Beginning Jan 1, 2003: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: chimera project (Mac OSX) Date: Fri, 03 Jan 2003 09:49:31 +0100 To: rasmol@lists.umass.edu Prospects for the future concerning the http://chimera.mozdev.org/ (etc.) browser(s) for use with the various incarnations of Rasmol? I came across this site again, while researching something else. A fantastic place for anyone interested in web programming! Lewis Edgel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: chimera project (Mac OSX) Date: Fri, 03 Jan 2003 11:10:14 -0500 To: rasmol@lists.umass.edu at 9:49 AM EDT on (Friday) 3 January 2003 Lewis Edgel said: > Prospects for the future concerning the http://chimera.mozdev.org/ (etc.) > browser(s) for use with the various incarnations of Rasmol? I came across > this site again, while researching something else. A fantastic place for > anyone interested in web programming! > > Lewis Edgel > hi Lewis, I see no way to configure Chimera to use helper apps yet. once that functionality appears, one should be able to use RasMol/SPV/DSViewer/Cn3D as helper apps just like with other browsers. I do have hope for this in Chimera, though; it is still a pre-1.0 browser, and a darn fine one at that IMHO. Chimera appears to handle modern plug-ins without much trouble. (I have QT5 and Flash in my Internet Plugins folder, for example, and they work okay in Chimera.) unfortunately, Chime does not work in Chimera, despite the similarity in name ;-) :aside: AFAIK from reading various mozilla and netscape docs, last-generation plug-ins like Chime require some re-tooling in order to function in the next generation of mozilla-like browsers. the docs make it sound like a minor fix, but what do I know? :/aside: Java applet mol vis viewers show promise. for example, the Java-based QuickPdb applet available at the PDB works great. MICE, however, does not, possibly b/c it requires a more complicated combination of Java plugins? I can not find a VRML viewer native to OS X. hope that helps! :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Frank Johnston Subject: VMRL in OSX Date: Fri, 03 Jan 2003 13:12:52 -0400 To: rasmol@lists.umass.edu Cc: timothy driscoll Tim Driscoll et al.: Cortona for OSX http://www.parallelgraphics.com/products/cortona/download/mac/ Works well with iCab and IE5.xx. I'll post a complrte compatibility matrix of my current survey. Yours Frank Johnston -- Frank P. Johnston 166 Basin ST Grand Falls NB Canada E3Z 2J1 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Frank Johnston Subject: Cortona download Date: Fri, 03 Jan 2003 13:20:16 -0400 To: rasmol@lists.umass.edu http://www.parallelgraphics.com/products/downloads , http://www.parallelgraphics.com/products/cortonamacosx/ -- Frank P. Johnston 166 Basin ST Grand Falls NB Canada E3Z 2J1 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: VMRL in OSX Date: Fri, 03 Jan 2003 12:27:12 -0500 To: Frank Johnston , LIST rasmol at 1:12 PM EDT on (Friday) 3 January 2003 Frank Johnston said: > Tim Driscoll et al.: > > Cortona for OSX > http://www.parallelgraphics.com/products/cortona/download/mac/ > > > Works well with iCab and IE5.xx. I'll post a complrte compatibility > matrix of my current survey. > intriguing. the Cortona installer is a Classic app, so I didn't bother to run it. I'd be interested to hear if you test it in Chimera. also, do you know if Cortona (in iCab-X or IE-X) works with the VRML resources at the PDB? regards, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Frank Johnston Subject: Re: VMRL in OSX Date: Fri, 03 Jan 2003 14:13:07 -0400 To: rasmol@lists.umass.edu Tim Driscoll: OSx version works well at the PDB site with iCab and IE5. Mozilla etc can be buggy, often crashing on quit or back execution. yours Frank Johnston >at 1:12 PM EDT on (Friday) 3 January 2003 Frank Johnston said: > >> Tim Driscoll et al.: >> >> Cortona for OSX >> http://www.parallelgraphics.com/products/cortona/download/mac/ >> >> >> Works well with iCab and IE5.xx. I'll post a complrte compatibility >> matrix of my current survey. >> > >intriguing. the Cortona installer is a Classic app, so I didn't bother to >run it. I'd be interested to hear if you test it in Chimera. also, do you >know if Cortona (in iCab-X or IE-X) works with the VRML resources at the >PDB? > >regards, > >:tim >-- >molvisions - molecular graphics & visualization > >usa:north carolina:wake forest > > > -- Frank P. Johnston 166 Basin ST Grand Falls NB Canada E3Z 2J1 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: VMRL in OSX Date: Fri, 03 Jan 2003 13:38:50 -0500 To: rasmol@lists.umass.edu at 2:13 PM EDT on (Friday) 3 January 2003 Frank Johnston said: > Tim Driscoll: > > OSx version works well at the PDB site with iCab and IE5. Mozilla etc > can be buggy, often crashing > on quit or back execution. > > yours > Frank Johnston > hi Frank, thanks for the info. I did not realize that to get the X version of Cortona, one needs to sign up as a beta tester. I'll add it to my list of potentially useful mol vis viewers. regards, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest > >at 1:12 PM EDT on (Friday) 3 January 2003 Frank Johnston said: > > > >> Tim Driscoll et al.: > >> > >> Cortona for OSX > >> http://www.parallelgraphics.com/products/cortona/download/mac/ > >> > >> > >> Works well with iCab and IE5.xx. I'll post a complrte compatibility > >> matrix of my current survey. > >> > > > >intriguing. the Cortona installer is a Classic app, so I didn't bother > >to run it. I'd be interested to hear if you test it in Chimera. also, > >do you know if Cortona (in iCab-X or IE-X) works with the VRML resources > >at the PDB? > > > >regards, > > > >:tim ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_s8ctxQn3lzNenq4s+MRexw)" References: ++++------+------+------+------+------+------+------+------+------+------+ From: Frank Johnston Subject: Re: VMRL in OSX Date: Fri, 03 Jan 2003 16:18:01 -0400 To: rasmol@lists.umass.edu --Boundary_(ID_s8ctxQn3lzNenq4s+MRexw) Tim Driscoll: The OSX version of the Cortona plugin* visualizes the VRML files at the PDB in in the following browsers PDB/VRML Stable iCab 2.8.2 + + IE5.2.2 + + Mozilla 1.2 + + Chimera 0.6 + + Omniweb 4.1.1 - Opera 6.0 + + * http://www.parallelgraphics.com/products/cortonamacosx/ under OSX 10.1.5. Cheers Frank Johnston -- >at 1:12 PM EDT on (Friday) 3 January 2003 Frank Johnston said: > >> Tim Driscoll et al.: >> >> Cortona for OSX >> http://www.parallelgraphics.com/products/cortona/download/mac/ >> >> >> Works well with iCab and IE5.xx. I'll post a complrte compatibility >> matrix of my current survey. >> > >intriguing. the Cortona installer is a Classic app, so I didn't bother to >run it. I'd be interested to hear if you test it in Chimera. also, do you >know if Cortona (in iCab-X or IE-X) works with the VRML resources at the >PDB? > >regards, > >:tim >-- >molvisions - molecular graphics & visualization > >usa:north carolina:wake forest > > > -- Frank P. Johnston 166 Basin ST Grand Falls NB Canada E3Z 2J1 ++++------+------+------+------+------+------+------+------+------+------+ From: Frank Johnston Subject: Re: VMRL in OSX Date: Fri, 03 Jan 2003 16:37:54 -0400 To: rasmol@lists.umass.edu Tim Driscoll: The OSX version of the Cortona plugin* visualizes the VRML files at the PDB in in the following browsers PDB/VRML Stable iCab 2.8.2 + + IE5.2.2 + + Mozilla 1.2 + + Chimera 0.6 + + Omniweb 4.1.1 - Opera 6.0 + + * http://www.parallelgraphics.com/products/cortonamacosx/ under OSX 10.1.5. Cheers Frank Johnston -- at 1:12 PM EDT on (Friday) 3 January 2003 Frank Johnston said: > Tim Driscoll et al.: > > Cortona for OSX > http://www.parallelgraphics.com/products/cortona/download/mac/ > > > Works well with iCab and IE5.xx. I'll post a complrte compatibility > matrix of my current survey. > intriguing. the Cortona installer is a Classic app, so I didn't bother to run it. I'd be interested to hear if you test it in Chimera. also, do you know if Cortona (in iCab-X or IE-X) works with the VRML resources at the PDB? regards, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest -- Frank P. Johnston 166 Basin ST Grand Falls NB Canada E3Z 2J1 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Microsoft-Entourage/10.1.0.2006 ++++------+------+------+------+------+------+------+------+------+------+ From: "James W. Caras" Subject: Re: chimera project (Mac OSX) Date: Fri, 03 Jan 2003 15:32:30 -0600 To: rasmol@lists.umass.edu Hi Everyone- One thing to note about the not-so-good state of Chime on modern browsers in Mac OS X. I came across a web page whose subject was on Netscape 7 for OS X and plug-ins. It was stated that the plug-ins have to be developed with OS X in mind (carbonized?) in order to function. I do not know if this is indeed true, for without testing I believe older plugins function in N7 when installed, but this might explain why I can't get Chime to run in OS X-native browsers no matter what I do. I can get Chime to run in Netscape 4 and 7 as well as Explorer in OS 9. I think that the onus falls upon MDL, and not the browsers. Jamie On 1/3/03 10:10 AM, "timothy driscoll" wrote: > at 9:49 AM EDT on (Friday) 3 January 2003 Lewis Edgel said: > >> Prospects for the future concerning the http://chimera.mozdev.org/ (etc.) >> browser(s) for use with the various incarnations of Rasmol? I came across >> this site again, while researching something else. A fantastic place for >> anyone interested in web programming! >> >> Lewis Edgel >> > > hi Lewis, > > I see no way to configure Chimera to use helper apps yet. once that > functionality appears, one should be able to use RasMol/SPV/DSViewer/Cn3D as > helper apps just like with other browsers. I do have hope for this in > Chimera, though; it is still a pre-1.0 browser, and a darn fine one at that > IMHO. > > Chimera appears to handle modern plug-ins without much trouble. (I have QT5 > and Flash in my Internet Plugins folder, for example, and they work okay in > Chimera.) unfortunately, Chime does not work in Chimera, despite the > similarity in name ;-) > > :aside: > AFAIK from reading various mozilla and netscape docs, last-generation > plug-ins like Chime require some re-tooling in order to function in the next > generation of mozilla-like browsers. the docs make it sound like a minor > fix, but what do I know? > :/aside: > > Java applet mol vis viewers show promise. for example, the Java-based > QuickPdb applet available at the PDB works great. MICE, however, does not, > possibly b/c it requires a more complicated combination of Java plugins? > > I can not find a VRML viewer native to OS X. > > > hope that helps! > > :tim ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' Dr. James Caras The Institute for Cellular and Molecular Biology The University of Texas at Austin MBB 3.122 2500 Speedway Austin, TX 78712 caras@mail.utexas.edu (512) 471-0416 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Trina Valencich Subject: Re: Visualization conference Date: Tue, 07 Jan 2003 09:35:58 -0700 To: rasmol@lists.umass.edu This sounds like me. I simulate collision dynamics for reactive systems. I want to learn about biochemistry & I always need a visual image, if only in my head, to understand chemistry. When I tried your web site, the page could not be found. We are between the Autumn & Spring semesters right now, so I'll try again later. Trina Valencich Chemistry Department University of Montana MIssoula, MT 59812 Office: 406-243-5227 FAX: 406-243-4227 At 05:24 PM 12/6/2002 -0500, you wrote: >Greetings from the Chair of the 2003 Gordon Conference on Visualization >in Science and Education. For those not familiar with the conference, >the focus is on creating visualizations that are accurate AND that help >students in learning concepts. (For more information, see the web site: >http://www.soton.ac.uk/~ecchemed/grc/). I am posting to this list >because I am trying to find someone who is involved with molecular-level >visualizations in biology or chemistry who is concerned with the >question of whether the visualizations help students learn or how they >help students learn? If this sounds like you, please email me >Mary.shultz@tufts.edu >(Note: no c in Shultz) >We can then talk further. Looking forward to hearing from you! > >Thanks >Mary Shultz > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: RE: VMRL in OSX Date: Tue, 07 Jan 2003 20:38:11 +0100 To: rasmol@lists.umass.edu Anyone follow the links from www.parallelgraphics.com to the http://www.parallelgraphics.com/products/cortona/best list of sites,which links to the http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm site? I think this site has been mentioned once before in this mailing list. I don't recall the visualizations offered in the current variety of formats - the last time I visited it. It's worth adding to your "links" if not already visited. I think it would be a very good idea for as many people as possible to write to Parallel concerning the direction their software development takes while they finish up the VRML Client 4.1 Beta. This should be of special interest to anyone working with OSX for Mac. Lewis Edgel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Frank Johnston Subject: RE: VMRL in OSX Date: Tue, 07 Jan 2003 16:53:37 -0400 To: rasmol@lists.umass.edu Lewis Edgel: The MOTM (Bristol) is the more eclectic of the two valuable MOTMs (http://www.rcsb.org/pdb/molecules/molecule_list.html). We should communicate our interests to Parallel Graphics as you suggest-I'm sure they will notice the number of downloads for the OSx Cortona plugin and that this will be persuasive if it is seen to be used. Cheers Frank Johnston >Anyone follow the links from www.parallelgraphics.com to the >http://www.parallelgraphics.com/products/cortona/best list of sites,which >links to the http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm site? I >think this site has been mentioned once before in this mailing list. I don't >recall the visualizations offered in the current variety of formats - the >last time I visited it. It's worth adding to your "links" if not already >visited. > >I think it would be a very good idea for as many people as possible to write >to Parallel concerning the direction their software development takes while >they finish up the VRML Client 4.1 Beta. This should be of special interest >to anyone working with OSX for Mac. > >Lewis Edgel > -- Frank P. Johnston 166 Basin ST Grand Falls NB Canada E3Z 2J1 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 X-MSMail-priority: Normal References: <5.2.0.9.0.20030107093210.03310c78@selway.umt.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Brian Foley Subject: Help modelling a sequence onto a known structure with a gap? Date: Thu, 09 Jan 2003 16:11:07 -0600 To: rasmol@lists.umass.edu Dear RasMol users, I would like to "map" or model the amino acid sequence of a HIV-1 gp120 envelope protein onto the known structure of another HIV-1 gp120 protein. SwissModel http://www.expasy.org/swissmod/SWISS-MODEL.html fails when I give it the amino acid sequence and the PDB file (19GM) because the 1G9M 3D structure was made from an env protein that had the variable loops removed. Thus the real sequence of HIV-1 gp120 has insertions relative to the 3D structure sequence. I don't expect, or even want, a "realistic" structure for these loops. I would be happy with any conformation in the loops. All I need is a 3D figure of gp120 that does not have these variable loops entirely missing. I have seen many figures indicating that the authors have done this sort of thing. For example: Kwong PD, Wyatt R, Majeed S, Robinson J, Sweet RW, Sodroski J, Hendrickson WA. Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates. Structure Fold Des. 2000 Dec 15;8(12):1329-39. PMID: 11188697 Shows a figure with the loops included. Is there any tool that helps people "invent" the 3D X-Y-Z coordinates for a segment of amino acids, given that the first amino acid needs to start with Cys126 here: ATOM 355 N CYS G 126 25.490 -4.700 61.405 1.00 72.28 N ATOM 356 CA CYS G 126 26.188 -4.085 60.270 1.00 78.01 C ATOM 357 C CYS G 126 26.107 -5.014 59.054 1.00 80.78 C ATOM 358 O CYS G 126 27.010 -5.823 58.824 1.00 81.12 O ATOM 359 CB CYS G 126 27.668 -3.853 60.582 1.00 79.71 C ATOM 360 SG CYS G 126 28.115 -3.229 62.233 1.00 82.97 S and end with CYS196 here: ATOM 387 N CYS G 196 26.818 1.002 60.259 1.00 86.32 N ATOM 388 CA CYS G 196 26.277 -0.036 61.129 1.00 84.01 C ATOM 389 C CYS G 196 24.940 0.380 61.728 1.00 82.05 C ATOM 390 O CYS G 196 24.884 1.273 62.574 1.00 82.37 O ATOM 391 CB CYS G 196 27.237 -0.327 62.280 1.00 84.47 C ATOM 392 SG CYS G 196 28.721 -1.315 61.912 1.00 85.15 S the "loop" which is missing in the structure has this amino acid sequence: CVSLKCTDLKNDTNTNSSSGRMIMEKGEIKNCSFNISTSIRGKVQKEYA FFYKLDIIPIDNDTTSYKLTSC beginning with C = CYS 126 and ending with C = CYS 196 Thanks for any help you can give me. Brian Foley, PhD HIV Genetic Sequences and Immunology Databases btf@lanl.gov (505) 665-1970 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Help modelling a sequence onto a known structure with a gap? Date: Thu, 09 Jan 2003 18:33:28 -0500 To: rasmol@lists.umass.edu hi Brian, SwissPdbViewer has Loop building tools built in, and a tutorial online. I have not gone through the process but it looks to be exactly what you want. and knowing SPDBV, I imagine the loops would be fairly realistic. check out the loop-building tutorial at the SPDV home page is hth, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest at 4:11 PM EDT on (Thursday) 9 January 2003 Brian Foley said: > Dear RasMol users, > > I would like to "map" or model the amino acid sequence of a > HIV-1 gp120 envelope protein onto the known structure of another > HIV-1 gp120 protein. > SwissModel > http://www.expasy.org/swissmod/SWISS-MODEL.html > fails when I give it the amino acid sequence and the > PDB file (19GM) because the 1G9M 3D structure was made > from an env protein that had the variable loops removed. > Thus the real sequence of HIV-1 gp120 has insertions relative > to the 3D structure sequence. > > I don't expect, or even want, a "realistic" structure for these > loops. I would be happy with any conformation in the loops. > All I need is a 3D figure of gp120 that does not have these > variable loops entirely missing. > > I have seen many figures indicating that the authors have > done this sort of thing. For example: > > Kwong PD, Wyatt R, Majeed S, Robinson J, Sweet RW, Sodroski J, > Hendrickson WA. > Structures of HIV-1 gp120 envelope glycoproteins from > laboratory-adapted > and primary isolates. > Structure Fold Des. 2000 Dec 15;8(12):1329-39. > PMID: 11188697 > > Shows a figure with the loops included. > > Is there any tool that helps people "invent" the 3D X-Y-Z > coordinates for a segment of amino acids, given that the > first amino acid needs to start with Cys126 here: > ATOM 355 N CYS G 126 25.490 -4.700 61.405 1.00 72.28 > N > ATOM 356 CA CYS G 126 26.188 -4.085 60.270 1.00 78.01 > C > ATOM 357 C CYS G 126 26.107 -5.014 59.054 1.00 80.78 > C > ATOM 358 O CYS G 126 27.010 -5.823 58.824 1.00 81.12 > O > ATOM 359 CB CYS G 126 27.668 -3.853 60.582 1.00 79.71 > C > ATOM 360 SG CYS G 126 28.115 -3.229 62.233 1.00 82.97 > S > > and end with CYS196 here: > > ATOM 387 N CYS G 196 26.818 1.002 60.259 1.00 86.32 > N > ATOM 388 CA CYS G 196 26.277 -0.036 61.129 1.00 84.01 > C > ATOM 389 C CYS G 196 24.940 0.380 61.728 1.00 82.05 > C > ATOM 390 O CYS G 196 24.884 1.273 62.574 1.00 82.37 > O > ATOM 391 CB CYS G 196 27.237 -0.327 62.280 1.00 84.47 > C > ATOM 392 SG CYS G 196 28.721 -1.315 61.912 1.00 85.15 > S > > > the "loop" which is missing in the structure has this amino acid > sequence: > > CVSLKCTDLKNDTNTNSSSGRMIMEKGEIKNCSFNISTSIRGKVQKEYA > FFYKLDIIPIDNDTTSYKLTSC > > beginning with C = CYS 126 and ending with C = CYS 196 > > > Thanks for any help you can give me. > > Brian Foley, PhD > HIV Genetic Sequences and Immunology Databases > btf@lanl.gov > (505) 665-1970 > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Mail-followup-to: Rasmol List Content-disposition: inline User-Agent: Mutt/1.4i X-OriginalArrivalTime: 15 Jan 2003 03:44:06.0312 (UTC) FILETIME=[5A942280:01C2BC48] ++++------+------+------+------+------+------+------+------+------+------+ From: Brian Salter-Duke Subject: Launching Rasmol from browser under linux Date: Wed, 15 Jan 2003 13:13:07 +0930 To: Rasmol List I am trying to launch Rasmol from a browser under linux when a pdb file is received. I have set up the preferences to recognise chemical/x-pdb mime types with extension pdb. Now if a pdb file comes off the internet it works fine with both netscape and mozilla. Rasmol is launched with the molecule displayed. However, if I try to load a local pdb file in the browser it works with netscape (Rasmol is launched fine) but does not work with mozilla (the text of the pdb file appears in the browser. Does anyone have any idea what is happening here? Netscape 4.78/U.S., 25-Jun-01; (c) 1995-2000 Netscape Communications Corp. Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.2.1) Gecko/20010901, build 2001090111 For mozilla I took the advice from:- http://www.dkfz-heidelberg.de/spec/sweet2/doc/plugin/fhelper.html and called rasmol from a wrapper script. Rasmol is:- Version 2.7.2.1 April 2001. Regards, Brian. -- Usenet is like a herd of performing elephants with diarrhea; massive, difficult to redirect, awe-inspiring, entertaining, and a source of mind-boggling amounts of excrement when you least expect it. -- Eugene Spafford. Brian Salter-Duke (Brian Duke) b_duke@octa4.net.au ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: RasTop 2.0.3 Date: Tue, 21 Jan 2003 22:21:14 -0800 To: pdb-l@rcsb.org, rasmol@lists.umass.edu Available for download at http://www.geneinfinity.org/rastop/download.htm. This is a tiny update; the code for povray script export is updated to povray, version 3.5. High quality pictures are now easily generated, even with multimolecules. Many thanks to John Wessel for his support. Feedback, bug reports, and suggestions always appreciated. Philippe Valadon ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: rlight Subject: IE 6 and chime Date: Fri, 24 Jan 2003 10:47:48 -0500 To: rasmol@lists.umass.edu I may have asked this question earlier, but haven't gotten a response so I thought I'd try again. At some point my IE 6 (actually 6.0.2800.1106.xpsp1.020828-1920) quit loading opening pdb files with chime and instead I get the file download dialogue: File name: xxxxxx.pdb File type: ChimeShimLibrary Object, Etc With the choice to open the file or save to the computer. I have the latest Chime plugin installed (npchime.dll version is 2.6.1.1, ChimeShim.dll is version 1.0.0.0). IE works fine with pdb files that are imbedded in a web page. It just won't open a pdb file directly. (And I seem to recall that it worked okay in the not too distant past, so there may have been an IE upgrade that fouled things up). My registry under HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Internet Explorer\Plugins\Extension\.pdb shows: Name Type Data (Default) REG_SZ MDL Chime 2.6 SP4 Content Type REG_SZ chemical/x-pdb Location REG_SZ C:\Program Files\Internet Explorer\Plugins\npchime.dll Version REG_SZ 2,6,1,1 And the npchime.dll is in the correct directory as indicated here. Incidentally, both Netscape 4.7 and Netscape 7.01 work just fine, opening the pdb file directly in the browser. Any ideas anyone? Robley Light ************************************************************* Robley J. Light Professor of Chemistry and Biochemistry Department of Chemistry Phone: (850) 644-3844 and Biochemistry Email: rlight@chem.fsu.edu Florida State University Fax: (850) 644-8281 Tallahassee, FL 32306-4390 Home Page: http://chemweb.chem.fsu.edu/editors/rlight --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.443 / Virus Database: 248 - Release Date: 1/10/2003 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: IE 6 and chime Date: Fri, 24 Jan 2003 10:45:05 -0600 (CST) To: rlight Cc: rasmol@lists.umass.edu Hi, Under Win 98 it works with IE6 and Chime SP3. I don't have current access to Win 200 or XP machine with the latest Chime. Have you uninstalled chime and then reinstalled it? Windows is very good at corrupting dll's or using incorrect version of them. Also, you may have to change a security setting in IE to open files. Regards Bruce On Fri, 24 Jan 2003, rlight wrote: > I may have asked this question earlier, but haven't gotten a response so I > thought I'd try again. > > At some point my IE 6 (actually 6.0.2800.1106.xpsp1.020828-1920) quit > loading opening pdb files with chime and instead I get the file download > dialogue: > > File name: xxxxxx.pdb > File type: ChimeShimLibrary Object, > Etc > With the choice to open the file or save to the computer. > > I have the latest Chime plugin installed (npchime.dll version is 2.6.1.1, > ChimeShim.dll is version 1.0.0.0). IE works fine with pdb files that are > imbedded in a web page. It just won't open a pdb file directly. (And I seem > to recall that it worked okay in the not too distant past, so there may have > been an IE upgrade that fouled things up). > > My registry under HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Internet > Explorer\Plugins\Extension\.pdb shows: > > Name Type Data > (Default) REG_SZ MDL Chime 2.6 SP4 > Content Type REG_SZ chemical/x-pdb > Location REG_SZ C:\Program Files\Internet Explorer\Plugins\npchime.dll > Version REG_SZ 2,6,1,1 > > And the npchime.dll is in the correct directory as indicated here. > > Incidentally, both Netscape 4.7 and Netscape 7.01 work just fine, opening > the pdb file directly in the browser. > > Any ideas anyone? > > Robley Light > ************************************************************* > Robley J. Light Professor of Chemistry and > Biochemistry > Department of Chemistry Phone: (850) 644-3844 > and Biochemistry Email: rlight@chem.fsu.edu > Florida State University Fax: (850) 644-8281 > Tallahassee, FL 32306-4390 Home Page: > http://chemweb.chem.fsu.edu/editors/rlight > > > --- > Outgoing mail is certified Virus Free. > Checked by AVG anti-virus system (http://www.grisoft.com). > Version: 6.0.443 / Virus Database: 248 - Release Date: 1/10/2003 > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-MSMail-priority: Normal References: <000a01c2c3bf$f553b9b0$a00cba80@lightbyte> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: IE 6 and chime Date: Fri, 24 Jan 2003 18:17:45 +0100 To: rasmol@lists.umass.edu In windows explorer, are pdb files associated with Internet Explorer ? (Tools, Options, files type, and then check for the pdb file type) My two cents... Paul ----- Original Message ----- Sent: Friday, January 24, 2003 4:47 PM From: "rlight" Subject: IE 6 and chime To: > I may have asked this question earlier, but haven't gotten a response so I > thought I'd try again. > > At some point my IE 6 (actually 6.0.2800.1106.xpsp1.020828-1920) quit > loading opening pdb files with chime and instead I get the file download > dialogue: > > File name: xxxxxx.pdb > File type: ChimeShimLibrary Object, > Etc > With the choice to open the file or save to the computer. > > I have the latest Chime plugin installed (npchime.dll version is 2.6.1.1, > ChimeShim.dll is version 1.0.0.0). IE works fine with pdb files that are > imbedded in a web page. It just won't open a pdb file directly. (And I seem > to recall that it worked okay in the not too distant past, so there may have > been an IE upgrade that fouled things up). > > My registry under HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Internet > Explorer\Plugins\Extension\.pdb shows: > > Name Type Data > (Default) REG_SZ MDL Chime 2.6 SP4 > Content Type REG_SZ chemical/x-pdb > Location REG_SZ C:\Program Files\Internet Explorer\Plugins\npchime.dll > Version REG_SZ 2,6,1,1 > > And the npchime.dll is in the correct directory as indicated here. > > Incidentally, both Netscape 4.7 and Netscape 7.01 work just fine, opening > the pdb file directly in the browser. > > Any ideas anyone? > > Robley Light ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: rlight Subject: RE: IE 6 and chime Date: Fri, 24 Jan 2003 12:49:53 -0500 To: rasmol@lists.umass.edu Yes, I forgot to mention that. .pdb files are associated with IE. ************************************************************* Robley J. Light Professor of Chemistry and Biochemistry Department of Chemistry Phone: (850) 644-3844 and Biochemistry Email: rlight@chem.fsu.edu Florida State University Fax: (850) 644-8281 Tallahassee, FL 32306-4390 Home Page: http://chemweb.chem.fsu.edu/editors/rlight > -----Original Message----- > From: owner-rasmol@lists.umass.edu > [mailto:owner-rasmol@lists.umass.edu] On Behalf Of Paul Pillot > Sent: Friday, January 24, 2003 12:18 PM > To: rasmol@lists.umass.edu > Subject: Re: IE 6 and chime > > > In windows explorer, are pdb files associated with Internet > Explorer ? (Tools, Options, files type, and then check for > the pdb file type) > > My two cents... > Paul > > ----- Original Message ----- > From: "rlight" > To: > Sent: Friday, January 24, 2003 4:47 PM > Subject: IE 6 and chime > > > > I may have asked this question earlier, but haven't gotten > a response > > so I thought I'd try again. > > > > At some point my IE 6 (actually > 6.0.2800.1106.xpsp1.020828-1920) quit > > loading opening pdb files with chime and instead I get the file > > download > > dialogue: > > > > File name: xxxxxx.pdb > > File type: ChimeShimLibrary Object, > > Etc > > With the choice to open the file or save to the computer. > > > > I have the latest Chime plugin installed (npchime.dll version is > > 2.6.1.1, ChimeShim.dll is version 1.0.0.0). IE works fine with pdb > > files that are imbedded in a web page. It just won't open > a pdb file > > directly. (And I > seem > > to recall that it worked okay in the not too distant past, so there > > may > have > > been an IE upgrade that fouled things up). > > > > My registry under HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Internet > > Explorer\Plugins\Extension\.pdb shows: > > > > Name Type Data > > (Default) REG_SZ MDL Chime 2.6 SP4 > > Content Type REG_SZ chemical/x-pdb > > Location REG_SZ C:\Program Files\Internet > Explorer\Plugins\npchime.dll > > Version REG_SZ 2,6,1,1 > > > > And the npchime.dll is in the correct directory as indicated here. > > > > Incidentally, both Netscape 4.7 and Netscape 7.01 work just fine, > > opening the pdb file directly in the browser. > > > > Any ideas anyone? > > > > Robley Light > > > -------------------------------------------------------------- > --rasmol-+ > > To change your address, unsubscribe, view previous > messages/history, receive messages as weekly digests, or for > any other information about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > -------------------------------------------------------------- > --rasmol-- > > --- > Incoming mail is certified Virus Free. > Checked by AVG anti-virus system (http://www.grisoft.com). > Version: 6.0.443 / Virus Database: 248 - Release Date: 1/10/2003 > > --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.443 / Virus Database: 248 - Release Date: 1/10/2003 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime's "show pdbheader" crashes Internet Explorer Date: Sun, 26 Jan 2003 15:29:06 -0500 To: rasmol@lists.umass.edu Dear Chimeleons: At my request, Jean Holt of MDL kindly added a new command to Chime 2.6, "show pdbheader". This command returns the entire PDB file header (all lines before the first ATOM line) as a single message via MessageCallback, thereby making the header accessible to javascript. (The header string is returned with formfeeds delimiting lines.) We have been developing a display of information in the PDB file header (resolution, date of release, experimental method, sites described and identified by the authors, etc.) within Protein Explorer, and testing it in Netscape with the expectation of being able to get this to work also in Internet Explorer. I didn't test the 'show pdbheader' command in Internet Explorer until now, when Paul Pillot alerted me that it doesn't work. This appears to preclude use of 'show pdbheader' in Internet Explorer unless and until MDL fixes this problem. (We will probably use another method to get the PDB header into IE's javascript, but it will be more laborious and cumbersome.) I have confirmed that sending the 'show pdbheader' command to Chime causes Internet Explorer to crash with 100% reproducibility. If anyone comes up with a way to work around this, please let me know! The crash happens even in the simplest implementation I can envision, which is demonstrated at http://www.umass.edu/microbio/chime/beta/headtest/ (can be run on-line, and from which site there is also a link to download this test). This implementation avoids attempting to display the (long) header string in a form textarea, which itself is problematic even in Netscape -- any message longer than 1,000 bytes is put directly into a javascript string variable. If there is no PDB header in the PDB file (as for 1atom.pdb, loaded in the invocation of Chime in my test site), Chime returns the message 'No pdb header available' in both Netscape and IE, without any problems. If there is a PDB header, it is returned without problems in Netscape. The largest header I know of (1jj2.pdb, 290 Kbytes) is returned in a few seconds, and can be parsed in javascript in less than 30 seconds on an 800 MHz computer. My tests with IE went as follows: Windows 98, IE 6.0 SP1, Chime 2.6 SP4: IE crashes and often crashes Windows as well. Windows 2000, IE 6.0 SP1, Chime 2.6 SP4: IE crashes (Windows survives). Windows XP, IE 6.0 (no SP), Chime 2.6 SP3: IE crashes (Windows survives). All tests were done from local files. Windows 98 was also tested on-line from the above URL with the same results. In Windows 98, IE also crashed with debugscript=off, and when 'show pdbheader' was sent from a static Chime button instead of via IMBIF. The static button spared Windows 98 in my tests, unlike IMBIF. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6249.0 Thread-Topic: Can RasMol be used in a commercial application? Thread-Index: AcLE9/RO+9kxBx9BSMCj25HozT/CRQBEG5eQ content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Mitch Barker Subject: Can RasMol be used in a commercial application? Date: Mon, 27 Jan 2003 08:42:49 -0500 To: rasmol@lists.umass.edu We are developing an application for users in chemical R&D. Our focus is on automating lab equipment and organizing data from lab instrumentation. In many places we display a chemical structure, and up until now, we've been using our client's ChemDraw plug-in. We need to be independent of ChemDraw (not all clients have ChemDraw). Essentially all we need is a program, or piece of code, that turns a mol file into an image (bmp, wmf or whatever). Nothing very fancy, a simple 2-D view is sufficient. I think that Rasmol would be good fit, or at least a good starting point. Is anyone familiar enough with the license to comment on whether or not we could adapt rasmol for our application? We can supply the full Rasmol with the app, and will give credit to rasmol. Comments? Can anyone suggest another piece of code that can convert a mol file to an image? We're willing to pay a one time developer fee, but a run-time royalty is not very workable. Our platform is MS and our primary tool is C#. Thanks. Mitch Barker Avantium Technologies Inc. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Can RasMol be used in a commercial application? Date: Mon, 27 Jan 2003 09:28:05 -0500 (EST) To: rasmol@lists.umass.edu The RasMol 2.7 series is open source, with the following license: ================================================================ Subject to your acceptance of the conditions stated [in the notices that come with RasMol], and your respect, if you are not going to make any modifications or create derived works, you are given permission to freely copy and distribute this package, provided you do the following: * 1. Either include the complete documentation, especially the file NOTICE, with what you distribute or provide a clear indication where people can get a copy of the documentation; and * 2. Give credit where credit is due citing the version and original authors properly; and * 3. Do not give anyone the impression that the original authors are providing a warranty of any kind. In addition, you may also modify this package and create derived works provided you do the following: * 4. Explain in your documentation how what you did differs from this version of RasMol; and * 5. Make your modified source code available. ====================================================================== Since you are not proposing to modify RasMol, you free to redistribute RasMol under terms 1, 2 and 3, above, either including the full documentation, or pointing to the web site: http://www.RasMol.org In addition to the appropriate versions of the binary (we recommend 2.7.2.1), you will want to include at a minimum rasmol.hlp, raswin.hlp, NOTICE and the English html version of the manual and the Spanish html version of the manual. Please contact me if you have any difficulty setting up your distribution. Regards, Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 27 Jan 2003, Mitch Barker wrote: > We are developing an application for users in chemical R&D. Our focus is > on automating lab equipment and organizing data from lab > instrumentation. In many places we display a chemical structure, and up > until now, we've been using our client's ChemDraw plug-in. We need to be > independent of ChemDraw (not all clients have ChemDraw). > > Essentially all we need is a program, or piece of code, that turns a mol > file into an image (bmp, wmf or whatever). Nothing very fancy, a simple > 2-D view is sufficient. I think that Rasmol would be good fit, or at > least a good starting point. Is anyone familiar enough with the license > to comment on whether or not we could adapt rasmol for our application? > We can supply the full Rasmol with the app, and will give credit to > rasmol. > > Comments? Can anyone suggest another piece of code that can convert a > mol file to an image? We're willing to pay a one time developer fee, but > a run-time royalty is not very workable. > > Our platform is MS and our primary tool is C#. > > Thanks. > > Mitch Barker > Avantium Technologies Inc. > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Command line size limit Date: Mon, 27 Jan 2003 15:28:08 +0000 (GMT) To: rasmol@lists.umass.edu This is the first post of a bounced message. > Sorry if this question has been answered, > because I couldn't see a post in the last > three years, and then I gave up reading > about all kinds of limitation, limited > testing and all the other limits that > people have been talking about.... there > were quite a lot! > > Any way, when scripting, I somtimes get the > message error message... > > line 314: Script command line too long! > (it is a long script!) > > I would like to know exactly how long this line > can be, so I can issue another define command... > > I was doing every thing with growing define commands, > for example > > define domain1 100a > define domain1 domain1, 101a > define domain1 domain1, 102a > define domain1 domain1, 103a, > ... > > I was doing it like this because of the command line limit > wouldn't allow a single big define... > > Now I am using some code from the perl Set::Range > module, so I can just issue a few > > define domain1 100-200a, 300-400a > > type commands, I switched over to this style because > the fomer was really slow to load a big script. > > However, some of the latter are still too long for a > single line.! > > I guess I have the answer - just curious now. Cheers, Dan. > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: Can RasMol be used in a commercial application? Date: Mon, 27 Jan 2003 09:41:37 -0600 (CST) To: rasmol@lists.umass.edu Hi, This is not a simple question and is not trivial! So this is only my opinion that you take at your own risk - I am not a lawyer! RasMol is an open source project. You can obtain the open version at http://openrasmol.org/ as well as the license information. There are a few 'strings' attached that may not suit your company. VERY IMPORTANT: OpenRasMol is open source - you MUST release or provide access to the source code by anyone who wants it! The short answer is yes provided you follow the license terms. So I strongly recommend finding a lawyer because of the issues involved - especially if you modify it. Some pointers to information: In the FAQ are: 1) http://openrasmol.org/FAQ.html#distribution Can RasMol be distributed freely, on CD-ROMs, and used freely even for commercial purposes? 2) Does this mean I can't make a commercial graphics program based on RasMol? http://openrasmol.org/FAQ.html#infectious Also, there are also issues if you get the code written for you especially if the code of other programs that do what you want have been seen by those writing the code. Regards Bruce On Mon, 27 Jan 2003, Mitch Barker wrote: > We are developing an application for users in chemical R&D. Our focus is > on automating lab equipment and organizing data from lab > instrumentation. In many places we display a chemical structure, and up > until now, we've been using our client's ChemDraw plug-in. We need to be > independent of ChemDraw (not all clients have ChemDraw). > > Essentially all we need is a program, or piece of code, that turns a mol > file into an image (bmp, wmf or whatever). Nothing very fancy, a simple > 2-D view is sufficient. I think that Rasmol would be good fit, or at > least a good starting point. Is anyone familiar enough with the license > to comment on whether or not we could adapt rasmol for our application? > We can supply the full Rasmol with the app, and will give credit to > rasmol. > > Comments? Can anyone suggest another piece of code that can convert a > mol file to an image? We're willing to pay a one time developer fee, but > a run-time royalty is not very workable. > > Our platform is MS and our primary tool is C#. > > Thanks. > > Mitch Barker > Avantium Technologies Inc. > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Command line size limit Date: Mon, 27 Jan 2003 10:54:43 -0500 To: rasmol@lists.umass.edu At 1/27/03, you wrote: > > Any way, when scripting, I somtimes get the > > message error message... > >line 314: Script command line too long! The way I avoid long lines when defining large sets is by breaking up the select commands into multiple lines: select a, b, c, d, e, f ... select selected or g, h, i, j, k, ... select selected or l, m, n, o, p, q, ... define newtoken selected -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: Command line size limit Date: Mon, 27 Jan 2003 15:55:28 +0000 (GMT) To: rasmol@lists.umass.edu How many lines do I need to break it up into? When should I choose to break a line? Thanks, Dan. On Mon, 27 Jan 2003, Eric Martz wrote: > At 1/27/03, you wrote: > > > Any way, when scripting, I somtimes get the > > > message error message... > > >line 314: Script command line too long! > > > The way I avoid long lines when defining large sets is by breaking up the > select commands into multiple lines: > > select a, b, c, d, e, f ... > select selected or g, h, i, j, k, ... > select selected or l, m, n, o, p, q, ... > define newtoken selected > > -Eric > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: Command line size limit Date: Mon, 27 Jan 2003 15:55:58 +0000 (GMT) To: rasmol@lists.umass.edu Will this technique speed up reading a script file? Ta, Dan. On Mon, 27 Jan 2003, Eric Martz wrote: > At 1/27/03, you wrote: > > > Any way, when scripting, I somtimes get the > > > message error message... > > >line 314: Script command line too long! > > > The way I avoid long lines when defining large sets is by breaking up the > select commands into multiple lines: > > select a, b, c, d, e, f ... > select selected or g, h, i, j, k, ... > select selected or l, m, n, o, p, q, ... > define newtoken selected > > -Eric > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: Can RasMol be used in a commercial application? Date: Mon, 27 Jan 2003 22:11:16 -0800 To: rasmol@lists.umass.edu RasMol open source license is GPL-like. This means that if you link your software with rasmol you must open your software code under the same license (infectivity). If this is too restrictive for your company, rasmol 2.6.4 code is probably ok for your purpose and is in the public domain. Best regards, Philippe Valadon ----- Original Message ----- Sent: Monday, January 27, 2003 5:42 AM From: "Mitch Barker" Subject: Can RasMol be used in a commercial application? To: > We are developing an application for users in chemical R&D. Our focus is > on automating lab equipment and organizing data from lab > instrumentation. In many places we display a chemical structure, and up > until now, we've been using our client's ChemDraw plug-in. We need to be > independent of ChemDraw (not all clients have ChemDraw). > > Essentially all we need is a program, or piece of code, that turns a mol > file into an image (bmp, wmf or whatever). Nothing very fancy, a simple > 2-D view is sufficient. I think that Rasmol would be good fit, or at > least a good starting point. Is anyone familiar enough with the license > to comment on whether or not we could adapt rasmol for our application? > We can supply the full Rasmol with the app, and will give credit to > rasmol. > > Comments? Can anyone suggest another piece of code that can convert a > mol file to an image? We're willing to pay a one time developer fee, but > a run-time royalty is not very workable. > > Our platform is MS and our primary tool is C#. > > Thanks. > > Mitch Barker > Avantium Technologies Inc. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Why is rasmol so slow... Date: Tue, 28 Jan 2003 09:16:15 +0000 (GMT) To: rasmol@lists.umass.edu Why is rasmol so slow to read script files? perl for example can parse a million lines of a sequence database in less than 2 min. ? Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: Can RasMol be used in a commercial application? Date: Tue, 28 Jan 2003 08:30:55 -0600 (CST) To: rasmol@lists.umass.edu Hi, No, the OpenRasMol license is not GPL-like! The only similarity is that it is based on the part of the GPL's spirit. There are many misconceptions regarding the GPL especially in terms of what the goal is and what it actual provides. There are rather obvious differences between the licenses include: The GPL forces/demands that you to make the code available. In contrast, the OpenRasMol license request (uses please a lot) that you make it available. The OpenRasMol license requires you to tell the user where it differs from the original. The latest GPL only requires you to provide the modified code (earlier version has different requirements - always check the license used!). The OpenRasMol license tells you that you have to give credit by citation. There is no such requirement in the GPL. The OpenRasMol license tells you that you have to provide complete documentation or where to get it. There is no such requirement in the GPL. This is not meant to say what they are doing is bad but that I think the license is weak. Better Open Source licenses can be found at http://www.opensource.org. Regards Bruce On Mon, 27 Jan 2003, Philippe wrote: > RasMol open source license is GPL-like. This means that if you link your > software with rasmol you must open your software code under the same license > (infectivity). If this is too restrictive for your company, rasmol 2.6.4 > code is probably ok for your purpose and is in the public domain. > > Best regards, > Philippe Valadon > > > > ----- Original Message ----- > From: "Mitch Barker" > To: > Sent: Monday, January 27, 2003 5:42 AM > Subject: Can RasMol be used in a commercial application? > > > > We are developing an application for users in chemical R&D. Our focus is > > on automating lab equipment and organizing data from lab > > instrumentation. In many places we display a chemical structure, and up > > until now, we've been using our client's ChemDraw plug-in. We need to be > > independent of ChemDraw (not all clients have ChemDraw). > > > > Essentially all we need is a program, or piece of code, that turns a mol > > file into an image (bmp, wmf or whatever). Nothing very fancy, a simple > > 2-D view is sufficient. I think that Rasmol would be good fit, or at > > least a good starting point. Is anyone familiar enough with the license > > to comment on whether or not we could adapt rasmol for our application? > > We can supply the full Rasmol with the app, and will give credit to > > rasmol. > > > > Comments? Can anyone suggest another piece of code that can convert a > > mol file to an image? We're willing to pay a one time developer fee, but > > a run-time royalty is not very workable. > > > > Our platform is MS and our primary tool is C#. > > > > Thanks. > > > > Mitch Barker > > Avantium Technologies Inc. > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Can RasMol be used in a commercial application? Date: Tue, 28 Jan 2003 11:01:18 -0500 (EST) To: rasmol@lists.umass.edu Actually, the current RasMol license is GPL-like, and, the first release we make after moving the GIF code out into a separate module will in fact be explicitly GPL. The plan to move RasMol under the GPL has been discussed with Richard Stallman and Roger Sayle, and the old problem with the IUCr CIF patent vs. GPL has been resolved. The points raised are interesting, but do not represent a substantive conflict with the GPL. Both the GPL and the RasMol license make use of an interesting aspect of the law, that it is important for all internet software users to understand: Unless you have an explicit license to do so, you have no right to copy any document you encounter. There are some limited exceptions to this rule, but, especially for major programs, you need permission to make copies. If you read the RasMol notices carefully, you will find that, despite the polite language, the only way you may properly make a copy is by respecting the open source requirements. We consider the documentation an important part of RasMol as a program. Much of it even has its own source file (rasmol.doc). If you do not consider the non-source code portions of an open source release to be covered by the licenses in the package, then you have no right to copy or modify that material at all. Most developers I know treat the documentation of open source programs as part of the source. The programs diff and patch make compliance with our requirement to provide changes functionally equivalent to the GPL requirement to provide modified code, and in practice I have cheerfully accepted modified code instead of changes. I have had requests to distribute variants of RasMol without the long and growing list of credits. I am a stickler on giving credit where credit is due, so I prefer to retain such credit lists. Even when we move under the GPL, that will be a requirement in making copies of RasMol, as will the requirements on the documentation. Please note that the strength of all these licenses lies in the Copyright law. To avoid any misunderstanding arising from the assertion that the current license is "weak", be assured that we have enforced the RasMol license in the past and will enforce it in the future. The RasMol 2.7 series is open source and will remain so. Regards, Herbert J. Bernstein ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Tue, 28 Jan 2003 southey@ux1.cso.uiuc.edu wrote: > Hi, > > No, the OpenRasMol license is not GPL-like! The only similarity is that > it is based on the part of the GPL's spirit. There are many > misconceptions regarding the GPL especially in terms of what the goal is > and what it actual provides. > > There are rather obvious differences between the licenses include: > > The GPL forces/demands that you to make the code available. In > contrast, the OpenRasMol license request (uses please a lot) that you make > it available. > > The OpenRasMol license requires you to tell the user where it differs from > the original. The latest GPL only requires you to provide the modified > code (earlier version has different requirements - always check the > license used!). > > The OpenRasMol license tells you that you have to give credit by citation. > There is no such requirement in the GPL. > > The OpenRasMol license tells you that you have to provide complete > documentation or where to get it. There is no such requirement in the GPL. > > This is not meant to say what they are doing is bad but that I think the > license is weak. Better Open Source licenses can be found at > http://www.opensource.org. > > Regards > Bruce > > On Mon, 27 Jan 2003, Philippe wrote: > > > RasMol open source license is GPL-like. This means that if you link your > > software with rasmol you must open your software code under the same license > > (infectivity). If this is too restrictive for your company, rasmol 2.6.4 > > code is probably ok for your purpose and is in the public domain. > > > > Best regards, > > Philippe Valadon > > > > > > > > ----- Original Message ----- > > From: "Mitch Barker" > > To: > > Sent: Monday, January 27, 2003 5:42 AM > > Subject: Can RasMol be used in a commercial application? > > > > > > > We are developing an application for users in chemical R&D. Our focus is > > > on automating lab equipment and organizing data from lab > > > instrumentation. In many places we display a chemical structure, and up > > > until now, we've been using our client's ChemDraw plug-in. We need to be > > > independent of ChemDraw (not all clients have ChemDraw). > > > > > > Essentially all we need is a program, or piece of code, that turns a mol > > > file into an image (bmp, wmf or whatever). Nothing very fancy, a simple > > > 2-D view is sufficient. I think that Rasmol would be good fit, or at > > > least a good starting point. Is anyone familiar enough with the license > > > to comment on whether or not we could adapt rasmol for our application? > > > We can supply the full Rasmol with the app, and will give credit to > > > rasmol. > > > > > > Comments? Can anyone suggest another piece of code that can convert a > > > mol file to an image? We're willing to pay a one time developer fee, but > > > a run-time royalty is not very workable. > > > > > > Our platform is MS and our primary tool is C#. > > > > > > Thanks. > > > > > > Mitch Barker > > > Avantium Technologies Inc. > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Why is rasmol so slow... (fwd) Date: Tue, 28 Jan 2003 11:16:30 -0500 (EST) To: rasmol@lists.umass.edu Cc: Dan Bolser Please provide a samples of slow script and I'll investigate the problem. If the data files being read are not standard PDb entries, please remember to include them. -- HJB ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== > ---------- Forwarded message ---------- > Date: Tue, 28 Jan 2003 09:16:15 +0000 (GMT) > From: Dan Bolser > Reply-To: rasmol@lists.umass.edu > To: rasmol@lists.umass.edu > Subject: Why is rasmol so slow... > > > Why is rasmol so slow > to read script files? > > perl for example can parse > a million lines of a > sequence database in less > than 2 min. > > ? > Dan. > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: Can RasMol be used in a commercial application? Date: Tue, 28 Jan 2003 11:04:43 -0600 (CST) To: rasmol@lists.umass.edu Hi, Yes they ARE a conflict with the GPL! Please reread the GPL and you will see this. Let me very clear and say I don't have a problem with the OpenRasMol license in the 'spirit' of the GPL. But the 'spirit' aspect of the GPL carries no legal weight. What I have the problem with is the OpenRasMol license being called GPL-like when it is clearly NOT in the license view. Can the OpenRasMol conform to the GPL? Not in the present state and that is why is can not be considered GPL-like from a license view. Otherwise Stallman would love the BSD and similar licenses - which is far from the case. Bruce On Tue, 28 Jan 2003, Herbert J. Bernstein wrote: > Actually, the current RasMol license is GPL-like, and, the first release > we make after moving the GIF code out into a separate module will in fact > be explicitly GPL. The plan to move RasMol under the GPL has been > discussed with Richard Stallman and Roger Sayle, and the old problem with > the IUCr CIF patent vs. GPL has been resolved. > > The points raised are interesting, but do not represent a substantive > conflict with the GPL. Both the GPL and the RasMol license make use > of an interesting aspect of the law, that it is important for all > internet software users to understand: > > Unless you have an explicit license to do so, you have no right > to copy any document you encounter. > > There are some limited exceptions to this rule, but, especially for major > programs, you need permission to make copies. If you read the RasMol > notices carefully, you will find that, despite the polite language, > the only way you may properly make a copy is by respecting the open > source requirements. > > We consider the documentation an important part of RasMol as a program. > Much of it even has its own source file (rasmol.doc). If you do not > consider the non-source code portions of an open source release to be > covered by the licenses in the package, then you have no right to copy or > modify that material at all. Most developers I know treat the > documentation of open source programs as part of the source. > > The programs diff and patch make compliance with our requirement to > provide changes functionally equivalent to the GPL requirement to provide > modified code, and in practice I have cheerfully accepted modified code > instead of changes. > > I have had requests to distribute variants of RasMol without the long > and growing list of credits. I am a stickler on giving credit where > credit is due, so I prefer to retain such credit lists. Even when we > move under the GPL, that will be a requirement in making copies of > RasMol, as will the requirements on the documentation. > > Please note that the strength of all these licenses lies in the Copyright > law. To avoid any misunderstanding arising from the assertion that the > current license is "weak", be assured that we have enforced the RasMol > license in the past and will enforce it in the future. The RasMol 2.7 > series is open source and will remain so. > > Regards, > Herbert J. Bernstein > > ===================================================== > Herbert J. Bernstein, Professor of Computer Science > Dowling College, Kramer Science Center, KSC 020 > Idle Hour Blvd, Oakdale, NY, 11769 > > +1-631-244-3035 > yaya@dowling.edu > ===================================================== > > On Tue, 28 Jan 2003 southey@ux1.cso.uiuc.edu wrote: > > > Hi, > > > > No, the OpenRasMol license is not GPL-like! The only similarity is that > > it is based on the part of the GPL's spirit. There are many > > misconceptions regarding the GPL especially in terms of what the goal is > > and what it actual provides. > > > > There are rather obvious differences between the licenses include: > > > > The GPL forces/demands that you to make the code available. In > > contrast, the OpenRasMol license request (uses please a lot) that you make > > it available. > > > > The OpenRasMol license requires you to tell the user where it differs from > > the original. The latest GPL only requires you to provide the modified > > code (earlier version has different requirements - always check the > > license used!). > > > > The OpenRasMol license tells you that you have to give credit by citation. > > There is no such requirement in the GPL. > > > > The OpenRasMol license tells you that you have to provide complete > > documentation or where to get it. There is no such requirement in the GPL. > > > > This is not meant to say what they are doing is bad but that I think the > > license is weak. Better Open Source licenses can be found at > > http://www.opensource.org. > > > > Regards > > Bruce > > > > On Mon, 27 Jan 2003, Philippe wrote: > > > > > RasMol open source license is GPL-like. This means that if you link your > > > software with rasmol you must open your software code under the same license > > > (infectivity). If this is too restrictive for your company, rasmol 2.6.4 > > > code is probably ok for your purpose and is in the public domain. > > > > > > Best regards, > > > Philippe Valadon > > > > > > > > > > > > ----- Original Message ----- > > > From: "Mitch Barker" > > > To: > > > Sent: Monday, January 27, 2003 5:42 AM > > > Subject: Can RasMol be used in a commercial application? > > > > > > > > > > We are developing an application for users in chemical R&D. Our focus is > > > > on automating lab equipment and organizing data from lab > > > > instrumentation. In many places we display a chemical structure, and up > > > > until now, we've been using our client's ChemDraw plug-in. We need to be > > > > independent of ChemDraw (not all clients have ChemDraw). > > > > > > > > Essentially all we need is a program, or piece of code, that turns a mol > > > > file into an image (bmp, wmf or whatever). Nothing very fancy, a simple > > > > 2-D view is sufficient. I think that Rasmol would be good fit, or at > > > > least a good starting point. Is anyone familiar enough with the license > > > > to comment on whether or not we could adapt rasmol for our application? > > > > We can supply the full Rasmol with the app, and will give credit to > > > > rasmol. > > > > > > > > Comments? Can anyone suggest another piece of code that can convert a > > > > mol file to an image? We're willing to pay a one time developer fee, but > > > > a run-time royalty is not very workable. > > > > > > > > Our platform is MS and our primary tool is C#. > > > > > > > > Thanks. > > > > > > > > Mitch Barker > > > > Avantium Technologies Inc. > > > > > > > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Can RasMol be used in a commercial application? Date: Tue, 28 Jan 2003 13:12:56 -0500 (EST) To: rasmol@lists.umass.edu Dear Bruce, There is a difference between a conflict and simply having some additional license terms which do not conflict with keeping the program open source. Requiring someone to keep the documentation available or to cite authors does not "conflict" with the GPL. The place where the RasMol license and the GPL have a substantive difference is an area in which the RasMol license is silent: patents. That issue has now been resolved, and, as I said, we will be adopting the GPL as the license for the first release of RasMol after we segregate the GIF code. Please do not confuse the RasMol license with the BSD license. The RasMol license (like the GPL license) is "infectious", requires you to make source code available and applies to programs you derive from RasMol. The current BSD and MIT licenses are much less infectious, only requiring you to carry forward some notices. There are arguments pro and con on the two approaches. For RasMol, we have chosen to follow Stallman's approach. It seems to be appropriate for the tools used in science. I would suggest that, as a courtesy to the others on this list, if you have further discussion on the details of this particular license, we take it off-line from the list for a while, and, then, is something interesting arises from the discussion, we post one (or two) summary messages back to the list when we are done. Regards, Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Tue, 28 Jan 2003 southey@ux1.cso.uiuc.edu wrote: > Hi, > > Yes they ARE a conflict with the GPL! Please reread the GPL and you will > see this. Let me very clear and say I don't have a problem with the > OpenRasMol license in the 'spirit' of the GPL. But the 'spirit' aspect of > the GPL carries no legal weight. What I have the problem with is the > OpenRasMol license being called GPL-like when it is clearly NOT in the > license view. Can the OpenRasMol conform to the GPL? Not in the present > state and that is why is can not be considered GPL-like from a license > view. Otherwise Stallman would love the BSD and similar licenses - which > is far from the case. > > Bruce > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: valadon@ix.netcom.com Subject: Re: Can RasMol be used in a commercial application? Date: Tue, 28 Jan 2003 11:07:00 -0800 (PST) To: rasmol@lists.umass.edu Please, keep this discussion in clear on the list. It might be to technical for many, but it is important for the record to have these points explained and discussed in details. I realize that it is an elusive goal to try to classify open source licenses on their behavior so dramatic can be the effect of just changing one word. I used the term GLP-like regarding the infectivity. I think we agree that rasmol license is infective. For those who wonder what infectivity means, let's take a practical example. If you incorporate rasmol code into your own software, then your entire software becomes a derivative work and must be released under the rasmol license, not just the modifications you made to rasmol code. Philippe Valadon ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Markus Winter Subject: Installing MolMol on MacOS X Date: Wed, 29 Jan 2003 14:23:32 +1300 To: rasmol@lists.umass.edu Hi all, my apologies if this is not the right place to ask, but after long years on the Mac I feel somewhat lost on OS X. I would like to install MolMol and some other molecular biology apps on OS X. I installed Apples X11 beta, and afterwards installed MolMol - but when I start it I get an error: "MenuBar file could not be opened, check installation (setting of MOLMOLHOME)" ... I'm at a loss (aka I'm not even sure what to ask here). How do I get MolMol to run? Any advice would be highly appreciated. Best Regards Markus -- Dr. Markus Winter Tel: 0064 (0)9 373 7599 (wait for message then type extension) 83960 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Douglas Kojetin Subject: RE: Installing MolMol on MacOS X Date: Tue, 28 Jan 2003 21:01:29 -0500 To: rasmol@lists.umass.edu I do not run OS X myself, but found some info via google (for MOLMOL and scientific apps): http://dryden.biol.yorku.ca/darwin.html http://www.apple.com/scitech/unixports/ search google for your error to, using some sort of variation of "check installation MOLMOLHOME" -- I saw a few things that might help you out but first, make sure you have the following file: ./molmol/setup/MenuBar if not, that could be the source of your problem hope that helps- Doug > -----Original Message----- > From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu] > On Behalf Of Markus Winter > Sent: Tuesday, January 28, 2003 8:24 PM > To: rasmol@lists.umass.edu > Subject: Installing MolMol on MacOS X > > Hi all, > > my apologies if this is not the right place to ask, but after long years > on > the Mac I feel somewhat lost on OS X. I would like to install MolMol and > some other molecular biology apps on OS X. I installed Apples X11 beta, > and > afterwards installed MolMol - but when I start it I get an error: "MenuBar > file could not be opened, check installation (setting of MOLMOLHOME)" ... > I'm at a loss (aka I'm not even sure what to ask here). How do I get > MolMol > to run? > > Any advice would be highly appreciated. > > Best Regards > > Markus > > -- > > Dr. Markus Winter > Tel: 0064 (0)9 373 7599 (wait for message then type extension) 83960 > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Douglas Kojetin Subject: secondary structure prediction Date: Tue, 28 Jan 2003 21:43:01 -0500 To: rasmol@lists.umass.edu Hi All- Quick question: does anyone know of a secondary structure prediction program that will output a formatted file (postscript, etc.) with "graphic" helices/sheets (similar to ESPript postscript output). Note: I need it for a prediction; not to read and output from a pdb file Thanks! Doug ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: Can RasMol be used in a commercial application? Date: Tue, 28 Jan 2003 21:49:15 -0800 To: rasmol@lists.umass.edu ----- Original Message ----- From: "Herbert J. Bernstein" /.../ > I have had requests to distribute variants of RasMol without the long > and growing list of credits. I am a stickler on giving credit where > credit is due, so I prefer to retain such credit lists. /.../> Regards, > Herbert J. Bernstein > The license states: "Give credit where credit is due citing the version and original authors properly", but does not say that each author and each variant name, variant version and variant date must listed in each source file of the distribution and that each source file should be updated each time a new version is released. RasMol would be curiously alone in the open source world with such a requirement (That would definitively transform Mozilla in Godzilla!). On the other hand, I noticed that we tend to over-credit main contributors, where I see around me several open sources with a single list of credited people that is more extended and precise, and rewarding for those who committed themselves in very small, but fundamental contributions. If we ever switch to GPL, we should consider rewriting the credit line. I quote also: > Please do not confuse the RasMol license with the BSD license. The RasMol > license (like the GPL license) is "infectious", requires you to make > source code available and applies to programs you derive from RasMol. > The current BSD and MIT licenses are much less infectious, only requiring > you to carry forward some notices. There are arguments pro and con on the > two approaches. For RasMol, we have chosen to follow Stallman's > approach. It seems to be appropriate for the tools used in science. I guess most people in this list ask at this point if we shall ever make something Chime-like out of the nouveau rasmol. Can a browser plug-in be under the GPL? I'd like to be sure before we commit rasmol under the GPL. Can anyone shed some light here? Philippe Valadon ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Can RasMol be used in a commercial application? Date: Wed, 29 Jan 2003 07:35:33 -0500 (EST) To: rasmol@lists.umass.edu The only tricky part of creating a plug-in version of RasMol is that, to avoid legal tangles, it needs to be done by somebody who has never downloaded or used Chime, so that there cannot be any possibility that they have reversed engineered their code. This is call "clean-room" development. Any volunteers? ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Tue, 28 Jan 2003, Philippe wrote: > ----- Original Message ----- > From: "Herbert J. Bernstein" > > /.../ > > I have had requests to distribute variants of RasMol without the long > > and growing list of credits. I am a stickler on giving credit where > > credit is due, so I prefer to retain such credit lists. > /.../> Regards, > > Herbert J. Bernstein > > > > The license states: "Give credit where credit is due citing the version and > original authors properly", but does not say that each author and each > variant name, variant version and variant date must listed in each source > file of the distribution and that each source file should be updated each > time a new version is released. RasMol would be curiously alone in the open > source world with such a requirement (That would definitively transform > Mozilla in Godzilla!). On the other hand, I noticed that we tend to > over-credit main contributors, where I see around me several open sources > with a single list of credited people that is more extended and precise, and > rewarding for those who committed themselves in very small, but fundamental > contributions. If we ever switch to GPL, we should consider rewriting the > credit line. > > I quote also: > > > Please do not confuse the RasMol license with the BSD license. The RasMol > > license (like the GPL license) is "infectious", requires you to make > > source code available and applies to programs you derive from RasMol. > > The current BSD and MIT licenses are much less infectious, only requiring > > you to carry forward some notices. There are arguments pro and con on the > > two approaches. For RasMol, we have chosen to follow Stallman's > > approach. It seems to be appropriate for the tools used in science. > > I guess most people in this list ask at this point if we shall ever make > something Chime-like out of the nouveau rasmol. Can a browser plug-in be > under the GPL? I'd like to be sure before we commit rasmol under the GPL. > Can anyone shed some light here? > > Philippe Valadon > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: rasmol 2.7? Date: Wed, 29 Jan 2003 13:51:14 +0000 (GMT) To: rasmol@lists.umass.edu Is there a call for functionality? Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Joseph Mazurkiewicz Subject: Re: secondary structure prediction Date: Wed, 29 Jan 2003 12:00:12 -0500 To: rasmol@lists.umass.edu You could try the GCG Wisconsin Package. It has a protein analysis module called PeptideStructure that makes secondary structure predictions. PlotStructure then displays the predictions graphically. http://www.accelrys.com/products/gcg_wisconsin_package/ I have no financial interest in GCG, just use the program. Joseph E. Mazurkiewicz, Ph.D. Center for Neuropharmacology and Neuroscience Mail Code 136 Albany Medical College Albany, NY 12208 Phone: 518-262-5381 FAX: 518-262-5799 e-mail: mazurkj@mail.amc.edu >>> djkojeti@unity.ncsu.edu 01/28/03 09:43PM >>> Hi All- Quick question: does anyone know of a secondary structure prediction program that will output a formatted file (postscript, etc.) with "graphic" helices/sheets (similar to ESPript postscript output). Note: I need it for a prediction; not to read and output from a pdb file Thanks! Doug ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Molecular Machinery poster Date: Wed, 29 Jan 2003 14:37:19 -0600 (CST) To: rasmol@lists.umass.edu Hi, >From the PDB molecule of the month site: http://www.rcsb.org/pdb/molecules/molecule_list.html For copies of the poster, "Molecular Machinery: A Tour of the Protein Data Bank", please send your postal address to info@rcsb.org . A 2-sided, 8 1/2" x 11" quick reference guide--showing the images and their structure names and PDB ID's. There is also a link to a pdf version - about 5,113KB! Regards Bruce ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 boundary="Boundary_(ID_YQYnV/p97KCx3d1YOZnBgw)" Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Robert Bateman Subject: molecular 3D literacy Date: Wed, 29 Jan 2003 17:29:51 -0600 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_YQYnV/p97KCx3d1YOZnBgw) Colleagues: Those teaching and performing research in the molecular sciences, especially chemistry and biochemistry, are aware of the need for both students and practitioners to possess a kind of "literacy" which is based on multiple dimensions, both spatial and temporal. It is difficult to define precisely what skills one must possess before one can be considered literate in this manner, but it is important to do so from a pedagogical point of view. I have posted a draft list of such skills at http://orca.st.usm.edu/~rbateman/kinemage/mol-literacy.htm and would appreciate feedback from this list to refine it. Sincerely, Bob Bateman Robert C. Bateman, Jr. Professor and Chair Department of Chemistry and Biochemistry University of Southern Mississippi Hattiesburg, MS 39406-5043 Robert.Bateman@usm.edu www.chem.usm.edu 601-266-4701 (department office) 601-266-6075 (fax) ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Why is rasmol so slow... Date: Wed, 29 Jan 2003 20:30:00 -0500 To: rasmol@lists.umass.edu [[ I am posting this message from Roger Sayle to the list to circumvent technical difficulties with the original transmission. -Eric Martz]] ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: Why is rasmol so slow... Date: Tue, 28 Jan 2003 10:58:55 -0700 (MST) To: Dan Bolser Cc: rasmol@lists.umass.edu [I'm Cc'ing this response to the RasMol list as some of the hints and tricks to speeding up scripts may not be generally known.] To answer one of your original questions, the maximum command line length in RasMol is 256 characters (though this may have been increased in later versions). I'll explain a little of how RasMol works under the surface. The RasMol "define" command is implemented underneath the surface as a single symbolic name for a linked list of pointer to atoms. It actually does slightly better than a linked list, by chunking the list into blocks of upto ten atom pointers at a time. First tip, "define id1 id2", i.e. creating a synonym for a set of atoms is actually quite expensive. i.e. this requires two separate lists to be stored. RasMol could switch to reference counting like Perl, but it was assumed that duplicate lists would be rare. Hence, I'd recommend removing the "SUNID_*" and "SID_*" identifier synonyms. Grouping defines together in batches is a huge performance win. define D4 526A define D4 D4, 558A is much slower than define D4 526A, 558A In the first example, RasMol traverses the molecule querying each atom to determine if "526A" is true, and if so adds it to the linked list for the set D4. Then on the second line, it runs through every atom in the molecule again testing whether "D4, 558A" is true. To make things worse, "D4" is implemented by searching through the D4 linked list to see if the atom being tested is a member of the set. The alternative "define D4 526A,558A,758A" traverses the molecule only once, testing the expression "526A,558A,758A" at each atom, and doesn't ever have to test set membership. Most of your D# sets can be defined on a single line, and the remaining few can be split across lines should you reach 200 characters or so. When defining large sets it also make sense to use RasMol's selection mechanism. Selecting atoms and bonds in RasMol is, unlike user-defined sets, stored by representing a true or false flag in each atom. Hence "define D5 selected, 526B" is much faster than "define D5 D4, 526B" as testing for membership in "selected" is almost instantaneous. Hence, the sequence: select 525, 526, 527, 528, 529, 530 select selected, 531, 532, 533, 534 define D6 selected, 535, 536, 537, 538 is the optimal way to build up large RasMol sets. This also has the advantage that "define foo foo,bar", as described above, generates a copy rather than appends to a list. i.e. tmp = allocate (foo, bar) deallocate (foo) foo = tmp i.e. there's a lot of memory intensive allocation and deallocation going on, that doesn't occur using "select". I'm sure with the "optmization hints" provided above you should be able to create a version of your script that takes a fraction of the time, i.e. a second or two rather than over a minute. I hope this helps. Roger -- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Toobers in Science Education Date: Sat, 01 Feb 2003 12:30:03 -0500 To: rasmol@lists.umass.edu Dear Educators and Students: I first learned about "toobers" from Tim Herman and Michael Patrick in their SEPA Workshops for high-school teachers. Toobers are soft, flexible, inexpensive foam plastic rods about a meter long, and as big around as a good-sized carrot. They are easily bent and hold their shape, due to an aluminum wire running down the center. Originally designed as a component of toys named Toobers and Zots, they are manufactured by Hands-On Toys. Last year I bought a bunch of toobers and as I taught my immunology class, I kept finding new ways to use them to illustrate structural concepts in lecture, especially protein structural concepts. Concepts that were iffy to convey with static slides and hand-waving came across much more clearly with toobers. Examples include discontinuous protein epitopes made of multiple loops, heat denaturation of discontinuous epitopes, buried linear epitopes for MHC and T cells, the six CDR's in antibody, and how they line up in multiple sequence alignments as hypervariable regions. I have just made a website with some photos and three short movie clips illustrating how I use toobers in lectures - http://www.umass.edu/molvis/toobers/ I know that the Herman & Patrick group in Wisconsin is very actively using toobers and will soon have some information about their work on the web. Meanwhile, if you know of related resources please let me know so I can link them to my toobers website (see links at the bottom of the page). Sincerely, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6249.0 Thread-Topic: Can RasMol be used in a commercial application? Thread-Index: AcLLkvWRfDHehRWSTkS3cUP1nPetWA== content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Mitch Barker Subject: RE: Can RasMol be used in a commercial application? Date: Mon, 03 Feb 2003 09:45:56 -0500 To: rasmol@lists.umass.edu I guess I'm most confused about the "infectivity" of the license. If for example we modify part of rasmol to run under windows .Net (a new MS "platform"), we'd gladly give these mods back to the rasmol, and would comply with any requirements to give credit and supply documentation. But does this mean that ALL the source code of our product now must itself be open source? I've been a commercial software developer of scientific software for 15 years, and the current surge of open source is quite interesting. The concept is compelling, but the rules seem a bit opaque. I don't know how modular rasmol is, but I would think that we'd only pick off a piece or two of it's functionality. (we could still provide the entire package intact though if that were a license requirement). Any comments on using just a single module of rasmol. Thanks. Mitch ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: RE: Can RasMol be used in a commercial application? Date: Mon, 03 Feb 2003 10:24:53 -0500 (EST) To: rasmol@lists.umass.edu Dear Mitch, The RasMol license is just as infectious as the GPL. So, if you modify RasMol to make a new program, that new program is covered by the RasMol license. If you make a new, independent, program which only calls RasMol through its specified external interfaces, e.g. by creating scripts and allowing RasMol to run them, the license status of that new program _might_ not be controlled by the RasMol license. As they say, "God and the Devil are in the details." The only way to be certain if a use of RasMol is sufficiently independent of RasMol to avoid the infectious nature of the license is to have all the details of the proposed use. If you effectively integrate any signficant portion of RasMol (whether binary, source code or documentation) into a new package, creating what is called in law a "derived work", then the entirety of that new package is covered by the RasMol license. For example, if you strip out some portion of RasMol, make it into a library or DDL, and use that to make your new program function, then your new program is infected. I know this sounds complicated, and it definitely needs a lawyer to untangle, but that only becomes an issue if you are trying to create closed source proprietary products out of the community's open source resources. As long as you keep making open source programs out of open source programs, things are quite simple. In other words, if you want to make a closed source proprietary molecular graphics program, you are probably better off starting from a different base than RasMol. To repeat the answer in the FAQ: Does this mean I can't make a commercial graphics program based on RasMol? If what you mean by "commercial" is that you want to distribute binary versions and keep the source code as a secret, no, you may not do that, but if what you mean by "commercial" is that you wish to sell programs and services based on RasMol, that you certainly may do. Just remember that your new and wonderful program has to include or reference all the original source code and documentation, including the file NOTICE, which will allow other people to copy your program. In other words the rules for distributing copies of RasMol that you have taken advantage of will also apply to people who wish to make copes of your program. A lot of people find it easy to work within this framework, but if you need to do commerical development which does not fit the open source model, you may not make use of any substantial portion of the RasMol 2.7 series to develop your own product. Regards, Herbert J. Bernstein ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 3 Feb 2003, Mitch Barker wrote: > I guess I'm most confused about the "infectivity" of the license. If for > example we modify part of rasmol to run under windows .Net (a new MS > "platform"), we'd gladly give these mods back to the rasmol, and would > comply with any requirements to give credit and supply documentation. > But does this mean that ALL the source code of our product now must > itself be open source? > > I've been a commercial software developer of scientific software for 15 > years, and the current surge of open source is quite interesting. The > concept is compelling, but the rules seem a bit opaque. > > I don't know how modular rasmol is, but I would think that we'd only > pick off a piece or two of it's functionality. (we could still provide > the entire package intact though if that were a license requirement). > Any comments on using just a single module of rasmol. > > Thanks. > > Mitch > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en,es-ES References: <0H9O00KL30L2XA@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: shalpine@earthlink.net Subject: Re: molecular 3D literacy Date: Mon, 03 Feb 2003 12:10:56 -0800 To: Robert Bateman , rasmol@lists.umass.edu Hello Bob: Thank you for raising this important issue. I believe the spatial "literacy" now required in biochemistry has traditionally been reserved for artist, specifically sculptors, architects, and other 3D professionals. If we are truly interested in expanding spatial literacy, we must extend science literacy to segments of the population usually put-off by the standard approach to science education. For example, future scientist should not be put through a "linear thought" filter (such as text-based tests) and then be expected to excel in spatial, visual-motor skills. This integration of disparate skillsets is the basis for a program I've developed called STArt! teaching Science Through Art. Using hands-on models and molecular visualization, I've introduced third graders to the concept of atoms and molecules, as now required by the new California science curriculum standards. An additional bonus: young students get very excited and interested in science. Best regards, Susana Susana Maria Halpine Artist-Biochemist Candle Light Productions 239 Sunridge Street Playa del Rey, CA 90293 (310) 306-8399 shalpine@earthlink.net http://home.earthlink.net/~shalpine Women Chemists Committee Chair American Chemical Society, Los Angeles Section --------------------------------------------------------------- > > Subject: molecular 3D literacy > Date: Wed, 29 Jan 2003 17:29:51 -0600 > From: Robert Bateman > To: rasmol@lists.umass.edu > > Colleagues: > > Those teaching and performing research in the molecular sciences, > especially chemistry and biochemistry, are aware of the need for both > students and practitioners to possess a kind of "literacy" which is > based on multiple dimensions, both spatial and temporal. It is > difficult to define precisely what skills one must possess before one > can be considered literate in this manner, but it is important to do > so from a pedagogical point of view. I have posted a draft list of > such skills at > > > > http://orca.st.usm.edu/~rbateman/kinemage/mol-literacy.htm > > > > and would appreciate feedback from this list to refine it. > > > > Sincerely, > > Bob Bateman > > > > > > Robert C. Bateman, Jr. > > Professor and Chair > > Department of Chemistry and Biochemistry > > University of Southern Mississippi > > Hattiesburg, MS 39406-5043 > > Robert.Bateman@usm.edu > > www.chem.usm.edu > > 601-266-4701 (department office) > > 601-266-6075 (fax) > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: List History Update Date: Mon, 03 Feb 2003 15:31:04 -0500 To: rasmol@lists.umass.edu I have updated the history archives for this email list (separating the 2002 file from the current file for 2003). Also, I moved the history archives to a new server (click on the link labeled "View/Search Past Discussion on the List" at the URL below, which has not changed). The subscribership has plateaued for the past year at about 600 addresses. In 2002, we averaged 1.2 messages/day or 9 messages/week. - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 Molecular Visualization Freeware EMail Discussion List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable from the above link. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: pdb format from Cn3D/VAST? Date: Mon, 03 Feb 2003 17:51:15 -0500 To: rasmol@lists.umass.edu [This reply is redirected from Steve Bryant of NCBI regarding Tim Driscoll's question below (paraphrased) "Can a VAST alignment be obtained in PDB format?" Other options for obtaining alignments in PDB format are explained at http://www.umass.edu/microbio/chime/morpher/morphmtd.htm#am Due to problems I had with my email in January, posting this reply to the list was delayed one month. My apologies.] Hi Eric, Thanks for your question! The quick answer is "no", unfortunately. Our VAST alignment server doesn't any longer try to present structure alignment results in PDB format. Older versions did something like this, up to a few months ago. But we dropped the feature because it wasn't used much - most of our users have Cn3D - and because it was difficult to explain what was going on. What the old version did, if I recall correctly, was to send a PDB file for the first of the selected structure neighbors, rotated and translated so as to superimpose on the query domain. Users had to concatenate these files themselves, using MODEL/ENDMDL or different chain codes, as required for the viewer they wanted to use. The current VAST server version does have a feature that may be of interest. The "ASN1" display option will send a compact file that gives alignment information only, in print-format (text) ASN1. It's easy to parse the rotation-translation matrix from this file. So without too much effort one can write a program or server that reads this matrix and PDB files for the structure neighbors, does the rotation and translation, and then writes out concatenated PDB files with whatever secondary processing one prefers, like inserting MODEL/ENDMDL. As you know, I can't offer to take on user support for viewers other than Cn3D. But if you or other developers want to make something like this, to show VAST alignments with other viewers, I'll be happy to advise as best I can. Steve -----Original Message----- Sent: Monday, December 30, 2002 2:10 PM From: Eric Martz [mailto:emartz@microbio.umass.edu] Subject: Fwd: pdb format from Cn3D/VAST? To: bryant@ncbi.nlm.nih.gov Cc: driscoll@molvisions.com Hi, Steve. The inquiry below was sent to the RasMol list (600 subscribers) by Tim Driscoll, who wrote the Chime websites for Lehninger's Principles of Biochem, Stryer's Biochem, and Garland's Biol of the Cell by Alberts et al. I'm interested in the answer, too. I know you now offer ASN.1 reformatted as PDB on your structure site for single asymmetric units, but I'm not sure about VAST alignments. If you do, it would be ideal for RasMol/Chime/PE to include MODEL #/ENDMDL records between models in the alignments. If you don't mind, I'll forward the answer to the RasMol list. -Eric >Date: Sun, 29 Dec 2002 18:23:10 -0500 >From: timothy driscoll >Subject: pdb format from Cn3D/VAST? >Sender: owner-rasmol@lists.umass.edu >To: LIST rasmol >Reply-to: rasmol@lists.umass.edu >X-Mailer: Mailsmith 1.5.3 (Blindsider) > >hi, > >I used VAST at the NCBI Web site >(http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml) to align two 3d >structures. I downloaded the alignment and viewed it using Cn3D, and it >looks great. now I'd like to be able to save it as a simple pdb file (text >format with atom records) for use in rasmol/chime/spv/wlvp. does anyone >know how to do this, or if it is even possible? > >thanks! > >:tim >-- >molvisions - molecular graphics & visualization > >usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <007f01c2c75a$28b04560$1ed4fea9@Tranquilo> ++++------+------+------+------+------+------+------+------+------+------+ From: "Peter C. McCluskey" Subject: Re: Can RasMol be used in a commercial application? Date: Mon, 10 Feb 2003 11:47:05 -0800 (PST) To: rasmol@lists.umass.edu yaya@bernstein-plus-sons.com (Herbert J. Bernstein) writes: >The only tricky part of creating a plug-in version of RasMol is that, >to avoid legal tangles, it needs to be done by somebody who has never >downloaded or used Chime, so that there cannot be any possibility that >they have reversed engineered their code. This is call "clean-room" >development. Any volunteers? I'm potentially interested, but as I've never used Chime (I've only seen a brief demo) I don't have much of an idea how hard it would take to make a plug-in with power comparable to Chime. >> I guess most people in this list ask at this point if we shall ever make >> something Chime-like out of the nouveau rasmol. Can a browser plug-in be >> under the GPL? I'd like to be sure before we commit rasmol under the GPL. >> Can anyone shed some light here? A quick google for GPL'd plug-in's suggests that there are quite a few. http://www.gnu.org/licenses/gpl-faq.html#GPLAndPlugins indicates that whether such plug-in's can be used with proprietary browsers depends on how those browsers call the plug-in, which might be hard to determine. It adds: "However, you can resolve that legal problem by adding an exception to your program's license which gives permission to link it with the non-free main program." I think that switching to a well understood license such as GPL would be a clear improvement over an obscure license that looks substantially less precise than what a lawyer would write. It might be a good idea to add an exception for linking with proprietary browsers. Or it might be even better to use the LGPL license. -- ------------------------------------------------------------------------------ Peter McCluskey | http://www.rahul.net/pcm | ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: <5.2.0.9.2.20030201120525.00a7c9a0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Cindy Klevickis Subject: Quick Script Date: Tue, 18 Feb 2003 09:29:43 -0500 To: rasmol@lists.umass.edu, "milesjj@jmu.edu" This is a multi-part message in MIME format. --Boundary_(ID_FyPudftbJ+X+kafRVAb7kw) Hello to All, One of my students, Peter Miles, has written a Visual Basic program that automatically generates Rasmol scripts for a number of different kinds of animation. We tested this with the students in one of my classes with good success. Peter would be interested in any feedback you have on whether this program might be more generally useful. He would like to add more features and would like to hear from you about features that might be useful. This program can be downloaded from his web page at: http://www.isat.jmu.edu/users/klevicca/milespjPortfolio/Main.html (Click on his "Programs" icon to go directly to the download location.) (It is called "Quick Script") You can send feedback to Peter from the mailto link on his page or directly at milesjj@jmu.edu Thanks in advance for your help. Cindy Klevickis --Boundary_(ID_FyPudftbJ+X+kafRVAb7kw) Content-description: Card for Cindy Klevickis Content-disposition: attachment; filename=klevicca.vcf begin:vcard n:Klevickis;Cindy tel;home:office phone: 540-568-2726 tel;work:James Madison University x-mozilla-html:FALSE adr:;;;;;; version:2.1 email;internet:klevicca@jmu.edu x-mozilla-cpt:;-22192 fn:Cindy Klevickis end:vcard --Boundary_(ID_FyPudftbJ+X+kafRVAb7kw)-- References: <5.2.0.9.2.20030201120525.00a7c9a0@marlin.bio.umass.edu> <3E524357.FECA98B6@jmu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Judy Voet Subject: Re: Quick Script Date: Wed, 19 Feb 2003 08:31:38 -0400 To: rasmol@lists.umass.edu, "milesjj@jmu.edu" Dear Cindy, Will this program run on Macs as well as PCs? I tried to download it and it was an exe file (not mac). How do I get it for Mac? Judy At 9:29 AM -0500 2/18/03, Cindy Klevickis wrote: >Hello to All, > >One of my students, Peter Miles, has written a Visual Basic program that >automatically generates Rasmol scripts for a number of different kinds of >animation. We tested this with the students in one of my classes with good >success. > >Peter would be interested in any feedback you have on whether this program >might be more generally useful. He would like to add more features and would >like to hear from you about features that might be useful. > >This program can be downloaded from his web page at: > >http://www.isat.jmu.edu/users/klevicca/milespjPortfolio/Main.html >(Click on his "Programs" icon to go directly to the download location.) > >(It is called "Quick Script") > >You can send feedback to Peter from the mailto link on his page or directly at >milesjj@jmu.edu > >Thanks in advance for your help. > >Cindy Klevickis > >Content-type: text/x-vcard; name=klevicca.vcf; charset=us-ascii >Content-description: Card for Cindy Klevickis >Content-disposition: attachment; filename=klevicca.vcf >Content-transfer-encoding: 7BIT > >Attachment converted: Macintosh HD:klevicca.vcf 19 (TEXT/MSWD) (0004889E) -- Judith G. Voet, J. H. Hammons Professor Swarthmore College jvoet1@swarthmore.edu Department of Chemistry 610-328-8520 500 College Avenue FAX 610-328-7355 Swarthmore, PA 19081-1390 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Announcement: DSMM: a Database of Simulated Molecular Motions Date: Wed, 19 Feb 2003 11:05:00 -0500 To: rasmol@lists.umass.edu Dear All, If you are interested in finding movies resulting from biomolecular simulation studies, please take a look at this new website: http://projects.villa-bosch.de/mcm/database/dsmm where you will find: "DSMM: a Database of Simulated Molecular Motions". You can read about it in Finocchiaro, G. , Wang, T., Hoffmann, R., Gonzalez, A., Wade, R.C. Nucleic Acids Research, 2003, 31, 456. at: http://nar.oupjournals.org/cgi/content/abstract/31/1/456. Please do submit your own molecular movies and email your feedback to dsmm@eml.villa-bosch.de. Rebecca Wade wade@EMBL-Heidelberg.DE European Media Laboratory, Heidelberg European Molecular Biology Laboratory, Heidelberg dsmm@eml.villa-bosch.de ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Dave Hurley Subject: Re: Quick Script Date: Wed, 19 Feb 2003 08:46:35 -0800 To: rasmol@lists.umass.edu Visual Basic doesn't compile for the Mac. If REALbasic (http://www.realsoftware.com) were used instead, then this would be possible. Maybe the author would consider porting their code to the Mac using this language. The development environment is currently Mac only, but sometime this quarter they will release a Windows version that will also cross-compile for Windows, Mac Classic, and Mac OS X. There is even a VB to RB code conversion utility that comes with the current version. Dave Hurley Biology Department University of Washington On Wednesday, February 19, 2003, at 04:31 AM, Judy Voet wrote: > Dear Cindy, > Will this program run on Macs as well as PCs? I tried to download it > and it was an exe file (not mac). How do I get it for Mac? > Judy > > At 9:29 AM -0500 2/18/03, Cindy Klevickis wrote: >> Hello to All, >> >> One of my students, Peter Miles, has written a Visual Basic program >> that >> automatically generates Rasmol scripts for a number of different >> kinds of >> animation. We tested this with the students in one of my classes >> with good >> success. >> >> Peter would be interested in any feedback you have on whether this >> program >> might be more generally useful. He would like to add more features >> and would >> like to hear from you about features that might be useful. >> >> This program can be downloaded from his web page at: >> >> http://www.isat.jmu.edu/users/klevicca/milespjPortfolio/Main.html >> (Click on his "Programs" icon to go directly to the download >> location.) >> >> (It is called "Quick Script") >> >> You can send feedback to Peter from the mailto link on his page or >> directly at >> milesjj@jmu.edu >> >> Thanks in advance for your help. >> >> Cindy Klevickis >> >> Content-type: text/x-vcard; name=klevicca.vcf; charset=us-ascii >> Content-description: Card for Cindy Klevickis >> Content-disposition: attachment; filename=klevicca.vcf >> Content-transfer-encoding: 7BIT >> >> Attachment converted: Macintosh HD:klevicca.vcf 19 (TEXT/MSWD) >> (0004889E) > > > -- > Judith G. Voet, J. H. Hammons Professor Swarthmore College > jvoet1@swarthmore.edu Department of > Chemistry > 610-328-8520 500 College Avenue > FAX 610-328-7355 Swarthmore, > PA 19081-1390 > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eugen Leitl Subject: Re: Quick Script Date: Wed, 19 Feb 2003 17:59:21 +0100 (CET) To: rasmol@lists.umass.edu On Wed, 19 Feb 2003, Dave Hurley wrote: > Visual Basic doesn't compile for the Mac. If REALbasic > (http://www.realsoftware.com) were used instead, then this would be > possible. Maybe the author would consider porting their code to the Mac > using this language. The development environment is currently Mac only, I haven't seen the code, but I very much doubt it's hard to port to Perl, Python or Ruby. These are crossplatform languages, open source. > but sometime this quarter they will release a Windows version that will > also cross-compile for Windows, Mac Classic, and Mac OS X. There is > even a VB to RB code conversion utility that comes with the current > version. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: <5.2.0.9.2.20030219110357.024bc6d0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Cindy Klevickis Subject: Reseting Rasmol inbetween scripts Date: Wed, 19 Feb 2003 19:44:29 -0500 To: rasmol@lists.umass.edu Cc: hellermj@jmu.edu This is a multi-part message in MIME format. --Boundary_(ID_YtEsTOty89Kk20it9epW3w) Hello to All from Cindy Klevickis, My students are writing Rasmol scripts in teams that collaborate with each other. They have found that sometimes they can have a script that runs perfectly on its own. But, when it is executed following a different script it has many error messages that say "unable to allocate shade." They have tried including "zap" and "reset" at the end of the first script with no success. Closing Rasmol entirely and opening it up again before running the second script fixes this problem. In trying to troubleshoot their difficulties, they sent me this question. "Within the RasMol command line, is there a command or set of command that could be used to "reset" all of the setting in RasMol established by previous scripts? By "reset" I mean to set up RasMol just as it would be if the program were closed and re-opened." Thank you in advance for any advice you might have. --Boundary_(ID_YtEsTOty89Kk20it9epW3w) Content-description: Card for Cindy Klevickis Content-disposition: attachment; filename=klevicca.vcf begin:vcard n:Klevickis;Cindy tel;home:office phone: 540-568-2726 tel;work:James Madison University x-mozilla-html:FALSE adr:;;;;;; version:2.1 email;internet:klevicca@jmu.edu x-mozilla-cpt:;-22192 fn:Cindy Klevickis end:vcard --Boundary_(ID_YtEsTOty89Kk20it9epW3w)-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Reseting Rasmol inbetween scripts Date: Wed, 19 Feb 2003 20:52:47 -0500 To: rasmol@lists.umass.edu at 7:44 PM EDT on (Wednesday) 19 February 2003 Cindy Klevickis said: > Hello to All from Cindy Klevickis, > > My students are writing Rasmol scripts in teams that collaborate with > each other. They have found that sometimes they can have a script that > runs perfectly on its own. But, when it is executed following a > different script it has many error messages that say "unable to allocate > shade." They have tried including "zap" and "reset" at the end of the > first script with no success. Closing Rasmol entirely and opening it up > again before running the second script fixes this problem. In trying to > troubleshoot their difficulties, they sent me this question. > > "Within the RasMol command line, is there a command or set of command > that could be used to "reset" all of the setting in RasMol established by > previous scripts? By "reset" I mean to set up RasMol just as it would be > if the program were closed and re-opened." > > Thank you in advance for any advice you might have. > I believe you can fix the allocate shade error with color white which clears the palette. otherwise, I know of no single command except a load command that clears everything. maybe someone else does? :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Cindy Klevickis Subject: Re: Reseting Rasmol inbetween scripts Date: Wed, 19 Feb 2003 21:57:35 -0500 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_l9T2z88QtlPkKeu6FD+SBA) Thanks VERY much. This sounds good. It worked when I tested it on my computer here at home and I forwarded this to my students so that they can test them on the picky school computers. Cindy Klevickis timothy driscoll wrote: > at 7:44 PM EDT on (Wednesday) 19 February 2003 Cindy Klevickis said: > > > Hello to All from Cindy Klevickis, > > > > My students are writing Rasmol scripts in teams that collaborate with > > each other. They have found that sometimes they can have a script that > > runs perfectly on its own. But, when it is executed following a > > different script it has many error messages that say "unable to allocate > > shade." They have tried including "zap" and "reset" at the end of the > > first script with no success. Closing Rasmol entirely and opening it up > > again before running the second script fixes this problem. In trying to > > troubleshoot their difficulties, they sent me this question. > > > > "Within the RasMol command line, is there a command or set of command > > that could be used to "reset" all of the setting in RasMol established by > > previous scripts? By "reset" I mean to set up RasMol just as it would be > > if the program were closed and re-opened." > > > > Thank you in advance for any advice you might have. > > > > I believe you can fix the allocate shade error with > > color white > > which clears the palette. otherwise, I know of no single command except a > load command that clears everything. maybe someone else does? > > :tim > -- > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > --Boundary_(ID_l9T2z88QtlPkKeu6FD+SBA) Content-description: Card for Cindy Klevickis Content-disposition: attachment; filename=klevicca.vcf begin:vcard n:Klevickis;Cindy tel;home:office phone: 540-568-2726 tel;work:James Madison University x-mozilla-html:FALSE adr:;;;;;; version:2.1 email;internet:klevicca@jmu.edu x-mozilla-cpt:;-22192 fn:Cindy Klevickis end:vcard --Boundary_(ID_l9T2z88QtlPkKeu6FD+SBA)-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Bruce Branchini Subject: Re:selective display Date: Thu, 20 Feb 2003 11:19:43 +0100 To: rasmol@lists.umass.edu Hello All, Does anyone know a way in Rasmol to display only a selected area of a protein structure. I have tried coloring all residues I don't want to display black using a black background and this works OK, except that with certain views the black lines make it difficult to see certain features like H bonding. I have also tried a white background with whited colored residues with no improvement. Thanks in advance for your help. Bruce Branchini ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_wz5S2rYzIdspPhGmcSGheg)" ++++------+------+------+------+------+------+------+------+------+------+ From: adriano ceccarelli Subject: rasmol 2.7.2 install in Mac OSX Date: Thu, 20 Feb 2003 12:15:20 +0100 To: rasmol@lists.umass.edu --Boundary_(ID_wz5S2rYzIdspPhGmcSGheg) Dear colleagues, I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 (beta=20= version) and, not being exactly a guru of UNIX systems/subsistems I got=20= lost. Is there a manual with easier instructions (something that goes=20 beyond " ...set the CFLAGS for your platform...."? Thanks for any help. Sincerely Adriano Ceccarelli Prof. Adriano Ceccarelli Facolt=E0 di Medicina e Chirurgia Dip. Scienze Cliniche e Biologiche Osp. S. Luigi Gonzaga - Orbassano Torino - ITALY phone +39116708109 fax +39119038639 email adriano.ceccarelli@unito.it= --Boundary_(ID_wz5S2rYzIdspPhGmcSGheg) Dear colleagues, I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 (beta version) and, not being exactly a guru of UNIX systems/subsistems I got lost. Is there a manual with easier instructions (something that goes beyond " ...set the CFLAGS for your platform...."? Thanks for any help. Sincerely Adriano Ceccarelli Prof. Adriano Ceccarelli Facolt=E0 di Medicina e Chirurgia Dip. Scienze Cliniche e Biologiche Osp. S. Luigi Gonzaga - Orbassano Torino - ITALY phone +39116708109 fax +39119038639 email adriano.ceccarelli@unito.it= --Boundary_(ID_wz5S2rYzIdspPhGmcSGheg)-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re:selective display Date: Thu, 20 Feb 2003 06:22:32 -0500 To: rasmol@lists.umass.edu hi Bruce, try "restrict". for example, restrict none will make everything disappear. hth, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest at 11:19 AM EDT on (Thursday) 20 February 2003 Bruce Branchini said: > Hello All, > > Does anyone know a way in Rasmol to display only a selected area of a > protein structure. I have tried coloring all residues I don't want to > display black using a black background and this works OK, except that with > certain views the black lines make it difficult to see certain features > like H bonding. I have also tried a white background with whited colored > residues with no improvement. > > Thanks in advance for your help. > > Bruce Branchini > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Thu, 20 Feb 2003 06:24:52 -0500 To: rasmol@lists.umass.edu at 12:15 PM EDT on (Thursday) 20 February 2003 adriano ceccarelli said: > Dear colleagues, > I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 (beta > version) and, not being exactly a guru of UNIX systems/subsistems I got > lost. Is there a manual with easier instructions (something that goes > beyond " ...set the CFLAGS for your platform...."? > I have not found anything helpful for myself, being quite the novice unix weenie. but please, if you find something more helpful, I would love to hear about it! thanks, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Mathy Froeyen Subject: multiple molecules in rasmol 2.7.2.1 Date: Thu, 20 Feb 2003 13:50:10 +0100 To: "rasmol@lists.umass.edu" Dear all, In rasmol 2.7.2.1 there is a possibility to load several molecules at the same time. However when I load more than one molecule, each molecule is centered individually to its own center point. This is a problem if you do structure comparisons where you have overlayed the structures (by an external program) and want to look at RMS differences. I looked in the c-code and tried to patch the centering routines but had only partial success ( My code destroys the zooming functions). Any ideas? regards, Mathy Froeyen ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <5.2.0.9.2.20030219110357.024bc6d0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Reseting Rasmol inbetween scripts Date: Thu, 20 Feb 2003 07:44:06 -0500 To: rasmol@lists.umass.edu At 2/19/03, Cindy Klevickis wrote: >"unable to allocate shade." Chime and RasMol 2.6 (2.7?) both suffer from this limitation. This can be corrected with: select all color [any single plain color, e.g. white] [now apply a new color scheme] When the "unable to allocate shade" error occurs in Protein Explorer, the above information is offered automatically, including: "The best way to avoid the "Unable to allocate shade" problem is to start with simple color schemes (plain colors or Element/CPK), and end with complex ones that use up lots of colors (notably "N->C Rainbow" aka "Group", or Temperature)." (The problem arises when you apply a complex color scheme that "uses up" RasMol's internal palette, and then try to add additional colors by selecting a subset of the atoms and applying a different color scheme.) In Chime, if you have generated a surface and applied multiple colors to it, you may need to delete the surface in order to avoid "unable to allocate shade". -Eric ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <3E54441E.806948E6@jmu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re:selective display Date: Thu, 20 Feb 2003 07:52:39 -0500 To: rasmol@lists.umass.edu On 2/20/03, Bruce Branchini asked how to hide subsets of the atoms in a PDB file. Tim's recommendation to use the 'restrict' command is correct. In Protein Explorer, you can select what you want to see (from the SELECT menu), then open the DISPLAY menu and select "Only" (display only what is selected). This hides non-selected atoms. Alternatively, select what you don't want to see, then open the DISPLAY menu and select *Hide*. You are then presented with a list of options: Hide everything Hide hydrogen bonds in selected atoms. Hide disulfide (SS) bonds in selected atoms. Hide dots for all atoms. Hide selected atoms and bonds. Hide non-selected atoms and bonds (same as DISPLAY Only [selected]). Delete surface. Such menu operations generate the appropriate RasMol/Chime commands and send them to Chime. The commands are displayed in the message box. Watching the commands generated by Protein Explorer is a good way to learn which commands to use for a particular purpose in RasMol. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Antivirus: scanned by sophie at shiva.jussieu.fr ++++------+------+------+------+------+------+------+------+------+------+ From: christian.simon@ppce.jussieu.fr (Christian Simon) Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Thu, 20 Feb 2003 13:38:49 +0100 (FRA Hiver) To: rasmol@lists.umass.edu Dear Adriano, > Dear colleagues, > I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 (beta > version) and, not being exactly a guru of UNIX systems/subsistems I got > lost. Is there a manual with easier instructions (something that goes > beyond " ...set the CFLAGS for your platform...."? Why do not you install it through Fink ? Fink is a package holder that allows you to download-patch-compile THOUSANDS of softwares (essentially from Unix/Linux world), including rasmol, xmgrace, gnuplot, x11, TeX, even KDE, Gimp, etc... AUTOMATICALLY, with little knowledge. Sounds magic ? http://fink.sourceforge.net/ Personnally, I installed Rasmol in few minutes... without effort. Furthermore, Fink webpage gives hints to port softs to OSX... and the values for CFLAGS you are looking for... If you really insist to do it by hand... -- Christian ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_3EuRCK5ve0TrEgrD1tsfDQ)" User-Agent: Microsoft-Entourage/10.1.1.2418 X-OriginalArrivalTime: 20 Feb 2003 14:48:39.0288 (UTC) FILETIME=[27986F80:01C2D8EF] ++++------+------+------+------+------+------+------+------+------+------+ From: Warren Gallagher Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Thu, 20 Feb 2003 08:48:53 -0600 To: rasmol@lists.umass.edu > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --Boundary_(ID_3EuRCK5ve0TrEgrD1tsfDQ) 20 February, 2003 Adriano, On 2/20/03 5:15 AM, "adriano ceccarelli" wrote: > I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 (beta > version) and, not being exactly a guru of UNIX systems/subsistems I got > lost. Is there a manual with easier instructions (something that goes > beyond " ...set the CFLAGS for your platform...."? !~~~~~~~~~~~~~~~~~~ I have been using RasMol 2.7.2 under X11 and found the following set-up works pretty well: 1. First, I created a folder within my =B3Documents=B2 folder called =B3pdb_files= =B2 where I place all my pdb files. The path to this folder is =B3~/Documents/pdb_files=B2 2. Second, I placed the rasmol folder that I downloaded in the =B3Applications=B2 folder. The path to the executable is =B3/Applications/rasmol/bin/rasmol-32=B2 3. Third, I launched X11 and selected =B3Customize=B2 from the =B3Applications=B2 menu and pressed the =B3New=B2 button. Under the =B3Name=B2 column I typed in =B3RasMol=B2, and under the =B3Command=B2 column I typed in =B3cd ~/Documents/pdb_files; xterm -e /Applications/rasmol/bin/rasmol-32=B2. This will create an item named =B3RasMol=B2 in the X11 =B3Applications=B2 menu. 4. When I want to run Rasmol, I launch X11 and select =B3RasMol=B2 from the =B3Applications=B2 menu. This changes the working directory to the folder containing my pdb files and then launches rasmol within an xterm session. The purpose behind changing the working directory to the folder containing the pdb files is that I only need to type in the name of the pdb file without its path when loading files. I hope this is helpful. Warren !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Warren Gallagher Associate Professor Chemistry Department University of Wisconsin-Eau Claire Eau Claire, WI 54702 TEL: (715) 836-5388 FAX: (715) 836-4979 --Boundary_(ID_3EuRCK5ve0TrEgrD1tsfDQ) Re: rasmol 2.7.2 install in Mac OSX 20 February, 2003

Adriano,

On 2/20/03 5:15 AM, "adriano ceccarelli" <adriano.ceccarelli@unito.it> wrote:
> I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 (beta
> version) and, not being exactly a guru of UNIX systems/subsistems I got
> lost. Is there a manual with easier instructions (something that goes
> beyond " ...set the CFLAGS for your platform...."?
!~~~~~~~~~~~~~~~~~~

    I have been using RasMol 2.7.2 under X11 and found the following set-up works pretty well:

  1. First, I created a folder within my “Documents” folder called “pdb_files” where I place all my pdb files.  The path to this folder is “~/Documents/pdb_files”
  2. Second, I placed the rasmol folder that I downloaded in the “Applications” folder.  The path to the executable is “/Applications/rasmol/bin/rasmol-32”
  3. Third, I launched X11 and selected “Customize” from the “Applications” menu and pressed the “New” button.  Under the “Name” column I typed in “RasMol”, and under the “Command” column I typed in “cd ~/Documents/pdb_files; xterm -e /Applications/rasmol/bin/rasmol-32”.  This will  create an item named “RasMol” in the X11 “Applications” menu.
  4. When I want to run Rasmol,  I launch X11 and select “RasMol” from the “Applications” menu.  This changes the working directory to the folder containing my pdb files and then launches rasmol within an xterm session.  The purpose behind changing the working directory to the folder containing the pdb files is that I only need to type in the name of the pdb file without its path when loading files.

I hope this is helpful.

Warren

!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Warren Gallagher
Associate Professor
Chemistry Department
University of Wisconsin-Eau Claire
Eau Claire, WI 54702
TEL: (715) 836-5388
FAX: (715) 836-4979

 --Boundary_(ID_3EuRCK5ve0TrEgrD1tsfDQ)-- Originator-info: login-token=Mulberry:01YaOmUNgQ1sBzES7WqCTWrfQDIX3s1x/OGNS1lyM=; token_authority=postmaster@andrew.cmu.edu Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: will mcclure Subject: Re: multiple molecules in rasmol 2.7.2.1 Date: Thu, 20 Feb 2003 11:46:16 -0500 To: rasmol@lists.umass.edu What works in RasMol 2.6 (and Chime) is to make separate MODELs of each superposed coordinate set in one file. This requires the addition of dividers in the superposed file. For two sets of coordinates, use: MODEL 1 coordinates for first structure ENDMDL MODEL 2 coordinates for second structure ENDMDL END Then use, 'load nmrpdb filename.pdb' The various models are displayed, etc. with 'select ::1' or 'restrict ::2', etc. -Will McClure --On Thursday, February 20, 2003 1:50 PM +0100 Mathy Froeyen wrote: > Dear all, > > In rasmol 2.7.2.1 there is a possibility to load several molecules > at the same time. > > However when I load more than one molecule, > each molecule is centered individually to its own center point. > This is a problem if you do structure comparisons where you > have overlayed the structures (by an external program) and > want to look at RMS differences. > > I looked in the c-code and tried to patch the centering routines > but had only partial success > ( My code destroys the zooming functions). > > Any ideas? > > regards, > Mathy Froeyen > > > ----------------------------------------------------------------ras > mol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ----------------------------------------------------------------ras > mol-- > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Info: This message was accepted for relay by smtp03.mrf.mail.rcn.net as the sender used SMTP authentication X-Trace: UmFuZG9tSVagQoWmCZHCBwIXgiDJ8mUp6czyZB7WdTkLaqQd3CUiznejebGGrap3 X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id h1KHjvf19671 ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Masi Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Thu, 20 Feb 2003 12:45:53 -0500 To: rasmol@lists.umass.edu As others have suggested, installing Fink will take some time, but Fink makes installing a large number of Unix applications very easy. One minor annoyance I have with the RasMol installed via Fink (I assume the same thing happens if RasMol is installed by other means) is that RasMol is very picky about the form of a file's name. If the path to the file that is to be displayed contains a space, RasMol will not be able to find the file (I tried escaping with \ and I tried putting quotes around any folder name that contains spaces). I haven't done much with it yet, but PyMol, which can be installed using Fink, doesn't have a problem with non-Unix-y file names. It might be a good alternative/supplement to RasMol. Chris On Thursday, February 20, 2003, at 06:15 AM, adriano ceccarelli wrote: > Dear colleagues, > I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 (beta > version) and, not being exactly a guru of UNIX systems/subsistems I > got lost. Is there a manual with easier instructions (something that > goes beyond " ...set the CFLAGS for your platform...."? > > Thanks for any help. > > Sincerely > > Adriano Ceccarelli > > > > Prof. Adriano Ceccarelli > Facoltà di Medicina e Chirurgia > Dip. Scienze Cliniche e Biologiche > Osp. S. Luigi Gonzaga - Orbassano > Torino - ITALY > phone +39116708109 > fax +39119038639 > email adriano.ceccarelli@unito.it ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <3E54441E.806948E6@jmu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Ian Musgrave Subject: Re:selective display Date: Fri, 21 Feb 2003 09:40:50 +1030 To: rasmol@lists.umass.edu G'Day All At 11:19 20/02/2003 +0100, you wrote: >Hello All, > >Does anyone know a way in Rasmol to display only a selected area of a >protein structure. I have tried coloring all residues I don't want to >display black using a black background and this works OK, except that with >certain views the black lines make it difficult to see certain features >like H bonding. I have also tried a white background with whited colored >residues with no improvement. There are two basic ways to do this, Tim Driscol has mentioned one, using restrict, and the other is using select. Both are approximately the same, but have a few quirks. [load protein file, say on with multiple chains and a ligand bound to it] The default display is in wireframe, so we will stick with this at the moment. restrict *A [restricts to chain A, looks good] restrict 100-200A [restricts to amino acids 100-200 in A] restrict lys123A [restricts to just the lysine 123 in chain A, nice zoom in] This is all fine and dandy, now lets try and go back restrict 100-200A [this gives the message 232 atoms selected, but the display hasn't changed, RESTRICT turns off the WIREFRAME (or CARTOON or SPACEFILL) so you have to turn on the WIREFRAME again] wireframe on [restores your previous view] Similar sequence using select select all wireframe off select *A wireframe on wireframe off select 100-200A wireframe on wireframe off select lys123A wireframe on wireframe off select 100-200A wireframe on Restrict is more efficient than select, so long as you remember to turn wireframe ON when backing out of a zoom-in sequence, or if you want to swap from wireframe to some other view. Also, if you have got your selected portion of the protein set up, then want to show a ligand binding to it, you have to use select to turn on the hetero group, as restrict will make your protein disaster. eg. [load protein file, say on with multiple chains and a ligand bound to it] restrict 100-200A [restricts to amino acids 100-200 in A] select hetero wireframe on Cheers! Ian (see http://home.mira.net/~reynella/chime/adr_tuta.htm for a limited version of the above) =============================================================== Ian F. Musgrave Ph.D, ian.musgrave@adelaide.edu.au Senior Lecturer, Dept. Clinical and Experimental Pharmacology University of Adelaide, SA, 5005, Australia Phone +61 8 83033905 Fax +61 8 8224 0685 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_8TOHxmozh+9+GDmBRdO35g)" ++++------+------+------+------+------+------+------+------+------+------+ From: adriano ceccarelli Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Fri, 21 Feb 2003 09:26:15 +0100 To: rasmol@lists.umass.edu --Boundary_(ID_8TOHxmozh+9+GDmBRdO35g) Dear Chris and all the ones who sent helpful suggestions, which I have followed the most carefully I could, I am afraid I still =20= am in troubles. I have downloaded and installed Fink with no pain at all. I already had =20= installed X11 package from Apple (beta test version). I followed fink =20= instructions to download and install rasmol as source package and I was =20= prompted with the need to install 5 more packages, including =20 xfree86-rootless. But while installing, it stopped with an error =20 message: "configure: error: no acceptable cc in $PATH" I have looked in =20= all the troubleshooting docs I could find but coudn't solve the =20 problem. As far as my knowledge of UNIX goes, that means it cannot find =20= a compiler. Correct? However, I couldn't locate gcc or cc anywhere in =20= my directories. Is that normal, am I missing some sw, or have I messed =20= it up by reinstalling xfree86 on a preexisting x11 installation? I will be grateful for more help. Thanks Adriano Gioved=EC, 20 Feb 2003, alle 18:45 Europe/Rome, Christopher Masi ha =20 scritto: > As others have suggested, installing Fink will take some time, but =20= > Fink makes installing a large number of Unix applications very easy. =20= > One minor annoyance I have with the RasMol installed via Fink (I =20 > assume the same thing happens if RasMol is installed by other means) =20= > is that RasMol is very picky about the form of a file's name. > If the path to the file that is to be displayed contains a space, =20= > RasMol will not be able to find the file (I tried escaping with \ and =20= > I tried putting quotes around any folder name that contains spaces). > I haven't done much with it yet, but PyMol, which can be installed =20= > using Fink, doesn't have a problem with non-Unix-y file names. It =20 > might be a good alternative/supplement to RasMol. > > Chris > > > On Thursday, February 20, 2003, at 06:15 AM, adriano ceccarelli = wrote: > >> Dear colleagues, >> I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 =20 >> (beta version) and, not being exactly a guru of UNIX =20 >> systems/subsistems I got lost. Is there a manual with easier =20 >> instructions (something that goes beyond " ...set the CFLAGS for your = =20 >> platform...."? >> >> Thanks for any help. >> >> Sincerely >> >> Adriano Ceccarelli >> >> >> >> Prof. Adriano Ceccarelli >> Facolt=E0 di Medicina e Chirurgia >> Dip. Scienze Cliniche e Biologiche >> Osp. S. Luigi Gonzaga - Orbassano >> Torino - ITALY >> phone +39116708109 >> fax +39119038639 >> email adriano.ceccarelli@unito.it > ----------------------------------------------------------------=20 > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ----------------------------------------------------------------=20 > rasmol-- > > Prof. Adriano Ceccarelli Facolt=E0 di Medicina e Chirurgia Dip. Scienze Cliniche e Biologiche Osp. S. Luigi Gonzaga - Orbassano Torino - ITALY phone +39116708109 fax +39119038639 email adriano.ceccarelli@unito.it --Boundary_(ID_8TOHxmozh+9+GDmBRdO35g) Dear Chris and all the ones who sent helpful suggestions, which I have followed the most carefully I could, I am afraid I still am in troubles. I have downloaded and installed Fink with no pain at all. I already had installed X11 package from Apple (beta test version). I followed fink instructions to download and install rasmol as source package and I was prompted with the need to install 5 more packages, including xfree86-rootless. But while installing, it stopped with an error message: "configure: error: no acceptable cc in $PATH" I have looked in all the troubleshooting docs I could find but coudn't solve the problem. As far as my knowledge of UNIX goes, that means it cannot find a compiler. Correct? However, I couldn't locate gcc or cc anywhere in my directories. Is that normal, am I missing some sw, or have I messed it up by reinstalling xfree86 on a preexisting x11 installation? I will be grateful for more help. Thanks Adriano Gioved=EC, 20 Feb 2003, alle 18:45 Europe/Rome, Christopher Masi ha scritto: As others have suggested, installing Fink will take some time, but Fink makes installing a large number of Unix applications very easy. One minor annoyance I have with the RasMol installed via Fink (I assume the same thing happens if RasMol is installed by other means) is that RasMol is very picky about the form of a file's name. If the path to the file that is to be displayed contains a space, RasMol will not be able to find the file (I tried escaping with \ and I tried putting quotes around any folder name that contains spaces). I haven't done much with it yet, but PyMol, which can be installed using Fink, doesn't have a problem with non-Unix-y file names. It might be a good alternative/supplement to RasMol. Chris On Thursday, February 20, 2003, at 06:15 AM, adriano ceccarelli wrote: Dear colleagues, I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 (beta version) and, not being exactly a guru of UNIX systems/subsistems I got lost. Is there a manual with easier instructions (something that goes beyond " ...set the CFLAGS for your platform...."? Thanks for any help. Sincerely Adriano Ceccarelli Prof. Adriano Ceccarelli Facolt=E0 di Medicina e Chirurgia Dip. Scienze Cliniche e Biologiche Osp. S. Luigi Gonzaga - Orbassano Torino - ITALY phone +39116708109 fax +39119038639 email adriano.ceccarelli@unito.it = ----------------------------------------------------------------= rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm Prof. Adriano Ceccarelli Facolt=E0 di Medicina e Chirurgia Dip. Scienze Cliniche e Biologiche Osp. S. Luigi Gonzaga - Orbassano Torino - ITALY phone +39116708109 fax +39119038639 email adriano.ceccarelli@unito.it --Boundary_(ID_8TOHxmozh+9+GDmBRdO35g)-- X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Mathy Froeyen Subject: [Fwd: Re: multiple molecules in rasmol 2.7.2.1] Date: Fri, 21 Feb 2003 10:33:39 +0100 To: "rasmol@lists.umass.edu" Dear Mathy I use to compare several PDB files with rasmol but after making the superposition of the structures with another program (SwissPDB Viewer is very good for this http://us.expasy.org/spdbv/ and is available for all platforms). The trick for distinguish the different superposed PDB from within RasMol is to label the coordinates for each PDB file with a different chain name (this can be easily done from within SwissPDB Viewer also). This allow you to use all the rich rasmol syntax to select which part of the structures do you want to work. If you have any doubts or more questions about this, please don't heasitate to e-mail me. Best regards Gerard PS: my you be so kind to redirect this message to the rasmol list? I have problems with the alias of my e-mail address and this mail is refused by the listserver -- =========================================================================== DR. GERARD PUJADAS BIOTECNOLOGIA COMPUTACIONAL DEPT. BIOQUIMICA I BIOTECNOLOGIA E-MAIL: pujadas@quimica.urv.es UNIV. ROVIRA I VIRGILI PHONE: 34-977 559565 PLAÇA IMPERIAL TARRACO 1 FAX: 34-977 559597 43005 TARRAGONA (CATALONIA) STATE: SPAIN (EUROPEAN UNION) =========================================================================== > >In rasmol 2.7.2.1 there is a possibility to load several molecules >at the same time. > >However when I load more than one molecule, >each molecule is centered individually to its own center point. >This is a problem if you do structure comparisons where you >have overlayed the structures (by an external program) and >want to look at RMS differences. > >I looked in the c-code and tried to patch the centering routines >but had only partial success >( My code destroys the zooming functions). > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Antivirus: scanned by sophie at shiva.jussieu.fr ++++------+------+------+------+------+------+------+------+------+------+ From: christian.simon@ppce.jussieu.fr (Christian Simon) Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Fri, 21 Feb 2003 09:56:46 +0100 (FRA Hiver) To: rasmol@lists.umass.edu Dear Adriano, > I have downloaded and installed Fink with no pain at all. I already had > installed X11 package from Apple (beta test version). Easy, isn'it ? > I followed fink > instructions to download and install rasmol as source package and I was > prompted with the need to install 5 more packages, including > xfree86-rootless. But while installing, it stopped with an error > message: "configure: error: no acceptable cc in $PATH" I have looked in > all the troubleshooting docs I could find but coudn't solve the > problem. As far as my knowledge of UNIX goes, that means it cannot find > a compiler. Correct? However, I couldn't locate gcc or cc anywhere in > my directories. Is that normal, am I missing some sw, or have I messed > it up by reinstalling xfree86 on a preexisting x11 installation? Yes it is normal. I am almost sure you did not installed Apple's SDK, did you ? (Soft Developpement Toolkit ? which include all these stuff and more, for free ?) But we should now go on with Fink's mailing list. See you there ! -- Christian ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id h1LAH3f23068 ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: [Fwd: Re: multiple molecules in rasmol 2.7.2.1] Date: Fri, 21 Feb 2003 05:15:33 -0500 To: rasmol@lists.umass.edu hi, I concur with Gerard - Swiss Pdb Viewer is wonderful for aligning multiple structures in seconds. if you use it, though, be aware that SPV is more picky than rasmol about non-standard pdb files and may have trouble with nucleic acids, carbohydrates, etc. on a more philosophical note (if I may), I prefer using multiple MODEL records for aligned structures in the same file, instead of chain designations. the issue is minor, and I have not found any practical pros or cons as far as implementing rasmol commands ("select :a" vs "select model=1"). but I instinctively regard different chains as belonging to the same structure, and different models as being somewhat more independent of each other. a blurry distinction, to be sure, and quite possibly bogus - but my two cents. if you work in graphics, I think of multiple models existing on different layers, with multiple chains being on the same layer. anyway... the drawback of course, is that creating multiple model files still requires editing the raw pdb file, at least as far as I know. but wil mcclure's instructions are easy to follow: at 11:46 AM EDT on (Thursday) 20 February 2003 will mcclure said: > > > > What works in RasMol 2.6 (and Chime) is to make separate MODELs of > > each superposed coordinate set in one file. This requires the > > addition of dividers in the superposed file. For two sets of > > coordinates, use: > > > > MODEL 1 > > coordinates for first structure > > ENDMDL > > MODEL 2 > > coordinates for second structure > > ENDMDL > > END if you have any trouble, you can email the files to me directly. I'll be happy to convert them to a multiple model file for you (it's that easy). in fact, I'm working on an online tool to do this sort of thing - you submit multiple sets of coordinates and it returns the coordinates in a multiple-model file. it's just not ready yet :-) best regards, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest --------original message-------- at 10:33 AM EDT on (Friday) 21 February 2003 Mathy Froeyen said: > Dear Mathy > > I use to compare several PDB files with rasmol but after making the > superposition of the structures with another program (SwissPDB Viewer > is very good for this http://us.expasy.org/spdbv/ and is available > for all platforms). The trick for distinguish the different > superposed PDB from within RasMol is to label the coordinates for > each PDB file with a different chain name (this can be easily done > from within SwissPDB Viewer also). This allow you to use all the rich > rasmol syntax to select which part of the structures do you want to > work. > > If you have any doubts or more questions about this, please don't > heasitate to e-mail me. > > Best regards > > Gerard > > PS: my you be so kind to redirect this message to the rasmol list? I > have problems with the alias of my e-mail address and this mail is > refused by the listserver > -- > =========================================================================== > DR. GERARD PUJADAS > BIOTECNOLOGIA COMPUTACIONAL > DEPT. BIOQUIMICA I BIOTECNOLOGIA E-MAIL: pujadas@quimica.urv.es > UNIV. ROVIRA I VIRGILI PHONE: 34-977 559565 > PLAÇA IMPERIAL TARRACO 1 FAX: 34-977 559597 > 43005 TARRAGONA (CATALONIA) > STATE: SPAIN (EUROPEAN UNION) > =========================================================================== > > > > > > >In rasmol 2.7.2.1 there is a possibility to load several molecules > >at the same time. > > > >However when I load more than one molecule, > >each molecule is centered individually to its own center point. > >This is a problem if you do structure comparisons where you > >have overlayed the structures (by an external program) and > >want to look at RMS differences. > > > >I looked in the c-code and tried to patch the centering routines > >but had only partial success > >( My code destroys the zooming functions). > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_Hox8YllcxqigB0EqLXacsw)" ++++------+------+------+------+------+------+------+------+------+------+ From: adriano ceccarelli Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Fri, 21 Feb 2003 13:08:57 +0100 To: rasmol@lists.umass.edu --Boundary_(ID_Hox8YllcxqigB0EqLXacsw) Dear Christian, I am not sure which one of the available lists you mean. I have=20 obviously subscribed to the beginners.... However, I did get the x11SDKForMAcOS.pkg, but when I install it it=20 says "disk space required =3D 0 Kb" so I suspect something is wrong = there. I will look for a reply on the fink list. Thanks Adriano Venerd=EC, 21 Feb 2003, alle 09:56 Europe/Rome, Christian Simon ha=20 scritto: > christian.simon@ppce.jussieu.fr (Christian Simon) Prof. Adriano Ceccarelli Facolt=E0 di Medicina e Chirurgia Dip. Scienze Cliniche e Biologiche Osp. S. Luigi Gonzaga - Orbassano Torino - ITALY phone +39116708109 fax +39119038639 email adriano.ceccarelli@unito.it --Boundary_(ID_Hox8YllcxqigB0EqLXacsw) Dear Christian, I am not sure which one of the available lists you mean. I have obviously subscribed to the beginners.... However, I did get the x11SDKForMAcOS.pkg, but when I install it it says "disk space required =3D 0 Kb" so I suspect something is wrong there. I will look for a reply on the fink list. Thanks Adriano Venerd=EC, 21 Feb 2003, alle 09:56 Europe/Rome, Christian Simon ha scritto: christian.simon@ppce.jussieu.fr (Christian Simon) Prof. Adriano Ceccarelli Facolt=E0 di Medicina e Chirurgia Dip. Scienze Cliniche e Biologiche Osp. S. Luigi Gonzaga - Orbassano Torino - ITALY phone +39116708109 fax +39119038639 email adriano.ceccarelli@unito.it --Boundary_(ID_Hox8YllcxqigB0EqLXacsw)-- References: <3E55F273.95604E1F@rega.kuleuven.ac.be> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: [Fwd: Re: multiple molecules in rasmol 2.7.2.1] Date: Fri, 21 Feb 2003 09:41:00 -0500 To: rasmol@lists.umass.edu At 2/21/03, Tim Driscoll wrote: >the drawback of course, is that creating multiple model files still requires >editing the raw pdb file, at least as far as I know. If you are satisfied with aligning two protein chains (not multiple-chain complexes) and you don't mind losing hetero atoms, you can do the alignment automatically at http://cl.sdsc.edu/ce.html (use the TWO CHAINS link). The result can be downloaded directly from that site in multiple-model (MODEL #/ENDMDL) PDB format ready for use in RasMol, PE, etc. The alignment at this site is akin to the iterative magic fit in DeepView. That is, it is intelligent about ignoring parts of the chains that don't align well, and aligning the remainder more closely. This kind of information is available in Protein Explorer's Help/Index/Glossary, e.g. http://molvis.sdsc.edu/protexpl/igloss.htm#alignments DeepView is more powerful and flexible, but takes longer. I think I have asked the DeepView authors to put MODEL #/ENDMDL records in the saved PDB files for multiple layers. Perhaps if more of us ask, they will do it. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6249.0 boundary="Boundary_(ID_LzyYbXOxAzQOvQaMwyzCfg)" Thread-Topic: Substructure search Thread-Index: AcLZyd7HOJ4gg8VtTPCPWFAViQh96A== content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Mitch Barker Subject: Substructure search Date: Fri, 21 Feb 2003 11:54:17 -0500 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_LzyYbXOxAzQOvQaMwyzCfg) This may be slightly off topic, but maybe someone can point me in the correct direction: Does anyone know of a technique to search a bunch of mol files looking for a "sub-structure"? One thought has been to convert the mol file to a SMILES string, then search the SMILES strings looking for a sub structure. Does this sound feasible? Does anyone know conceptually how some of the larger chem database companies do this? Thanks. Mitch --Boundary_(ID_LzyYbXOxAzQOvQaMwyzCfg) Message
This = may be slightly=20 off topic, but maybe someone can point me in the correct=20 direction:
 
Does = anyone know of=20 a technique to search a bunch of mol files looking for a=20 "sub-structure"?
 
One = thought has been=20 to convert the mol file to a SMILES string, then search the=20 SMILES strings
looking for a sub=20 structure. Does this sound feasible?
 
Does = anyone know=20 conceptually how
some = of the larger=20 chem database companies do this?
 
Thanks.
 
Mitch
=00 --Boundary_(ID_LzyYbXOxAzQOvQaMwyzCfg)-- X-Info: This message was accepted for relay by smtp03.mrf.mail.rcn.net as the sender used SMTP authentication X-Trace: UmFuZG9tSVbXKhjMKbaOzRhtvSPnv3+B+V6L8PybO5rMUFfyVrgZoLuFq9X7Cn4V X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id h1LHctf13548 ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Masi Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Fri, 21 Feb 2003 12:38:59 -0500 To: rasmol@lists.umass.edu Dear Adriano, First, I must add that I am NOT a Unix expert, I am a beginner. My guess is that Fink and X11 were installed OK, and that you are missing the X11 SDK, Apple's Development Tools, and Fink doesn't know that you have Apple's X11 application installed. The "no acceptable cc in $PATH" makes me think that you didn't install Apple's Developers tools? The comment by Fink that you need to install Xfree86-rootless makes me think that you didn't tell Fink that you have Apple's X11 application installed. The following page is a great source of information for getting thing up and going with XWindows and Fink http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html The quick run through to get things working is Install Apple's Developer Tools. Most people are recommending (it might be required) that the December 2002 Developer's tools be installed. Since I bought OS 10.2 before December I had to download the Dev Tools at http://developer.apple.com/tools/ The download is free. However, you have to sign up, and it is a 300+ MB download. Install Apple's X11 application (get the newest one. Feb 10 I think. The Feb 5 one doesn't start up with Apple's window manager) Install Apple's X11 Software Development Kit (SDK) When I launch the installer it says the installation requires 0 MB of disk space. Install Fink Tell Fink that you have installed Apple's X11 software (the page I mentioned up top tells you how to do this). Tell Fink to install a Fortran compiler (the page I mentioned at the top also tells you what to do here) and any of the other software that you want. I cannot stress how helpful this page http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html has been for me. Sincerely, Chris On Friday, February 21, 2003, at 03:26 AM, adriano ceccarelli wrote: > Dear Chris and all the ones who sent helpful suggestions, > which I have followed the most carefully I could, I am afraid I still > am in troubles. > > I have downloaded and installed Fink with no pain at all. I already > had installed X11 package from Apple (beta test version). I followed > fink instructions to download and install rasmol as source package and > I was prompted with the need to install 5 more packages, including > xfree86-rootless. But while installing, it stopped with an error > message: "configure: error: no acceptable cc in $PATH" I have looked > in all the troubleshooting docs I could find but coudn't solve the > problem. As far as my knowledge of UNIX goes, that means it cannot > find a compiler. Correct? However, I couldn't locate gcc or cc > anywhere in my directories. Is that normal, am I missing some sw, or > have I messed it up by reinstalling xfree86 on a preexisting x11 > installation? > > I will be grateful for more help. > > Thanks > > Adriano > > > > > > Giovedì, 20 Feb 2003, alle 18:45 Europe/Rome, Christopher Masi ha > scritto: > >> As others have suggested, installing Fink will take some time, but >> Fink makes installing a large number of Unix applications very easy. >> One minor annoyance I have with the RasMol installed via Fink (I >> assume the same thing happens if RasMol is installed by other means) >> is that RasMol is very picky about the form of a file's name. >> If the path to the file that is to be displayed contains a space, >> RasMol will not be able to find the file (I tried escaping with \ and >> I tried putting quotes around any folder name that contains spaces). >> I haven't done much with it yet, but PyMol, which can be installed >> using Fink, doesn't have a problem with non-Unix-y file names. It >> might be a good alternative/supplement to RasMol. >> >> Chris >> >> >> On Thursday, February 20, 2003, at 06:15 AM, adriano ceccarelli >> wrote: >> >>> Dear colleagues, >>> I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 >>> (beta version) and, not being exactly a guru of UNIX >>> systems/subsistems I got lost. Is there a manual with easier >>> instructions (something that goes beyond " ...set the CFLAGS for >>> your platform...."? >>> >>> Thanks for any help. >>> >>> Sincerely >>> >>> Adriano Ceccarelli >>> >>> >>> >>> Prof. Adriano Ceccarelli >>> Facoltà di Medicina e Chirurgia >>> Dip. Scienze Cliniche e Biologiche >>> Osp. S. Luigi Gonzaga - Orbassano >>> Torino - ITALY >>> phone +39116708109 >>> fax +39119038639 >>> email adriano.ceccarelli@unito.it >> ---------------------------------------------------------------- >> rasmol-+ >> >> To change your address, unsubscribe, view previous messages/history, >> receive messages as weekly digests, or for any other information >> about the RasMol EMail List, please go to >> http://www.umass.edu/microbio/rasmol/raslist.htm >> >> >> >> > Prof. Adriano Ceccarelli > Facoltà di Medicina e Chirurgia > Dip. Scienze Cliniche e Biologiche > Osp. S. Luigi Gonzaga - Orbassano > Torino - ITALY > phone +39116708109 > fax +39119038639 > email adriano.ceccarelli@unito.it ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: [Fwd: Re: multiple molecules in rasmol 2.7.2.1] Date: Fri, 21 Feb 2003 12:54:27 -0500 To: rasmol@lists.umass.edu at 9:41 AM EDT on (Friday) 21 February 2003 Eric Martz said: > At 2/21/03, Tim Driscoll wrote: > >the drawback of course, is that creating multiple model files still > >requires editing the raw pdb file, at least as far as I know. > > If you are satisfied with aligning two protein chains (not multiple-chain > complexes) and you don't mind losing hetero atoms, you can do the > alignment automatically at http://cl.sdsc.edu/ce.html (use the TWO CHAINS > link). > > The result can be downloaded directly from that site in multiple-model > (MODEL #/ENDMDL) PDB format ready for use in RasMol, PE, etc. > of course! CE is a great site, and I just used it recently. doh. thanks for the reminder, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Substructure search Date: Fri, 21 Feb 2003 12:56:45 -0500 To: rasmol@lists.umass.edu hi Mitch, can you clarify what you mean by sub-structure? do you mean domains and motifs, or a certain sequence, or...? sorry - the fog has not quite cleared yet today for me. thanks, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest at 11:54 AM EDT on (Friday) 21 February 2003 Mitch Barker said: > This may be slightly off topic, but maybe someone can point me in the > correct direction: > > Does anyone know of a technique to search a bunch of mol files looking > for a "sub-structure"? > > One thought has been to convert the mol file to a SMILES string, then > search the SMILES strings > looking for a sub structure. Does this sound feasible? > > Does anyone know conceptually how > some of the larger chem database companies do this? > > Thanks. > > Mitch ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6249.0 Thread-Topic: Substructure search Thread-Index: AcLZ06VK8pTLwKfNTnGNmr7pRIcj2wAA3kOw content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Mitch Barker Subject: RE: Substructure search Date: Fri, 21 Feb 2003 13:32:59 -0500 To: rasmol@lists.umass.edu >> can you clarify what you mean by sub-structure? >> do you mean domains and motifs, or a >>certain sequence, or...? For example, I may want to search for molecules that contain a benzene ring. The people who use our software work with molecules of lets say up to 50 atoms (excluding H's). Mitch at 11:54 AM EDT on (Friday) 21 February 2003 Mitch Barker said: > This may be slightly off topic, but maybe someone can point me in the > correct direction: > > Does anyone know of a technique to search a bunch of mol files looking > for a "sub-structure"? > > One thought has been to convert the mol file to a SMILES string, then > search the SMILES strings looking for a sub structure. Does this sound > feasible? > > Does anyone know conceptually how > some of the larger chem database companies do this? > > Thanks. > > Mitch ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: stereo projection technology Date: Sat, 22 Feb 2003 16:32:00 -0500 To: rasmol@lists.umass.edu I'm forwarding this from David Cassinelli (dcassinelli@jrti.com) as it may interest some subscribers. -Eric Martz Hello Professor Matrz: Is 3D Stereo visualization a technology that would help in your research projects? I'm hopeful that it is something you are interested in. I sell an affordable, portable, platform independent, passive 3D Immersive Large Screen Visualization system known as Viz EveryWhere (VEW). Here is a link for more information http://www.jrti.com/vew/viz3.html This system consists of a Workstation (one I could provide or an existing one), a Converter box, two projectors and a non-depolarizing screen. This is suitable for a classroom or an auditorium and as I said - portable. It is passive technology - so there is no need for expensive active goggles. It is a projection system - front or rear! Prices start at $30K for an XGA (1024x786) and $40K for an SXGA (1280x1024)solution. If your application supports frame sequential stereo then this solution is plug and play. Here is a link of applications that currently support this feature: http://www.stereographics.com/support/srsoftware/index.html If you would like to understand how this technology can accelerate the time to discovery I encourage you to contact me for more details. I look forward to hearing from you! David Cassinelli James River Technical 120 Quarry Dr Milford, MA 01757 508-381-6311 Office 508-667-3311 Cell 508-381-6981 Fax www.jrti.com ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Virus-Scanned: by amavisd-milter (http://amavis.org/) ++++------+------+------+------+------+------+------+------+------+------+ From: Harold Schranz Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Sun, 23 Feb 2003 14:01:09 +1100 To: rasmol@lists.umass.edu Cc: Harold Schranz On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli wrote: > Dear Chris and all the ones who sent helpful suggestions, > which I have followed the most carefully I could, I am afraid I still > am in troubles. Dear Adriano Hopefully I correctly understand your predicament! A simple approach MIGHT be the following (assuming you have OS X 10.2 or later): 1) In case the route involving getting the bits and pieces together as in Christopher Masi's post is too hard (at first) you could just download one of the precompiled executables from: http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ Mac_OS_X_10.2.2_PPC/ (e.g. the 32 bit one if your display covers that range) and the corresponding help file from: http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ rasmol.hlp.gz which I put both (after gunzipping) in /usr/local/bin (a little less elegant than the full Fink install procedure but it works). (see http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ for details) Of course, you will still need (for example) X11 for Mac OS X Public Beta, which is an implementation of the X Window System that makes it possible to run X11-based applications in Mac OS http://www.apple.com/downloads/macosx/apple/x11formacosx.html (41.8MB) 2) Eventually, if you do get the energy, (as stated by others) the following link is invaluable http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html to get all of the appropriate pieces together and use Fink for the compile/install procedures (rasmol executable will end up in /sw/bin/ and not overwrite /usr/local/bin/). Just a matter of being persistent and careful and a little patient. I've actually got Rasmol installed by both routes (but gave/linked them to unique names); don't ask why I bothered ... just bored I guess. 8-) I hope this helps! Good Luck Harry. ------------------------------------------------------------------------ ---- Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 6268 8919 School of Chemistry, University College (UNSW) Fax: +61 2 6268 8002 Australian Defence Force Academy Fax: +61 2 6268 8017 Canberra ACT 2600, Australia Email: Harold.Schranz@adfa.edu.au Visiting Fellow, Biophysics Group, Department of Theoretical Physics and ANU Supercomputer Facility and Research School of Chemistry Australian National University, Canberra ACT 0200, Australia Email: Harold.Schranz@anu.edu.au Phone: +61 2 6125 6533 ------------------------------------------------------------------------ ---- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Sat, 22 Feb 2003 23:09:52 -0500 (EST) To: rasmol@lists.umass.edu Cc: Harold Schranz Unfortunately, option 2 is a step backwards from option 1. Option 1 gives you RasMol 2.7.2.1, while Option 2 takes you back to RasMol 2.7.1.1. Judging by the current downloads, most people prefer 2.7.2.1 -- HJB ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Sun, 23 Feb 2003, Harold Schranz wrote: > On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli wrote: > > Dear Chris and all the ones who sent helpful suggestions, > > which I have followed the most carefully I could, I am afraid I still > > am in troubles. > > Dear Adriano > > Hopefully I correctly understand your predicament! > > A simple approach MIGHT be the following (assuming you have OS X 10.2 > or later): > > 1) In case the route involving getting the bits and pieces together as > in > Christopher Masi's post is too hard (at first) you could just download > one of the precompiled executables from: > http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > Mac_OS_X_10.2.2_PPC/ > (e.g. the 32 bit one if your display covers that range) > and the corresponding help file from: > http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > rasmol.hlp.gz > which I put both (after gunzipping) in /usr/local/bin > (a little less elegant than the full Fink install procedure but it > works). > (see > http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ for > details) > > Of course, you will still need (for example) X11 for Mac OS X Public > Beta, which > is an implementation of the X Window System that makes it possible to > run X11-based applications in Mac OS > http://www.apple.com/downloads/macosx/apple/x11formacosx.html (41.8MB) > > 2) Eventually, if you do get the energy, (as stated by others) the > following link is invaluable > http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html > to get all of the appropriate pieces together and use Fink for the > compile/install procedures > (rasmol executable will end up in /sw/bin/ and not overwrite > /usr/local/bin/). > Just a matter of being persistent and careful and a little patient. > > I've actually got Rasmol installed by both routes (but gave/linked them > to unique names); > don't ask why I bothered ... just bored I guess. 8-) > > I hope this helps! > > Good Luck > Harry. > > ------------------------------------------------------------------------ > ---- > Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 6268 > 8919 > School of Chemistry, University College (UNSW) Fax: +61 2 6268 > 8002 > Australian Defence Force Academy Fax: +61 2 6268 > 8017 > Canberra ACT 2600, Australia Email: > Harold.Schranz@adfa.edu.au > > Visiting Fellow, Biophysics Group, Department of Theoretical Physics > and ANU Supercomputer Facility and Research School of Chemistry > Australian National University, Canberra ACT 0200, Australia > Email: Harold.Schranz@anu.edu.au Phone: +61 2 6125 > 6533 > ------------------------------------------------------------------------ > ---- > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en References: <8918FD882FEE0344B2E8C6311140E06A0372A7@carbon.us.avantium.com> ++++------+------+------+------+------+------+------+------+------+------+ From: Ilan Samish Subject: Re: Substructure search Date: Sun, 23 Feb 2003 10:09:17 +0200 To: rasmol@lists.umass.edu Dear Mitch,

For proteins, much work was done to look for the 'common' substructure, as found in the 'structural neighbors' field in each protein entry in the RCSB PDB. For an efficient sequence-independent data-minig a pre-processing is needed, as done in the geometric hashing method. For more details (and some new downloadable algorithms for multiple structural alignment) see: http://bioinfo3d.cs.tau.ac.il/.

Best regards,

Ilan

~~~~~~~~~~~~~~~~~
Ilan Samish
Plant Sciences Dept.
Weizmann Institute of Science
Rehovot, Israel
Lab: 972-8-9344300
Cell: 972-53-321150
Fax: 972-8-9344181
ilan.samish@weizmann.ac.il

Mitch Barker wrote:
  
can you clarify what you mean by sub-structure?  
do you mean domains and motifs, or a >>certain sequence, or...?
      

For example, I may want to search for molecules that contain a benzene
ring. The people
who use our software work with molecules of lets say up to 50 atoms
(excluding H's).

Mitch

at 11:54 AM EDT on (Friday) 21 February 2003 Mitch Barker said:

  
This may be slightly off topic, but maybe someone can point me in the 
correct direction:
 
Does anyone know of a technique to search a bunch of mol files looking
    

  
for a "sub-structure"?
 
One thought has been to convert the mol file to a SMILES string, then 
search the SMILES strings looking for a sub structure. Does this sound
    

  
feasible?
 
Does anyone know conceptually how
some of the larger chem database companies do this?
 
Thanks.
 
Mitch

----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline User-Agent: Mutt/1.4i References: <8918FD882FEE0344B2E8C6311140E06A0372A7@carbon.us.avantium.com> <3E5881AD.7040002@weizmann.ac.il> ++++------+------+------+------+------+------+------+------+------+------+ From: Johannes Ranke Subject: Re: Substructure search Date: Sun, 23 Feb 2003 14:04:12 +0100 To: rasmol@lists.umass.edu Hi > Does anyone know of a technique to search a bunch of mol files looking > for a "sub-structure"? Sounds like a perfect task for the CACTVS tools: http://www2.ccc.uni-erlangen.de/software/cactvs/ They consist of a couple of tcl/tk extensions and work nicely under linux and SGI Irix. Unfortunately, very sparsely documented. I figured out how to do substructure searches only by corresponding with the author. But the tools are very powerful and free for academic purposes, unfortunately not open source at all. Hannes P.S.: In the future, the Java CDK might be a replacement. It already can do substructure searches http://cdk.sf.net > One thought has been to convert the mol file to a SMILES string, then > search the SMILES strings looking for a sub structure. Does this sound > feasible? > > Does anyone know conceptually how > some of the larger chem database companies do this? > > Thanks. > > Mitch > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Xu Yong Subject: select Date: Wed, 26 Feb 2003 09:56:17 +0800 To: "rasmol@lists.umass.edu" Dear rasmoler how to select specific residues which is within 5.0A from residue32/h2o10 I can select atom within this radius but not residues. thank you in advance xy ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: standards for mol vis Date: Thu, 27 Feb 2003 05:55:11 -0500 To: LIST rasmol hello all, I am compiling a list of standard representations used for molecular visualization. for example: depiction of protein secondary structures (helices are cylinders, strands are arrows); atoms as solid spheres and bonds as connecting rods; element coloring - cpk scheme; etc. if you have any others that you would like to share, I would be grateful! you can email me off-list if you prefer - . regards, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: standards for mol vis Date: Thu, 27 Feb 2003 12:50:54 +0000 (GMT) To: rasmol@lists.umass.edu timothy driscoll said: > hello all, > > I am compiling a list of standard representations used for molecular > visualization. for example: > > depiction of protein secondary structures (helices are cylinders, strands are > arrows); > atoms as solid spheres and bonds as connecting rods; > element coloring - cpk scheme; > etc. two basics, (in case replies have been low) is coloring - hydrophobicity / tipical pk of atoms depiction - surface representation some others are, structure factors - how well the molecule was resolved in x-ray for example. > > if you have any others that you would like to share, I would be grateful! you can > email me off-list if you prefer - . > > regards, > > :tim > -- > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: standards for mol vis Date: Thu, 27 Feb 2003 15:38:18 -0500 To: rasmol@lists.umass.edu hi Dan, thanks for the response, and to other list members who have sent me ideas off-list. I'll be working on this for the next few days, so if you think of any others please feel free to send them along. when I compile a fair list, I'll post the url for criticism and feedback. regards, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest at 12:50 PM EDT on (Thursday) 27 February 2003 Dan Bolser said: > timothy driscoll said: > > hello all, > > > > I am compiling a list of standard representations used for molecular > > visualization. for example: > > > > depiction of protein secondary structures (helices are cylinders, > > strands are arrows); atoms as solid spheres and bonds as connecting > > rods; element coloring - cpk scheme; etc. > > two basics, (in case replies have been low) is > > coloring - hydrophobicity / tipical pk of atoms > depiction - surface representation > > some others are, > structure factors - how well the molecule was resolved > in x-ray for example. > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: standards for mol vis Date: Sat, 01 Mar 2003 11:57:09 -0500 To: rasmol@lists.umass.edu --Boundary_(ID_rTL6TyFVtWfiF1yReLw8+g) At 2/27/03, you wrote: >I am compiling a list of standard representations used for molecular >visualization. Last summer I spent quite a bit of time writing some entries on this for a dictionary of bioinformatics that has yet to be published. I've attached them -- they may be useful. -Eric ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: oops Date: Sat, 01 Mar 2003 14:18:08 -0500 To: rasmol@lists.umass.edu My sincere apologies for burdening everyone on the list with a large attachment that I intended only for Tim Driscoll. -Eric Martz (red faced) ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: my favorite protein structure literature Date: Sat, 01 Mar 2003 15:20:40 -0500 To: rasmol@lists.umass.edu I have posted some of my favorite protein structure literature (books and journal articles) at http://molvis.sdsc.edu/protexpl/favlit.htm I particularly recommend two books just published: -- Structural Bioinformatics, edited by Bourne and Weissig -- Introduction to Bioinformatics, edited by Krawetz and Womble More about each book is at the above link. (This document is not yet included in the downloadable version of Protein Explorer. It will be included whenever the next numbered release occurs, probably sometime this summer.) -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: George Tzotzos Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Sun, 02 Mar 2003 04:35:07 -0800 To: rasmol@lists.umass.edu Cc: rasmol@lists.umass.edu, Harold Schranz Hi there, I followed Harold's option 1. X11 properly installed, rasmol 2.7.2.1 and rasmol.help both downloaded from arcib.dowling.edu and moved to the /usr/local/bin directory. Encountered the following problems: 1. On trying to open files with .pdb extension rasmol is overriden by iMol (native OSX program). 2. On trying to open rasmol scripted files (.ras extension), system OS9 is fired up and the file is open by RasMol 2.6 for system 9. Both of the above even if I reboot and try to open files from the X11 window. Would be grateful for any suggestions. George Dr George Tzotzos UNIDO, Vienna, Austria Tel: +43-1-26026 4336 Fax: +43-1-26026 6810 email: g.tzotzos@unido.org On Saturday, February 22, 2003, at 07:01PM, Harold Schranz wrote: >On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli wrote: >> Dear Chris and all the ones who sent helpful suggestions, >> which I have followed the most carefully I could, I am afraid I still >> am in troubles. > >Dear Adriano > >Hopefully I correctly understand your predicament! > >A simple approach MIGHT be the following (assuming you have OS X 10.2 >or later): > >1) In case the route involving getting the bits and pieces together as >in >Christopher Masi's post is too hard (at first) you could just download >one of the precompiled executables from: >http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >Mac_OS_X_10.2.2_PPC/ >(e.g. the 32 bit one if your display covers that range) >and the corresponding help file from: >http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >rasmol.hlp.gz >which I put both (after gunzipping) in /usr/local/bin >(a little less elegant than the full Fink install procedure but it >works). >(see >http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ for >details) > >Of course, you will still need (for example) X11 for Mac OS X Public >Beta, which >is an implementation of the X Window System that makes it possible to >run X11-based applications in Mac OS >http://www.apple.com/downloads/macosx/apple/x11formacosx.html (41.8MB) > >2) Eventually, if you do get the energy, (as stated by others) the >following link is invaluable >http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html >to get all of the appropriate pieces together and use Fink for the >compile/install procedures >(rasmol executable will end up in /sw/bin/ and not overwrite >/usr/local/bin/). >Just a matter of being persistent and careful and a little patient. > >I've actually got Rasmol installed by both routes (but gave/linked them >to unique names); >don't ask why I bothered ... just bored I guess. 8-) > >I hope this helps! > >Good Luck >Harry. > >------------------------------------------------------------------------ >---- >Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 6268 >8919 >School of Chemistry, University College (UNSW) Fax: +61 2 6268 >8002 >Australian Defence Force Academy Fax: +61 2 6268 >8017 >Canberra ACT 2600, Australia Email: >Harold.Schranz@adfa.edu.au > >Visiting Fellow, Biophysics Group, Department of Theoretical Physics >and ANU Supercomputer Facility and Research School of Chemistry >Australian National University, Canberra ACT 0200, Australia >Email: Harold.Schranz@anu.edu.au Phone: +61 2 6125 >6533 >------------------------------------------------------------------------ >---- > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Sun, 02 Mar 2003 09:04:35 -0500 To: rasmol@lists.umass.edu hi George, did you try the OSX method? just in case, here it is: single-click on any pdb file (in the Finder) and choose Get Info (control- or right-click, cmd-I, or File:Get Info at your discretion). switch to the "Open With" pane. from the option list there, choose rasmol 2.7.2.1 (if it is not present, there is an Other... option at the very bottom of the list that allows you browse to the app). click the Change All button to make this the default for all files of this type on your computer. repeat for ras files, scr files - any files you want to double-click and launch rasmol 2.7.2.1. hth, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest at 4:35 AM EDT on (Sunday) 2 March 2003 George Tzotzos said: > Hi there, > > I followed Harold's option 1. X11 properly installed, rasmol 2.7.2.1 and > rasmol.help both downloaded from arcib.dowling.edu and moved to the > /usr/local/bin directory. > > Encountered the following problems: > > 1. On trying to open files with .pdb extension rasmol is overriden by iMol > (native OSX program). > 2. On trying to open rasmol scripted files (.ras extension), system OS9 is > fired up and the file is open by RasMol 2.6 for system 9. > > Both of the above even if I reboot and try to open files from the X11 > window. > > Would be grateful for any suggestions. > > George > > Dr George Tzotzos > UNIDO, Vienna, Austria > > Tel: +43-1-26026 4336 > Fax: +43-1-26026 6810 > email: g.tzotzos@unido.org > > > > On Saturday, February 22, 2003, at 07:01PM, Harold Schranz > wrote: > > >On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli wrote: > >> Dear Chris and all the ones who sent helpful suggestions, > >> which I have followed the most carefully I could, I am afraid I still > >> am in troubles. > > > >Dear Adriano > > > >Hopefully I correctly understand your predicament! > > > >A simple approach MIGHT be the following (assuming you have OS X 10.2 > >or later): > > > >1) In case the route involving getting the bits and pieces together as > >in > >Christopher Masi's post is too hard (at first) you could just download > >one of the precompiled executables from: > >http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >Mac_OS_X_10.2.2_PPC/ > >(e.g. the 32 bit one if your display covers that range) > >and the corresponding help file from: > >http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >rasmol.hlp.gz > >which I put both (after gunzipping) in /usr/local/bin > >(a little less elegant than the full Fink install procedure but it > >works). > >(see > >http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ for > >details) > > > >Of course, you will still need (for example) X11 for Mac OS X Public > >Beta, which > >is an implementation of the X Window System that makes it possible to > >run X11-based applications in Mac OS > >http://www.apple.com/downloads/macosx/apple/x11formacosx.html (41.8MB) > > > >2) Eventually, if you do get the energy, (as stated by others) the > >following link is invaluable > >http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html > >to get all of the appropriate pieces together and use Fink for the > >compile/install procedures > >(rasmol executable will end up in /sw/bin/ and not overwrite > >/usr/local/bin/). > >Just a matter of being persistent and careful and a little patient. > > > >I've actually got Rasmol installed by both routes (but gave/linked them > >to unique names); > >don't ask why I bothered ... just bored I guess. 8-) > > > >I hope this helps! > > > >Good Luck > >Harry. > > > >------------------------------------------------------------------------ > >---- > >Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 6268 > >8919 > >School of Chemistry, University College (UNSW) Fax: +61 2 6268 > >8002 > >Australian Defence Force Academy Fax: +61 2 6268 > >8017 > >Canberra ACT 2600, Australia Email: > >Harold.Schranz@adfa.edu.au > > > >Visiting Fellow, Biophysics Group, Department of Theoretical Physics > >and ANU Supercomputer Facility and Research School of Chemistry > >Australian National University, Canberra ACT 0200, Australia > >Email: Harold.Schranz@anu.edu.au Phone: +61 2 6125 > >6533 > >------------------------------------------------------------------------ > >---- > > > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Info: This message was accepted for relay by smtp01.mrf.mail.rcn.net as the sender used SMTP authentication X-Trace: UmFuZG9tSVY2oqJAw/vty7q2XPP0MuSP7xPjEr4qT6UUSnriXM70ifZU+wy0jM2s ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Masi Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Sun, 02 Mar 2003 09:18:53 -0500 To: rasmol@lists.umass.edu I am starting with the assumption that you are double clicking the files to open them. Rasmol 2.7.2 is running on OS X's Darwin core, and the only way to interact with the program is by a terminal emulator (xTerm or Apple's Terminal). The only way to display the output is through an X 11 window. Essentially, OS X has a mild case of MPD. iMol is a full fledged OS X program. Rasmol 2.6 is a "Classic" application. Rasmol 2.7.2 is a Darwin application. The Finder only "knows" about Classic and OS X applications. It does not know about Darwin applications. When you double click the pdb file, the Finder looks for a program that has the correct creator type and tells that program to open the file. Since the Finder doesn't know that rasmol 2.7.2 exists the Finder instructs iMol to open the pdb file (iMol is newer than Rasmol 2.6). When you double click the .ras file, the Finder looks for an application to use. The Finder still doesn't know about Rasmol 2.7.2, and iMol cannot open (or at least the Finder doesn't think it can open) .ras files, so the Finder goes to the only application that it knows about that can open the .ras file, Rasmol 2.6. Because rasmol 2.7.2 was installed as a Darwin/Unix application it is not double clickable. Try finding rasmol 2.7.2 and double clicking it. It will not start. If everything is set up correctly, to use Rasmol 2.7.2 to open a pdb file you have to 1. have X11 running. Double click Apple's X11.app 2. in an xTerm window or (if configured the right way) or a Terminal.app window navigate to the directory that contains all the pbds that you want to view and type rasmol 3. in the window that was used to launch rasmol type load 1ADO.pdb where 1ADO.pdb is the name of the file that you want to open. Chris On Sunday, March 2, 2003, at 07:35 AM, George Tzotzos wrote: > Hi there, > > I followed Harold's option 1. X11 properly installed, rasmol 2.7.2.1 > and rasmol.help both downloaded from arcib.dowling.edu and moved to > the /usr/local/bin directory. > > Encountered the following problems: > > 1. On trying to open files with .pdb extension rasmol is overriden by > iMol (native OSX program). > 2. On trying to open rasmol scripted files (.ras extension), system > OS9 is fired up and the file is open by RasMol 2.6 for system 9. > > Both of the above even if I reboot and try to open files from the X11 > window. > > Would be grateful for any suggestions. > > George > > Dr George Tzotzos > UNIDO, Vienna, Austria > > Tel: +43-1-26026 4336 > Fax: +43-1-26026 6810 > email: g.tzotzos@unido.org > > > > On Saturday, February 22, 2003, at 07:01PM, Harold Schranz > wrote: > >> On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli wrote: >>> Dear Chris and all the ones who sent helpful suggestions, >>> which I have followed the most carefully I could, I am afraid I still >>> am in troubles. >> >> Dear Adriano >> >> Hopefully I correctly understand your predicament! >> >> A simple approach MIGHT be the following (assuming you have OS X 10.2 >> or later): >> >> 1) In case the route involving getting the bits and pieces together as >> in >> Christopher Masi's post is too hard (at first) you could just download >> one of the precompiled executables from: >> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >> Mac_OS_X_10.2.2_PPC/ >> (e.g. the 32 bit one if your display covers that range) >> and the corresponding help file from: >> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >> rasmol.hlp.gz >> which I put both (after gunzipping) in /usr/local/bin >> (a little less elegant than the full Fink install procedure but it >> works). >> (see >> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >> for >> details) >> >> Of course, you will still need (for example) X11 for Mac OS X Public >> Beta, which >> is an implementation of the X Window System that makes it possible to >> run X11-based applications in Mac OS >> http://www.apple.com/downloads/macosx/apple/x11formacosx.html (41.8MB) >> >> 2) Eventually, if you do get the energy, (as stated by others) the >> following link is invaluable >> http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html >> to get all of the appropriate pieces together and use Fink for the >> compile/install procedures >> (rasmol executable will end up in /sw/bin/ and not overwrite >> /usr/local/bin/). >> Just a matter of being persistent and careful and a little patient. >> >> I've actually got Rasmol installed by both routes (but gave/linked >> them >> to unique names); >> don't ask why I bothered ... just bored I guess. 8-) >> >> I hope this helps! >> >> Good Luck >> Harry. >> >> ---------------------------------------------------------------------- >> -- >> ---- >> Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 >> 6268 >> 8919 >> School of Chemistry, University College (UNSW) Fax: +61 2 >> 6268 >> 8002 >> Australian Defence Force Academy Fax: +61 2 >> 6268 >> 8017 >> Canberra ACT 2600, Australia Email: >> Harold.Schranz@adfa.edu.au >> >> Visiting Fellow, Biophysics Group, Department of Theoretical Physics >> and ANU Supercomputer Facility and Research School of Chemistry >> Australian National University, Canberra ACT 0200, Australia >> Email: Harold.Schranz@anu.edu.au Phone: +61 2 >> 6125 >> 6533 >> ---------------------------------------------------------------------- >> -- >> ---- >> >> >> >> > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Info: This message was accepted for relay by smtp01.mrf.mail.rcn.net as the sender used SMTP authentication X-Trace: UmFuZG9tSVbfqgFE7zVV7XtvFDE3O57/VM8ag58CFlwStA9VLDkAE/phuSgnxLr0 ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Masi Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Sun, 02 Mar 2003 11:39:13 -0500 To: rasmol@lists.umass.edu That doesn't work here. I installed 2.7.1 via Fink and 2.7.2 via the following link http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ Mac_OS_X_10.2.2_PPC/ and neither is recognized by OS X 10.2.4 as a suitable "Open with" application even when "All Applications" is selected in the Open with dialogue box. If you have found a way to make this work, I would love more details on how I might get my system to do it too. Thanks, Chris On Sunday, March 2, 2003, at 09:04 AM, timothy driscoll wrote: > hi George, > > did you try the OSX method? just in case, here it is: > > single-click on any pdb file (in the Finder) and choose Get Info > (control- > or right-click, cmd-I, or File:Get Info at your discretion). > > switch to the "Open With" pane. from the option list there, choose > rasmol > 2.7.2.1 (if it is not present, there is an Other... option at the very > bottom of the list that allows you browse to the app). > > click the Change All button to make this the default for all files of > this > type on your computer. > > repeat for ras files, scr files - any files you want to double-click > and > launch rasmol 2.7.2.1. > > > hth, > > :tim > -- > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > > > > > > at 4:35 AM EDT on (Sunday) 2 March 2003 George Tzotzos said: > >> Hi there, >> >> I followed Harold's option 1. X11 properly installed, rasmol 2.7.2.1 >> and >> rasmol.help both downloaded from arcib.dowling.edu and moved to the >> /usr/local/bin directory. >> >> Encountered the following problems: >> >> 1. On trying to open files with .pdb extension rasmol is overriden by >> iMol >> (native OSX program). >> 2. On trying to open rasmol scripted files (.ras extension), system >> OS9 is >> fired up and the file is open by RasMol 2.6 for system 9. >> >> Both of the above even if I reboot and try to open files from the X11 >> window. >> >> Would be grateful for any suggestions. >> >> George >> >> Dr George Tzotzos >> UNIDO, Vienna, Austria >> >> Tel: +43-1-26026 4336 >> Fax: +43-1-26026 6810 >> email: g.tzotzos@unido.org >> >> >> >> On Saturday, February 22, 2003, at 07:01PM, Harold Schranz >> wrote: >> >>> On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli wrote: >>>> Dear Chris and all the ones who sent helpful suggestions, >>>> which I have followed the most carefully I could, I am afraid I >>>> still >>>> am in troubles. >>> >>> Dear Adriano >>> >>> Hopefully I correctly understand your predicament! >>> >>> A simple approach MIGHT be the following (assuming you have OS X 10.2 >>> or later): >>> >>> 1) In case the route involving getting the bits and pieces together >>> as >>> in >>> Christopher Masi's post is too hard (at first) you could just >>> download >>> one of the precompiled executables from: >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >>> Mac_OS_X_10.2.2_PPC/ >>> (e.g. the 32 bit one if your display covers that range) >>> and the corresponding help file from: >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >>> rasmol.hlp.gz >>> which I put both (after gunzipping) in /usr/local/bin >>> (a little less elegant than the full Fink install procedure but it >>> works). >>> (see >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >>> for >>> details) >>> >>> Of course, you will still need (for example) X11 for Mac OS X Public >>> Beta, which >>> is an implementation of the X Window System that makes it possible to >>> run X11-based applications in Mac OS >>> http://www.apple.com/downloads/macosx/apple/x11formacosx.html >>> (41.8MB) >>> >>> 2) Eventually, if you do get the energy, (as stated by others) the >>> following link is invaluable >>> http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html >>> to get all of the appropriate pieces together and use Fink for the >>> compile/install procedures >>> (rasmol executable will end up in /sw/bin/ and not overwrite >>> /usr/local/bin/). >>> Just a matter of being persistent and careful and a little patient. >>> >>> I've actually got Rasmol installed by both routes (but gave/linked >>> them >>> to unique names); >>> don't ask why I bothered ... just bored I guess. 8-) >>> >>> I hope this helps! >>> >>> Good Luck >>> Harry. >>> >>> --------------------------------------------------------------------- >>> --- >>> ---- >>> Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 >>> 6268 >>> 8919 >>> School of Chemistry, University College (UNSW) Fax: +61 2 >>> 6268 >>> 8002 >>> Australian Defence Force Academy Fax: +61 2 >>> 6268 >>> 8017 >>> Canberra ACT 2600, Australia Email: >>> Harold.Schranz@adfa.edu.au >>> >>> Visiting Fellow, Biophysics Group, Department of Theoretical Physics >>> and ANU Supercomputer Facility and Research School of Chemistry >>> Australian National University, Canberra ACT 0200, Australia >>> Email: Harold.Schranz@anu.edu.au Phone: +61 2 >>> 6125 >>> 6533 >>> --------------------------------------------------------------------- >>> --- >>> ---- >>> >>> >>> >>> >> >> >> > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Sun, 02 Mar 2003 12:30:33 -0500 (EST) To: rasmol@lists.umass.edu If it is important to you to have the system allow you to double click files to have them opended by RasMol, then I would suggest you install the Mac Classic version of RasMol 2.7.2.1, instead of the X-windows based version you have installed. -- HJB ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Sun, 2 Mar 2003, Christopher Masi wrote: > That doesn't work here. > > I installed 2.7.1 via Fink and 2.7.2 via the following link > > http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > Mac_OS_X_10.2.2_PPC/ > > and neither is recognized by OS X 10.2.4 as a suitable "Open with" > application even when "All Applications" is selected in the Open with > dialogue box. If you have found a way to make this work, I would love > more details on how I might get my system to do it too. > > Thanks, > Chris > > On Sunday, March 2, 2003, at 09:04 AM, timothy driscoll wrote: > > > hi George, > > > > did you try the OSX method? just in case, here it is: > > > > single-click on any pdb file (in the Finder) and choose Get Info > > (control- > > or right-click, cmd-I, or File:Get Info at your discretion). > > > > switch to the "Open With" pane. from the option list there, choose > > rasmol > > 2.7.2.1 (if it is not present, there is an Other... option at the very > > bottom of the list that allows you browse to the app). > > > > click the Change All button to make this the default for all files of > > this > > type on your computer. > > > > repeat for ras files, scr files - any files you want to double-click > > and > > launch rasmol 2.7.2.1. > > > > > > hth, > > > > :tim > > -- > > molvisions - molecular graphics & visualization > > > > usa:north carolina:wake forest > > > > > > > > > > > > at 4:35 AM EDT on (Sunday) 2 March 2003 George Tzotzos said: > > > >> Hi there, > >> > >> I followed Harold's option 1. X11 properly installed, rasmol 2.7.2.1 > >> and > >> rasmol.help both downloaded from arcib.dowling.edu and moved to the > >> /usr/local/bin directory. > >> > >> Encountered the following problems: > >> > >> 1. On trying to open files with .pdb extension rasmol is overriden by > >> iMol > >> (native OSX program). > >> 2. On trying to open rasmol scripted files (.ras extension), system > >> OS9 is > >> fired up and the file is open by RasMol 2.6 for system 9. > >> > >> Both of the above even if I reboot and try to open files from the X11 > >> window. > >> > >> Would be grateful for any suggestions. > >> > >> George > >> > >> Dr George Tzotzos > >> UNIDO, Vienna, Austria > >> > >> Tel: +43-1-26026 4336 > >> Fax: +43-1-26026 6810 > >> email: g.tzotzos@unido.org > >> > >> > >> > >> On Saturday, February 22, 2003, at 07:01PM, Harold Schranz > >> wrote: > >> > >>> On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli wrote: > >>>> Dear Chris and all the ones who sent helpful suggestions, > >>>> which I have followed the most carefully I could, I am afraid I > >>>> still > >>>> am in troubles. > >>> > >>> Dear Adriano > >>> > >>> Hopefully I correctly understand your predicament! > >>> > >>> A simple approach MIGHT be the following (assuming you have OS X 10.2 > >>> or later): > >>> > >>> 1) In case the route involving getting the bits and pieces together > >>> as > >>> in > >>> Christopher Masi's post is too hard (at first) you could just > >>> download > >>> one of the precompiled executables from: > >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >>> Mac_OS_X_10.2.2_PPC/ > >>> (e.g. the 32 bit one if your display covers that range) > >>> and the corresponding help file from: > >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >>> rasmol.hlp.gz > >>> which I put both (after gunzipping) in /usr/local/bin > >>> (a little less elegant than the full Fink install procedure but it > >>> works). > >>> (see > >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >>> for > >>> details) > >>> > >>> Of course, you will still need (for example) X11 for Mac OS X Public > >>> Beta, which > >>> is an implementation of the X Window System that makes it possible to > >>> run X11-based applications in Mac OS > >>> http://www.apple.com/downloads/macosx/apple/x11formacosx.html > >>> (41.8MB) > >>> > >>> 2) Eventually, if you do get the energy, (as stated by others) the > >>> following link is invaluable > >>> http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html > >>> to get all of the appropriate pieces together and use Fink for the > >>> compile/install procedures > >>> (rasmol executable will end up in /sw/bin/ and not overwrite > >>> /usr/local/bin/). > >>> Just a matter of being persistent and careful and a little patient. > >>> > >>> I've actually got Rasmol installed by both routes (but gave/linked > >>> them > >>> to unique names); > >>> don't ask why I bothered ... just bored I guess. 8-) > >>> > >>> I hope this helps! > >>> > >>> Good Luck > >>> Harry. > >>> > >>> --------------------------------------------------------------------- > >>> --- > >>> ---- > >>> Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 > >>> 6268 > >>> 8919 > >>> School of Chemistry, University College (UNSW) Fax: +61 2 > >>> 6268 > >>> 8002 > >>> Australian Defence Force Academy Fax: +61 2 > >>> 6268 > >>> 8017 > >>> Canberra ACT 2600, Australia Email: > >>> Harold.Schranz@adfa.edu.au > >>> > >>> Visiting Fellow, Biophysics Group, Department of Theoretical Physics > >>> and ANU Supercomputer Facility and Research School of Chemistry > >>> Australian National University, Canberra ACT 0200, Australia > >>> Email: Harold.Schranz@anu.edu.au Phone: +61 2 > >>> 6125 > >>> 6533 > >>> --------------------------------------------------------------------- > >>> --- > >>> ---- > >>> > >>> > >>> > >>> > >> > >> > >> > > > > ---------------------------------------------------------------- > > rasmol-+ > > > > To change your address, unsubscribe, view previous messages/history, > > receive messages as weekly digests, or for any other information > > about the RasMol EMail List, please go to > > http://www.umass.edu/microbio/rasmol/raslist.htm > > > > ---------------------------------------------------------------- > > rasmol-- > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Sun, 02 Mar 2003 13:07:21 -0500 To: rasmol@lists.umass.edu at 11:39 AM EDT on (Sunday) 2 March 2003 Christopher Masi said: > That doesn't work here. > bummer. sorry. > I installed 2.7.1 via Fink and 2.7.2 via the following link > > http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > Mac_OS_X_10.2.2_PPC/ > > and neither is recognized by OS X 10.2.4 as a suitable "Open with" > application even when "All Applications" is selected in the Open with > dialogue box. If you have found a way to make this work, I would love > more details on how I might get my system to do it too. > um, no. I had neither time nor energy to try very hard, though ;-) I always have Classic running for one reason or another, so it is just as easy for me to use an older version of rasmol. hope you get it worked out, though! :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest > Thanks, > Chris > > On Sunday, March 2, 2003, at 09:04 AM, timothy driscoll wrote: > > > hi George, > > > > did you try the OSX method? just in case, here it is: > > > > single-click on any pdb file (in the Finder) and choose Get Info > > (control- > > or right-click, cmd-I, or File:Get Info at your discretion). > > > > switch to the "Open With" pane. from the option list there, choose > > rasmol > > 2.7.2.1 (if it is not present, there is an Other... option at the very > > bottom of the list that allows you browse to the app). > > > > click the Change All button to make this the default for all files of > > this > > type on your computer. > > > > repeat for ras files, scr files - any files you want to double-click > > and > > launch rasmol 2.7.2.1. > > > > > > hth, > > > > :tim > > -- > > molvisions - molecular graphics & visualization > > > > usa:north carolina:wake forest > > > > > > > > > > > > at 4:35 AM EDT on (Sunday) 2 March 2003 George Tzotzos said: > > > >> Hi there, > >> > >> I followed Harold's option 1. X11 properly installed, rasmol 2.7.2.1 > >> and > >> rasmol.help both downloaded from arcib.dowling.edu and moved to the > >> /usr/local/bin directory. > >> > >> Encountered the following problems: > >> > >> 1. On trying to open files with .pdb extension rasmol is overriden by > >> iMol > >> (native OSX program). > >> 2. On trying to open rasmol scripted files (.ras extension), system > >> OS9 is > >> fired up and the file is open by RasMol 2.6 for system 9. > >> > >> Both of the above even if I reboot and try to open files from the X11 > >> window. > >> > >> Would be grateful for any suggestions. > >> > >> George > >> > >> Dr George Tzotzos > >> UNIDO, Vienna, Austria > >> > >> Tel: +43-1-26026 4336 > >> Fax: +43-1-26026 6810 > >> email: g.tzotzos@unido.org > >> > >> > >> > >> On Saturday, February 22, 2003, at 07:01PM, Harold Schranz > >> wrote: > >> > >>> On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli wrote: > >>>> Dear Chris and all the ones who sent helpful suggestions, > >>>> which I have followed the most carefully I could, I am afraid I > >>>> still > >>>> am in troubles. > >>> > >>> Dear Adriano > >>> > >>> Hopefully I correctly understand your predicament! > >>> > >>> A simple approach MIGHT be the following (assuming you have OS X 10.2 > >>> or later): > >>> > >>> 1) In case the route involving getting the bits and pieces together > >>> as > >>> in > >>> Christopher Masi's post is too hard (at first) you could just > >>> download > >>> one of the precompiled executables from: > >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >>> Mac_OS_X_10.2.2_PPC/ > >>> (e.g. the 32 bit one if your display covers that range) > >>> and the corresponding help file from: > >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >>> rasmol.hlp.gz > >>> which I put both (after gunzipping) in /usr/local/bin > >>> (a little less elegant than the full Fink install procedure but it > >>> works). > >>> (see > >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >>> for > >>> details) > >>> > >>> Of course, you will still need (for example) X11 for Mac OS X Public > >>> Beta, which > >>> is an implementation of the X Window System that makes it possible to > >>> run X11-based applications in Mac OS > >>> http://www.apple.com/downloads/macosx/apple/x11formacosx.html > >>> (41.8MB) > >>> > >>> 2) Eventually, if you do get the energy, (as stated by others) the > >>> following link is invaluable > >>> http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html > >>> to get all of the appropriate pieces together and use Fink for the > >>> compile/install procedures > >>> (rasmol executable will end up in /sw/bin/ and not overwrite > >>> /usr/local/bin/). > >>> Just a matter of being persistent and careful and a little patient. > >>> > >>> I've actually got Rasmol installed by both routes (but gave/linked > >>> them > >>> to unique names); > >>> don't ask why I bothered ... just bored I guess. 8-) > >>> > >>> I hope this helps! > >>> > >>> Good Luck > >>> Harry. > >>> > >>> --------------------------------------------------------------------- > >>> --- > >>> ---- > >>> Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 > >>> 6268 > >>> 8919 > >>> School of Chemistry, University College (UNSW) Fax: +61 2 > >>> 6268 > >>> 8002 > >>> Australian Defence Force Academy Fax: +61 2 > >>> 6268 > >>> 8017 > >>> Canberra ACT 2600, Australia Email: > >>> Harold.Schranz@adfa.edu.au > >>> > >>> Visiting Fellow, Biophysics Group, Department of Theoretical Physics > >>> and ANU Supercomputer Facility and Research School of Chemistry > >>> Australian National University, Canberra ACT 0200, Australia > >>> Email: Harold.Schranz@anu.edu.au Phone: +61 2 > >>> 6125 > >>> 6533 > >>> --------------------------------------------------------------------- > >>> --- > >>> ---- > >>> > >>> > >>> > >>> > >> > >> > >> > > > > ---------------------------------------------------------------- > > rasmol-+ > > > > To change your address, unsubscribe, view previous messages/history, > > receive messages as weekly digests, or for any other information > > about the RasMol EMail List, please go to > > http://www.umass.edu/microbio/rasmol/raslist.htm > > > > ---------------------------------------------------------------- > > rasmol-- > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <5.2.0.9.2.20030301114541.024a9b90@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: standards for mol vis Date: Mon, 03 Mar 2003 00:51:40 +0000 (GMT) To: rasmol@lists.umass.edu Cc: emartz@microbio.umass.edu Eric Martz said: > At 2/27/03, you wrote: >>I am compiling a list of standard representations used for molecular >> visualization. > > Last summer I spent quite a bit of time writing some entries on this for a > dictionary of bioinformatics that has yet to be published. I've attached them -- > they may be useful. > > -Eric you couldnt post up an rtf version of this file could you? ;) ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 X-MSMail-priority: Normal X-Scanner: exiscan *18pjdz-0001aq-00*Lve11Eos4AE* (University of Pretoria, South Africa) References: <5.2.0.9.2.20030301141629.024bf7d0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Andrew Kiggundu Subject: Re: oops Date: Mon, 03 Mar 2003 08:43:27 +0200 To: rasmol@lists.umass.edu Any how it interesting to some of us new to Bioinformatics!!! ----- Original Message ----- Sent: Saturday, March 01, 2003 9:18 PM From: "Eric Martz" Subject: oops To: > My sincere apologies for burdening everyone on the list with a large > attachment that I intended only for Tim Driscoll. -Eric Martz (red faced) > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6249.0 Thread-Topic: rasmol 2.7.2 install in Mac OSX Thread-Index: AcLg6cyZSqxtvmlaT0mlmvQ0fpM3vAApJ4pg content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Mitch Barker Subject: RE: rasmol 2.7.2 install in Mac OSX Date: Mon, 03 Mar 2003 09:11:27 -0500 To: rasmol@lists.umass.edu Maybe you could use apple script? I installed another X windows application called "openOffice", and the package came with some double clickable scripts to start openOffice. I've never done any apple scripting; this is just kind of a guess... Mitch -----Original Message----- Sent: Sunday, March 02, 2003 1:07 PM From: timothy driscoll [mailto:listsub@molvisions.com] Subject: Re: rasmol 2.7.2 install in Mac OSX To: rasmol@lists.umass.edu at 11:39 AM EDT on (Sunday) 2 March 2003 Christopher Masi said: > That doesn't work here. > bummer. sorry. > I installed 2.7.1 via Fink and 2.7.2 via the following link > > http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > Mac_OS_X_10.2.2_PPC/ > > and neither is recognized by OS X 10.2.4 as a suitable "Open with" > application even when "All Applications" is selected in the Open with > dialogue box. If you have found a way to make this work, I would love > more details on how I might get my system to do it too. > um, no. I had neither time nor energy to try very hard, though ;-) I always have Classic running for one reason or another, so it is just as easy for me to use an older version of rasmol. hope you get it worked out, though! :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest > Thanks, > Chris > > On Sunday, March 2, 2003, at 09:04 AM, timothy driscoll wrote: > > > hi George, > > > > did you try the OSX method? just in case, here it is: > > > > single-click on any pdb file (in the Finder) and choose Get Info > > (control- > > or right-click, cmd-I, or File:Get Info at your discretion). > > > > switch to the "Open With" pane. from the option list there, choose > > rasmol > > 2.7.2.1 (if it is not present, there is an Other... option at the very > > bottom of the list that allows you browse to the app). > > > > click the Change All button to make this the default for all files > > of > > this > > type on your computer. > > > > repeat for ras files, scr files - any files you want to double-click > > and > > launch rasmol 2.7.2.1. > > > > > > hth, > > > > :tim > > -- > > molvisions - molecular graphics & visualization > > > > usa:north carolina:wake forest > > > > > > > > > > > > at 4:35 AM EDT on (Sunday) 2 March 2003 George Tzotzos said: > > > >> Hi there, > >> > >> I followed Harold's option 1. X11 properly installed, rasmol > >> 2.7.2.1 > >> and > >> rasmol.help both downloaded from arcib.dowling.edu and moved to the > >> /usr/local/bin directory. > >> > >> Encountered the following problems: > >> > >> 1. On trying to open files with .pdb extension rasmol is overriden > >> by > >> iMol > >> (native OSX program). > >> 2. On trying to open rasmol scripted files (.ras extension), system > >> OS9 is > >> fired up and the file is open by RasMol 2.6 for system 9. > >> > >> Both of the above even if I reboot and try to open files from the > >> X11 window. > >> > >> Would be grateful for any suggestions. > >> > >> George > >> > >> Dr George Tzotzos > >> UNIDO, Vienna, Austria > >> > >> Tel: +43-1-26026 4336 > >> Fax: +43-1-26026 6810 > >> email: g.tzotzos@unido.org > >> > >> > >> > >> On Saturday, February 22, 2003, at 07:01PM, Harold Schranz > >> wrote: > >> > >>> On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli > >>> wrote: > >>>> Dear Chris and all the ones who sent helpful suggestions, which I > >>>> have followed the most carefully I could, I am afraid I > >>>> still > >>>> am in troubles. > >>> > >>> Dear Adriano > >>> > >>> Hopefully I correctly understand your predicament! > >>> > >>> A simple approach MIGHT be the following (assuming you have OS X > >>> 10.2 or later): > >>> > >>> 1) In case the route involving getting the bits and pieces > >>> together > >>> as > >>> in > >>> Christopher Masi's post is too hard (at first) you could just > >>> download > >>> one of the precompiled executables from: > >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >>> Mac_OS_X_10.2.2_PPC/ > >>> (e.g. the 32 bit one if your display covers that range) > >>> and the corresponding help file from: > >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >>> rasmol.hlp.gz > >>> which I put both (after gunzipping) in /usr/local/bin > >>> (a little less elegant than the full Fink install procedure but it > >>> works). > >>> (see > >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >>> for > >>> details) > >>> > >>> Of course, you will still need (for example) X11 for Mac OS X > >>> Public Beta, which is an implementation of the X Window System > >>> that makes it possible to run X11-based applications in Mac OS > >>> http://www.apple.com/downloads/macosx/apple/x11formacosx.html > >>> (41.8MB) > >>> > >>> 2) Eventually, if you do get the energy, (as stated by others) the > >>> following link is invaluable > >>> http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html > >>> to get all of the appropriate pieces together and use Fink for the > >>> compile/install procedures (rasmol executable will end up in > >>> /sw/bin/ and not overwrite /usr/local/bin/). > >>> Just a matter of being persistent and careful and a little patient. > >>> > >>> I've actually got Rasmol installed by both routes (but gave/linked > >>> them > >>> to unique names); > >>> don't ask why I bothered ... just bored I guess. 8-) > >>> > >>> I hope this helps! > >>> > >>> Good Luck > >>> Harry. > >>> > >>> ------------------------------------------------------------------ > >>> --- > >>> --- > >>> ---- > >>> Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 > >>> 6268 > >>> 8919 > >>> School of Chemistry, University College (UNSW) Fax: +61 2 > >>> 6268 > >>> 8002 > >>> Australian Defence Force Academy Fax: +61 2 > >>> 6268 > >>> 8017 > >>> Canberra ACT 2600, Australia Email: > >>> Harold.Schranz@adfa.edu.au > >>> > >>> Visiting Fellow, Biophysics Group, Department of Theoretical > >>> Physics and ANU Supercomputer Facility and Research School of > >>> Chemistry Australian National University, Canberra ACT 0200, Australia > >>> Email: Harold.Schranz@anu.edu.au Phone: +61 2 > >>> 6125 > >>> 6533 > >>> ------------------------------------------------------------------ > >>> --- > >>> --- > >>> ---- > >>> > >>> > >>> > >>> > >> > >> > >> > > > > ---------------------------------------------------------------- > > rasmol-+ > > > > To change your address, unsubscribe, view previous messages/history, > > receive messages as weekly digests, or for any other information > > about the RasMol EMail List, please go to > > http://www.umass.edu/microbio/rasmol/raslist.htm > > > > ---------------------------------------------------------------- > > rasmol-- > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: George Tzotzos Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Tue, 04 Mar 2003 00:35:55 -0800 To: rasmol@lists.umass.edu Chris' solution works. Many thanks. George Dr George Tzotzos UNIDO Vienna, Austria Tel: +43-1-26026 4336 Fax: +43-1-26026 810 -------------- On Sunday, March 02, 2003, at 06:18AM, Christopher Masi wrote: >I am starting with the assumption that you are double clicking the >files to open them. > > Rasmol 2.7.2 is running on OS X's Darwin core, and the only way to >interact with the program is by a terminal emulator (xTerm or Apple's >Terminal). The only way to display the output is through an X 11 window. > Essentially, OS X has a mild case of MPD. iMol is a full fledged OS X >program. Rasmol 2.6 is a "Classic" application. Rasmol 2.7.2 is a >Darwin application. The Finder only "knows" about Classic and OS X >applications. It does not know about Darwin applications. > When you double click the pdb file, the Finder looks for a program >that has the correct creator type and tells that program to open the >file. Since the Finder doesn't know that rasmol 2.7.2 exists the Finder >instructs iMol to open the pdb file (iMol is newer than Rasmol 2.6). >When you double click the .ras file, the Finder looks for an >application to use. The Finder still doesn't know about Rasmol 2.7.2, >and iMol cannot open (or at least the Finder doesn't think it can open) >.ras files, so the Finder goes to the only application that it knows >about that can open the .ras file, Rasmol 2.6. > Because rasmol 2.7.2 was installed as a Darwin/Unix application it is >not double clickable. Try finding rasmol 2.7.2 and double clicking it. >It will not start. If everything is set up correctly, to use Rasmol >2.7.2 to open a pdb file you have to > >1. have X11 running. Double click Apple's X11.app >2. in an xTerm window or (if configured the right way) or a >Terminal.app window navigate to the directory that contains all the >pbds that you want to view and type rasmol >3. in the window that was used to launch rasmol type load 1ADO.pdb >where 1ADO.pdb is the name of the file that you want to open. > >Chris > >On Sunday, March 2, 2003, at 07:35 AM, George Tzotzos wrote: > >> Hi there, >> >> I followed Harold's option 1. X11 properly installed, rasmol 2.7.2.1 >> and rasmol.help both downloaded from arcib.dowling.edu and moved to >> the /usr/local/bin directory. >> >> Encountered the following problems: >> >> 1. On trying to open files with .pdb extension rasmol is overriden by >> iMol (native OSX program). >> 2. On trying to open rasmol scripted files (.ras extension), system >> OS9 is fired up and the file is open by RasMol 2.6 for system 9. >> >> Both of the above even if I reboot and try to open files from the X11 >> window. >> >> Would be grateful for any suggestions. >> >> George >> >> Dr George Tzotzos >> UNIDO, Vienna, Austria >> >> Tel: +43-1-26026 4336 >> Fax: +43-1-26026 6810 >> email: g.tzotzos@unido.org >> >> >> >> On Saturday, February 22, 2003, at 07:01PM, Harold Schranz >> wrote: >> >>> On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli wrote: >>>> Dear Chris and all the ones who sent helpful suggestions, >>>> which I have followed the most carefully I could, I am afraid I still >>>> am in troubles. >>> >>> Dear Adriano >>> >>> Hopefully I correctly understand your predicament! >>> >>> A simple approach MIGHT be the following (assuming you have OS X 10.2 >>> or later): >>> >>> 1) In case the route involving getting the bits and pieces together as >>> in >>> Christopher Masi's post is too hard (at first) you could just download >>> one of the precompiled executables from: >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >>> Mac_OS_X_10.2.2_PPC/ >>> (e.g. the 32 bit one if your display covers that range) >>> and the corresponding help file from: >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >>> rasmol.hlp.gz >>> which I put both (after gunzipping) in /usr/local/bin >>> (a little less elegant than the full Fink install procedure but it >>> works). >>> (see >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >>> for >>> details) >>> >>> Of course, you will still need (for example) X11 for Mac OS X Public >>> Beta, which >>> is an implementation of the X Window System that makes it possible to >>> run X11-based applications in Mac OS >>> http://www.apple.com/downloads/macosx/apple/x11formacosx.html (41.8MB) >>> >>> 2) Eventually, if you do get the energy, (as stated by others) the >>> following link is invaluable >>> http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html >>> to get all of the appropriate pieces together and use Fink for the >>> compile/install procedures >>> (rasmol executable will end up in /sw/bin/ and not overwrite >>> /usr/local/bin/). >>> Just a matter of being persistent and careful and a little patient. >>> >>> I've actually got Rasmol installed by both routes (but gave/linked >>> them >>> to unique names); >>> don't ask why I bothered ... just bored I guess. 8-) >>> >>> I hope this helps! >>> >>> Good Luck >>> Harry. >>> >>> ---------------------------------------------------------------------- >>> -- >>> ---- >>> Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 >>> 6268 >>> 8919 >>> School of Chemistry, University College (UNSW) Fax: +61 2 >>> 6268 >>> 8002 >>> Australian Defence Force Academy Fax: +61 2 >>> 6268 >>> 8017 >>> Canberra ACT 2600, Australia Email: >>> Harold.Schranz@adfa.edu.au >>> >>> Visiting Fellow, Biophysics Group, Department of Theoretical Physics >>> and ANU Supercomputer Facility and Research School of Chemistry >>> Australian National University, Canberra ACT 0200, Australia >>> Email: Harold.Schranz@anu.edu.au Phone: +61 2 >>> 6125 >>> 6533 >>> ---------------------------------------------------------------------- >>> -- >>> ---- >>> >>> >>> >>> >> >> ---------------------------------------------------------------- >> rasmol-+ >> >> To change your address, unsubscribe, view previous messages/history, >> receive messages as weekly digests, or for any other information >> about the RasMol EMail List, please go to >> http://www.umass.edu/microbio/rasmol/raslist.htm >> >> ---------------------------------------------------------------- >> rasmol-- >> > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: helgew@www.grajagan.net ++++------+------+------+------+------+------+------+------+------+------+ From: Helge Weissig Subject: book announcement: Structural Bioinformatics Date: Wed, 12 Mar 2003 09:53:47 -0800 (PST) To: Bioinformatics List: ; Dear Colleague, I am very pleased to announce the availability of a new text book with the title "Structural Bioinformatics" (Editors: P. E. Bourne and H. Weissig. Hoboken, NJ, John Wiley & Sons, Inc.). Chapters of interest to this list include "The Protein Data Bank", "Computational Aspects of High-throughput Crystallographic Macromolecular Structure Determination" and "Molecular Visualization." Other chapters cover areas such as Comparative Features, Structure and Functional Assignment, Proteins as Drug Targets and Structure Prediction. A full list of chapters together with the names of all authors and more is available at the book's companion web site http://www.structuralbioinformaticsbook.com We hope you will find this book of great relevance to your area of research and/or teaching and your comments and feedback are very welcome. Apologies in advance, should you have received this message multiple times. with best regards, h. /--------------------------------------------- / Helge Weissig, Ph.D. / Co-Editor, Structural Bioinformatics / http://www.structuralbioinformaticsbook.com ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20021120 Netscape/7.01 X-Accept-Language: en-us, en ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: rasmol and 4cpa Date: Fri, 28 Mar 2003 12:40:05 +0000 To: rasmol Hi, I dont't know if you know pdb 4cpa - It has a weird format, having some null chain and some named chain. As far as I know this is the only pdb to mix null and named chains. In rasmol is there any way to select just the null chain? I am guessing that this feature was not implemented, as it is almost never necessary. I asked at the PDB about this file, but they said they could not update the record, which seems a bit strange to me. Thanks, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20021120 Netscape/7.01 X-Accept-Language: en-us, en References: <3E8442A5.9030602@mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: tiny bug Date: Fri, 28 Mar 2003 12:54:20 +0000 To: rasmol@lists.umass.edu I just saw that select not all and select ! all doesn't work like select not * and select !* ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Gorga, Frank" Subject: RE: rasmol and 4cpa Date: Fri, 28 Mar 2003 08:14:45 -0500 To: "'rasmol@lists.umass.edu'" Dan, All that is needed is a little Boolean logic... Use the command "select not (*I and *G)" this will select just the enzyme and not the inhibitor or the glycine. You could modify this strategy to select a specific part of the enzyme. For example to select residue 7 in the enzyme without selecting residue 7 in the inhibitor you would use the command "select 7 and not 7I" Hope that this helps, --- Frank ---------------------------------------------------------------------------- - Frank R. Gorga, Ph.D. Department of Chemical Sciences Bridgewater State College Bridgewater, MA 02325 508-531-2827 / 508-531-1785 (fax) fgorga@bridgew.edu webhost.bridgew.edu/fgorga ---------------------------------------------------------------------------- Comfort the troubled; trouble the comfortable. -- Dietrich Bonhoeffer, 1906-1945 http://www.dbonhoeffer.org/who-was-db2.htm -----Original Message----- Sent: Friday, March 28, 2003 7:40 AM From: Dan Bolser [mailto:dmb@mrc-dunn.cam.ac.uk] Subject: rasmol and 4cpa To: rasmol Hi, I dont't know if you know pdb 4cpa - It has a weird format, having some null chain and some named chain. As far as I know this is the only pdb to mix null and named chains. In rasmol is there any way to select just the null chain? I am guessing that this feature was not implemented, as it is almost never necessary. I asked at the PDB about this file, but they said they could not update the record, which seems a bit strange to me. Thanks, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: rasmol and 4cpa Date: Fri, 28 Mar 2003 09:05:24 -0500 To: rasmol@lists.umass.edu At 3/28/03, you wrote: >Hi, I dont't know if you know pdb 4cpa - It has a weird format, >having some null chain and some named chain. As far as I know >this is the only pdb to mix null and named chains. > >In rasmol is there any way to select just the null chain? > >I am guessing that this feature was not implemented, as it is almost >never necessary. > >I asked at the PDB about this file, but they said they could not update >the record, which seems a bit strange to me. > >Thanks, Dan. Frank Gorga's Boolean solution is a good one. Alternatively, one can use DeepView to rename the unnamed chain. The result with chains A, G, I is available at http://molvis.sdsc.edu/pdb/4cpa_agi.pdb The procedure is: -Preferences, Loading Protein, uncheck Ignore solvent (lower left in dialog). [Unnecessary for 4cpa since it has no water.] -In the Control Panel, select the unnamed chain by clicking in the blank leftmost column. -Holding down Ctrl, click to deselect ZN1. -Edit, Rename current layer. -In that dialog, enter "A" in Rename Chain of Selected Groups -Click OK. -File, Save, Layer. -Remove the SPDB records inserted at the end by DeepView (optional - I did). -Copy the original header into the DeepView result (optional - I did). DeepView makes at least one other change: Residue 2 in chain I is GLX. This is a legal residue name in PDB format meaning either GLU or GLN (http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_82.html#Anchor-Amino-36680). DeepView changes this residue from ATOM to HETATM. Dan, I would be interested in seeing a copy of your inquiry to the PDB and their reply. -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-MSMail-priority: Normal References: <9F5E83E17008D31193DD0090274E75051319DCE9@mailhost.bridgew.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: rasmol and 4cpa Date: Fri, 28 Mar 2003 15:12:10 +0100 To: rasmol@lists.umass.edu Hi, you surelly meant "select not (*I or *G)" as *I and *G is empty. Paul ----- Original Message ----- Sent: Friday, March 28, 2003 2:14 PM From: "Gorga, Frank" Subject: RE: rasmol and 4cpa To: > Dan, > > All that is needed is a little Boolean logic... > > Use the command "select not (*I and *G)" this will select just the enzyme > and not the inhibitor or the glycine. > > You could modify this strategy to select a specific part of the enzyme. For > example to select residue 7 in the enzyme without selecting residue 7 in the > inhibitor you would use the command "select 7 and not 7I" > > Hope that this helps, > > --- Frank > > -------------------------------------------------------------------------- -- > - > Frank R. Gorga, Ph.D. > Department of Chemical Sciences > Bridgewater State College > Bridgewater, MA 02325 > 508-531-2827 / 508-531-1785 (fax) > fgorga@bridgew.edu > webhost.bridgew.edu/fgorga > -------------------------------------------------------------------------- -- > Comfort the troubled; trouble the comfortable. > -- Dietrich Bonhoeffer, 1906-1945 > http://www.dbonhoeffer.org/who-was-db2.htm > > > -----Original Message----- > From: Dan Bolser [mailto:dmb@mrc-dunn.cam.ac.uk] > Sent: Friday, March 28, 2003 7:40 AM > To: rasmol > Subject: rasmol and 4cpa > > > Hi, I dont't know if you know pdb 4cpa - It has a weird format, > having some null chain and some named chain. As far as I know > this is the only pdb to mix null and named chains. > > In rasmol is there any way to select just the null chain? > > I am guessing that this feature was not implemented, as it is almost > never necessary. > > I asked at the PDB about this file, but they said they could not update > the record, which seems a bit strange to me. > > Thanks, Dan. > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20021120 Netscape/7.01 X-Accept-Language: en-us, en References: <9F5E83E17008D31193DD0090274E75051319DCE9@mailhost.bridgew.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: rasmol and 4cpa Date: Fri, 28 Mar 2003 14:57:55 +0000 To: rasmol@lists.umass.edu Perfect, I guess I am getting slow in my old age! Dan. Gorga, Frank wrote: >Dan, > >All that is needed is a little Boolean logic... > >Use the command "select not (*I and *G)" this will select just the enzyme >and not the inhibitor or the glycine. > >You could modify this strategy to select a specific part of the enzyme. For >example to select residue 7 in the enzyme without selecting residue 7 in the >inhibitor you would use the command "select 7 and not 7I" > >Hope that this helps, > >--- Frank > >---------------------------------------------------------------------------- >- >Frank R. Gorga, Ph.D. >Department of Chemical Sciences >Bridgewater State College >Bridgewater, MA 02325 >508-531-2827 / 508-531-1785 (fax) >fgorga@bridgew.edu >webhost.bridgew.edu/fgorga >---------------------------------------------------------------------------- >Comfort the troubled; trouble the comfortable. > -- Dietrich Bonhoeffer, 1906-1945 > http://www.dbonhoeffer.org/who-was-db2.htm > > >-----Original Message----- >From: Dan Bolser [mailto:dmb@mrc-dunn.cam.ac.uk] >Sent: Friday, March 28, 2003 7:40 AM >To: rasmol >Subject: rasmol and 4cpa > > >Hi, I dont't know if you know pdb 4cpa - It has a weird format, >having some null chain and some named chain. As far as I know >this is the only pdb to mix null and named chains. > >In rasmol is there any way to select just the null chain? > >I am guessing that this feature was not implemented, as it is almost >never necessary. > >I asked at the PDB about this file, but they said they could not update >the record, which seems a bit strange to me. > >Thanks, Dan. > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_vkiRG+fml7gWFWwfqWEqZQ)" User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20021120 Netscape/7.01 X-Accept-Language: en-us, en ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Original mail to PDB:[Fwd: Fwd: 4cpa - unique format.] Date: Fri, 28 Mar 2003 15:00:17 +0000 To: rasmol --Boundary_(ID_vkiRG+fml7gWFWwfqWEqZQ) -------- Original Message -------- ++++------+------+------+------+------+------+------+------+------+------+ From: Shri Jain Subject: Fwd: 4cpa - unique format. Date: Thu, 16 Jan 2003 14:36:52 -0500 To: dmb@mrc-dunn.cam.ac.uk, SJ_INFO , "Jain, Shri" Hi, This is a very old file. Under the data uniformity project, the older files were fixed and are available in mmCIF format from the pdb site. The information about how to get the file and translate it to pdb format is available at http://www.rcsb.org/pdb/uniformity/index.html Hope this helps, Shri >>You wrote: >Hi, I don't know if this molecule breaks >the format specification, but it is unique >in that it has both a 'null' chain and a >chain with an identifier. > >I had asumed that any null chain was itself >indicative of a single chain pdb, with all >multi chain pdbs having chain id's in all >instances. > >Using the scop domain definition I found that >4cpa is unique in this respect. > >Thanks for any help you can give in this matter. >Dan. -- =========================================================== Shri C Jain, Ph.D. RCSB Protein Data Bank Department of Chemistry and Chemical Biology Rutgers The State University of New Jersey 610 Taylor Road Piscataway, NJ 08854-8087 Email: sjain@rcsb.rutgers.edu Phone: (732) 445-0103 Fax: (732)-445-4320 =========================================================== --Boundary_(ID_vkiRG+fml7gWFWwfqWEqZQ)

-------- Original Message --------
Subject: Fwd: 4cpa - unique format.
Date: Thu, 16 Jan 2003 14:36:52 -0500
From: Shri Jain <sjain@rcsb.rutgers.edu>
To: dmb@mrc-dunn.cam.ac.uk, SJ_INFO <info@rcsb.org>, "Jain, Shri" <sjain@rcsb.rutgers.edu> 


Hi,

	This is a very old file. Under the data uniformity project, the older files
were fixed and are available in mmCIF format from the pdb site. The information
about how to get the file and translate it to pdb format is available at
 
http://www.rcsb.org/pdb/uniformity/index.html

	Hope this helps,
	Shri

	

>>You wrote:

>Hi, I don't know if this molecule breaks
>the format specification, but it is unique
>in that it has both a 'null' chain and a
>chain with an identifier.
>
>I had asumed that any null chain was itself
>indicative of a single chain pdb, with all
>multi chain pdbs having chain id's in all
>instances.
>
>Using the scop domain definition I found that
>4cpa is unique in this respect.
>
>Thanks for any help you can give in this matter.
>Dan.
-- 
===========================================================
Shri C Jain, Ph.D.
RCSB Protein Data Bank
Department of Chemistry and Chemical Biology
Rutgers The State University of New Jersey
610 Taylor Road
Piscataway, NJ 08854-8087

Email:  sjain@rcsb.rutgers.edu
Phone:  (732) 445-0103  
Fax:    (732)-445-4320
===========================================================
--Boundary_(ID_vkiRG+fml7gWFWwfqWEqZQ)-- boundary="Boundary_(ID_r0eUW1rcC03DF1cFqCqE8Q)" User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20021120 Netscape/7.01 X-Accept-Language: en-us, en ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Original reply to that mail:[Fwd: Re: Fwd: 4cpa - unique format.] Date: Fri, 28 Mar 2003 15:01:13 +0000 To: rasmol --Boundary_(ID_r0eUW1rcC03DF1cFqCqE8Q) I didn't get any reply... :( -------- Original Message -------- , SJ_INFO References: <3E2709D4.DF0F9F8C@rcsb.rutgers.edu> <32808.81.100.89.186.1042753284.squirrel@www.mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Shri Jain Subject: Re: Fwd: 4cpa - unique format. Date: Fri, 17 Jan 2003 09:34:58 -0500 To: Dan Bolser , "Jain, Shri" If the changes are in the coordinate section, we are not permitted to change. IF there are any corrections in the header section, we do make changes and the updated file is re-released to appear in public domain. Shri Jain Dan Bolser wrote: > > So there is no plan to replace / update the original PDB? > > The problem is that the pdb is classified a certain way by > scop. Updating my local copy isn't the problem. > > Please let me know, > > Thanks for the reply, > > Dan. > > Shri Jain said: > > Hi, > > > > This is a very old file. Under the data uniformity project, the older files > > were fixed and are available in mmCIF format from the pdb site. The information > > about how to get the file and translate it to pdb format is available at > > > > http://www.rcsb.org/pdb/uniformity/index.html > > > > Hope this helps, > > Shri > > > > > > > > > > > >>>You wrote: > > > > > >>Hi, I don't know if this molecule breaks > >>the format specification, but it is unique > >>in that it has both a 'null' chain and a > >>chain with an identifier. > >> > >>I had asumed that any null chain was itself > >>indicative of a single chain pdb, with all > >>multi chain pdbs having chain id's in all > >>instances. > >> > >>Using the scop domain definition I found that > >>4cpa is unique in this respect. > >> > >>Thanks for any help you can give in this matter. > >>Dan. > > -- > > =========================================================== > > Shri C Jain, Ph.D. > > RCSB Protein Data Bank > > Department of Chemistry and Chemical Biology > > Rutgers The State University of New Jersey > > 610 Taylor Road > > Piscataway, NJ 08854-8087 > > > > Email: sjain@rcsb.rutgers.edu > > Phone: (732) 445-0103 > > Fax: (732)-445-4320 > > =========================================================== -- =========================================================== Shri C Jain, Ph.D. RCSB Protein Data Bank Department of Chemistry and Chemical Biology Rutgers The State University of New Jersey 610 Taylor Road Piscataway, NJ 08854-8087 Email: sjain@rcsb.rutgers.edu Phone: (732) 445-0103 Fax: (732)-445-4320 =========================================================== --Boundary_(ID_r0eUW1rcC03DF1cFqCqE8Q) I didn't get any reply... :(

-------- Original Message --------
Subject: Re: Fwd: 4cpa - unique format.
Date: Fri, 17 Jan 2003 09:34:58 -0500
From: Shri Jain <sjain@rcsb.rutgers.edu>
To: Dan Bolser <dmb@mrc-dunn.cam.ac.uk>, "Jain, Shri" <sjain@rcsb.rutgers.edu>, SJ_INFO <info@rcsb.org>
References: <3E2709D4.DF0F9F8C@rcsb.rutgers.edu> <32808.81.100.89.186.1042753284.squirrel@www.mrc-dunn.cam.ac.uk> 


	If the changes are in the coordinate section, we are not permitted to change.
IF there are any corrections in the header section, we do make changes and the
updated file is re-released to appear in public domain.

	Shri Jain

Dan Bolser wrote:
> 
> So there is no plan to replace / update the original PDB?
> 
> The problem is that the pdb is classified a certain way by
> scop. Updating my local copy isn't the problem.
> 
> Please let me know,
> 
> Thanks for the reply,
> 
> Dan.
> 
> Shri Jain said:
> > Hi,
> >
> >       This is a very old file. Under the data uniformity project, the older files
> > were fixed and are available in mmCIF format from the pdb site. The information
> > about how to get the file and translate it to pdb format is available at
> >
> > http://www.rcsb.org/pdb/uniformity/index.html
> >
> >       Hope this helps,
> >       Shri
> >
> >
> >
> >
> >
> >>>You wrote:
> >
> >
> >>Hi, I don't know if this molecule breaks
> >>the format specification, but it is unique
> >>in that it has both a 'null' chain and a
> >>chain with an identifier.
> >>
> >>I had asumed that any null chain was itself
> >>indicative of a single chain pdb, with all
> >>multi chain pdbs having chain id's in all
> >>instances.
> >>
> >>Using the scop domain definition I found that
> >>4cpa is unique in this respect.
> >>
> >>Thanks for any help you can give in this matter.
> >>Dan.
> > --
> > ===========================================================
> > Shri C Jain, Ph.D.
> > RCSB Protein Data Bank
> > Department of Chemistry and Chemical Biology
> > Rutgers The State University of New Jersey
> > 610 Taylor Road
> > Piscataway, NJ 08854-8087
> >
> > Email:  sjain@rcsb.rutgers.edu
> > Phone:  (732) 445-0103
> > Fax:    (732)-445-4320
> > ===========================================================

-- 
===========================================================
Shri C Jain, Ph.D.
RCSB Protein Data Bank
Department of Chemistry and Chemical Biology
Rutgers The State University of New Jersey
610 Taylor Road
Piscataway, NJ 08854-8087

Email:  sjain@rcsb.rutgers.edu
Phone:  (732) 445-0103  
Fax:    (732)-445-4320
===========================================================
--Boundary_(ID_r0eUW1rcC03DF1cFqCqE8Q)-- X-X-Sender: fcb@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Frances C. Bernstein" Subject: 4cpa Date: Fri, 28 Mar 2003 11:33:12 -0500 (EST) To: sjain@rcsb.rugers.edu Cc: jwest@rcsb.rutgers.edu, flippen@rcsb.rutgers.edu, rasmol@lists.umass.edu Hi, I saw the correspondence about 4cpa and am puzzled why it is not possible to correct the chain indentifier problem. This would not be a change to the coordinates but is rather a representation issue. Note that the format description (under SEQRES) indicates: Chain identifier. This may be any single legal character, including a blank which is used if there is only one chain. This implies that a blank cannot be used if there is more than one chain, which is the case in 4cpa. Thus the entry as it stands violates the PDB format. To take the argument about not changing coordinates to the extreme, would you not correct an entry with a misformatted ATOM record or with a spurious character in an ATOM record? Frances C. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Frances C. Bernstein * *** fcb@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20021120 Netscape/7.01 X-Accept-Language: en-us, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: 4cpa Date: Fri, 28 Mar 2003 18:20:30 +0000 To: rasmol@lists.umass.edu Cc: sjain@rcsb.rugers.edu, jwest@rcsb.rutgers.edu, flippen@rcsb.rutgers.edu exactly! What if the structure turned out to be wrong? Frances C. Bernstein wrote: >Hi, > > I saw the correspondence about 4cpa and am puzzled >why it is not possible to correct the chain indentifier >problem. This would not be a change to the coordinates >but is rather a representation issue. Note that the format >description (under SEQRES) indicates: > > Chain identifier. This may be any single legal character, > including a blank which is used if there is only one chain. > >This implies that a blank cannot be used if there is more >than one chain, which is the case in 4cpa. Thus the >entry as it stands violates the PDB format. > > To take the argument about not changing coordinates >to the extreme, would you not correct an entry with a >misformatted ATOM record or with a spurious character in >an ATOM record? > > Frances C. Bernstein >===================================================== >**** BERNSTEIN + SONS >* * INFORMATION SYSTEMS CONSULTANTS >**** P.O. BOX 177, BELLPORT, NY 11713-0177 >* * *** >**** * Frances C. Bernstein > * *** fcb@bernstein-plus-sons.com > *** * > * *** 1-631-286-1339 FAX: 1-631-286-1999 >===================================================== > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: Roy Carambula Subject: RE: 4cpa Date: Fri, 28 Mar 2003 13:50:30 -0500 To: "'rasmol@lists.umass.edu'" Hi list, It sounds like a "raw data" preservation-like concern. However I'm sure there must be a procedure to fix this, in any case this can't be the first time a mistake/error is found Roy Dan Bolser wrote: exactly! What if the structure turned out to be wrong? Frances C. Bernstein wrote: >Hi, > > I saw the correspondence about 4cpa and am puzzled >why it is not possible to correct the chain indentifier >problem. This would not be a change to the coordinates >but is rather a representation issue. Note that the format >description (under SEQRES) indicates: > > Chain identifier. This may be any single legal character, > including a blank which is used if there is only one chain. > >This implies that a blank cannot be used if there is more >than one chain, which is the case in 4cpa. Thus the >entry as it stands violates the PDB format. > > To take the argument about not changing coordinates >to the extreme, would you not correct an entry with a >misformatted ATOM record or with a spurious character in >an ATOM record? > > Frances C. Bernstein >===================================================== >**** BERNSTEIN + SONS >* * INFORMATION SYSTEMS CONSULTANTS >**** P.O. BOX 177, BELLPORT, NY 11713-0177 >* * *** >**** * Frances C. Bernstein > * *** fcb@bernstein-plus-sons.com > *** * > * *** 1-631-286-1339 FAX: 1-631-286-1999 >===================================================== > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-MSMail-priority: Normal References: <3E84926E.5020204@mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: 4cpa,... and 3cpa Date: Fri, 28 Mar 2003 19:50:51 +0100 To: rasmol@lists.umass.edu 3cpa has also a blank character as an identifier to the enzym chain, and a substrate chain identified by S Paul ----- Original Message ----- Sent: Friday, March 28, 2003 7:20 PM From: "Dan Bolser" Subject: Re: 4cpa To: Cc: ; ; > exactly! What if the structure turned out to be wrong? > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: fcb@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Frances C. Bernstein" Subject: Re: 4cpa (fwd) Date: Fri, 28 Mar 2003 16:21:02 -0500 (EST) To: Shri Jain Cc: jwest@rcsb.rutgers.edu, flippen@rcsb.rutgers.edu, rasmol@lists.umass.edu Dear Shri, I have been involved with CIF and mmCIF since 1990 and think that mmCIF will eventually become the standard format. However, I recognize the reality that almost everyone in the world who currently uses the PDB wants entries in PDB format. Perhaps you could provide statistics on the number of entries retrieved per month in mmCIF format versus the number retrieved per month in PDB format. This would help to establish whether your decision not to correct 4cpa in PDB format is in the best interests of the user community. Frances ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Frances C. Bernstein * *** fcb@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Fri, 28 Mar 2003, Shri Jain wrote: > Dear Frances, > > Thank you for your email. The 4CPA file was fixed for chain id and is available > from the site BETAmmCIF site as mmcif file: > > ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF/ > > Shri > > > > "Frances C. Bernstein" wrote: > > > > Sorry I mistyped your address the first time. > > > > Frances > > > > ===================================================== > > **** BERNSTEIN + SONS > > * * INFORMATION SYSTEMS CONSULTANTS > > **** P.O. BOX 177, BELLPORT, NY 11713-0177 > > * * *** > > **** * Frances C. Bernstein > > * *** fcb@bernstein-plus-sons.com > > *** * > > * *** 1-631-286-1339 FAX: 1-631-286-1999 > > ===================================================== > > > > ---------- Forwarded message ---------- > > Date: Fri, 28 Mar 2003 11:33:12 -0500 (EST) > > From: Frances C. Bernstein > > To: sjain@rcsb.rugers.edu > > Cc: jwest@rcsb.rutgers.edu, flippen@rcsb.rutgers.edu, rasmol@lists.umass.edu > > Subject: 4cpa > > Hi, > > > > I saw the correspondence about 4cpa and am puzzled > > why it is not possible to correct the chain indentifier > > problem. This would not be a change to the coordinates > > but is rather a representation issue. Note that the format > > description (under SEQRES) indicates: > > > > Chain identifier. This may be any single legal character, > > including a blank which is used if there is only one chain. > > > > This implies that a blank cannot be used if there is more > > than one chain, which is the case in 4cpa. Thus the > > entry as it stands violates the PDB format. > > > > To take the argument about not changing coordinates > > to the extreme, would you not correct an entry with a > > misformatted ATOM record or with a spurious character in > > an ATOM record? > > > > Frances C. Bernstein > > ===================================================== > > **** BERNSTEIN + SONS > > * * INFORMATION SYSTEMS CONSULTANTS > > **** P.O. BOX 177, BELLPORT, NY 11713-0177 > > * * *** > > **** * Frances C. Bernstein > > * *** fcb@bernstein-plus-sons.com > > *** * > > * *** 1-631-286-1339 FAX: 1-631-286-1999 > > ===================================================== > > -- > =========================================================== > Shri C Jain, Ph.D. > RCSB Protein Data Bank > Department of Chemistry and Chemical Biology > Rutgers The State University of New Jersey > 610 Taylor Road > Piscataway, NJ 08854-8087 > > Email: sjain@rcsb.rutgers.edu > Phone: (732) 445-0103 > Fax: (732)-445-4320 > =========================================================== > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_wbyT9DRRWWCPYGumXPL7Gg)" User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20021120 Netscape/7.01 X-Accept-Language: en-us, en References: <9F5E83E17008D31193DD0090274E75051319DCE9@mailhost.bridgew.edu> <000501c2f534$0f0d7580$0100a8c0@zig> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: rasmol and 4cpa Date: Mon, 31 Mar 2003 09:54:29 +0100 To: rasmol@lists.umass.edu --Boundary_(ID_wbyT9DRRWWCPYGumXPL7Gg) Cheers, Paul Pillot wrote: >Hi, > >you surelly meant "select not (*I or *G)" as *I and *G is empty. > >Paul >----- Original Message ----- >From: "Gorga, Frank" >To: >Sent: Friday, March 28, 2003 2:14 PM >Subject: RE: rasmol and 4cpa > > > > >>Dan, >> >>All that is needed is a little Boolean logic... >> >>Use the command "select not (*I and *G)" this will select just the enzyme >>and not the inhibitor or the glycine. >> >>You could modify this strategy to select a specific part of the enzyme. >> >> >For > > >>example to select residue 7 in the enzyme without selecting residue 7 in >> >> >the > > >>inhibitor you would use the command "select 7 and not 7I" >> >>Hope that this helps, >> >>--- Frank >> >>-------------------------------------------------------------------------- >> >> >-- > > >>- >>Frank R. Gorga, Ph.D. >>Department of Chemical Sciences >>Bridgewater State College >>Bridgewater, MA 02325 >>508-531-2827 / 508-531-1785 (fax) >>fgorga@bridgew.edu >>webhost.bridgew.edu/fgorga >>-------------------------------------------------------------------------- >> >> >-- > > >>Comfort the troubled; trouble the comfortable. >> -- Dietrich Bonhoeffer, 1906-1945 >> http://www.dbonhoeffer.org/who-was-db2.htm >> >> >>-----Original Message----- >>From: Dan Bolser [mailto:dmb@mrc-dunn.cam.ac.uk] >>Sent: Friday, March 28, 2003 7:40 AM >>To: rasmol >>Subject: rasmol and 4cpa >> >> >>Hi, I dont't know if you know pdb 4cpa - It has a weird format, >>having some null chain and some named chain. As far as I know >>this is the only pdb to mix null and named chains. >> >>In rasmol is there any way to select just the null chain? >> >>I am guessing that this feature was not implemented, as it is almost >>never necessary. >> >>I asked at the PDB about this file, but they said they could not update >>the record, which seems a bit strange to me. >> >>Thanks, Dan. >> >> >> >> >> >> > > > > --Boundary_(ID_wbyT9DRRWWCPYGumXPL7Gg) Cheers,

Paul Pillot wrote:
Hi,

you surelly meant "select not (*I or *G)" as *I and *G is empty.

Paul
----- Original Message -----
Sent: Friday, March 28, 2003 2:14 PM
From: "Gorga, Frank" <FGORGA@bridgew.edu>
Subject: RE: rasmol and 4cpa
To: <rasmol@lists.umass.edu>

  
Dan,

All that is needed is a little Boolean logic...

Use the command "select not (*I and *G)" this will select just the enzyme
and not the inhibitor or the glycine.

You could modify this strategy to select a specific part of the enzyme.
    
For
  
example to select residue 7 in the enzyme without selecting residue 7 in
    
the
  
inhibitor you would use the command "select 7 and not 7I"

Hope that this helps,

--- Frank

--------------------------------------------------------------------------
    
--
  
-
Frank R. Gorga, Ph.D.
Department of Chemical Sciences
Bridgewater State College
Bridgewater, MA 02325
508-531-2827 / 508-531-1785 (fax)
fgorga@bridgew.edu
webhost.bridgew.edu/fgorga
--------------------------------------------------------------------------
    
--
  
Comfort the troubled; trouble the comfortable.
       -- Dietrich Bonhoeffer, 1906-1945
          http://www.dbonhoeffer.org/who-was-db2.htm

-----Original Message-----
Sent: Friday, March 28, 2003 7:40 AM
From: Dan Bolser [mailto:dmb@mrc-dunn.cam.ac.uk]
Subject: rasmol and 4cpa
To: rasmol

Hi, I dont't know if you know pdb 4cpa - It has a weird format,
having some null chain and some named chain. As far as I know
this is the only pdb to mix null and named chains.

In rasmol is there any way to select just the null chain?

I am guessing that this feature was not implemented, as it is almost
never necessary.

I asked at the PDB about this file, but they said they could not update
the record, which seems a bit strange to me.

Thanks, Dan.

--Boundary_(ID_wbyT9DRRWWCPYGumXPL7Gg)-- charset=us-ascii X-Accept-Language: en X-OriginalArrivalTime: 31 Mar 2003 15:24:00.0348 (UTC) FILETIME=[8DF4C1C0:01C2F799] ++++------+------+------+------+------+------+------+------+------+------+ From: Brian White Subject: Using chime with Yellowdog Linux Date: Mon, 31 Mar 2003 10:31:54 -0500 To: rasmol@lists.umass.edu Hi - Has anyone tried chime using Mac On Linux on Yellowdog linux (or any other linux)? Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://intro.bio.umb.edu/BW/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: Using chime with Yellowdog Linux Date: Mon, 31 Mar 2003 11:16:10 -0600 (CST) To: rasmol@lists.umass.edu Hi, I think you will be out of luck with the combination of Linux and Mac. It might work if you can emulate the Mac OS under Linux in some way (eg Mac on Linux). The issues appear to relate to communication between the browser, chime and the OS. It would be easier to get the browser to run another viewer. Regards Bruce On Mon, 31 Mar 2003, Brian White wrote: > Hi - > Has anyone tried chime using Mac On Linux on Yellowdog linux (or any > other linux)? > > Brian > > -- > Prof. Brian White > Biology Department > University of Massachusetts, Boston > 100 Morrissey Blvd > Boston MA 02125 > (617) 287-6630 > fax:(617) 287-6650 > brian.white@umb.edu > http://intro.bio.umb.edu/BW/ > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4920.2300 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: 4cpa Date: Tue, 01 Apr 2003 15:43:56 +0200 To: rasmol@lists.umass.edu Exactly. In addition, not 4cpa is the only file with blank or odd chain identifiers. Quite often the water molecules are marked with blank. It is not uncommon either that the identifier changes from one letter to another or to blank somewhere between TERs. Because column 22 in the pdb file is for the chain identifier - as FCB cites - its correctness should be checked more rigorously at PDB before the publication of an entry. How Rasmol & the others behave in this case? If between TERs the identifier changes from A to B, on selecting the second chain, atoms with identifier B are selected or from the appropriate TER until the next TER? Tamas E. Gunda ---------------------------- Dr. Tamas E. Gunda Department of Pharmaceutical Chemistry Medical and Health Center University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tamasgunda@tigris.klte.hu ----- Original Message ----- Sent: Friday, March 28, 2003 18:33 From: "Frances C. Bernstein" Subject: 4cpa To: Cc: ; ; > Hi, > > I saw the correspondence about 4cpa and am puzzled > why it is not possible to correct the chain indentifier > problem. This would not be a change to the coordinates > but is rather a representation issue. Note that the format > description (under SEQRES) indicates: > > Chain identifier. This may be any single legal character, > including a blank which is used if there is only one chain. > > This implies that a blank cannot be used if there is more > than one chain, which is the case in 4cpa. Thus the > entry as it stands violates the PDB format. > > To take the argument about not changing coordinates > to the extreme, would you not correct an entry with a > misformatted ATOM record or with a spurious character in > an ATOM record? > > Frances C. Bernstein > ===================================================== > **** BERNSTEIN + SONS > * * INFORMATION SYSTEMS CONSULTANTS > **** P.O. BOX 177, BELLPORT, NY 11713-0177 > * * *** > **** * Frances C. Bernstein > * *** fcb@bernstein-plus-sons.com > *** * > * *** 1-631-286-1339 FAX: 1-631-286-1999 > ===================================================== > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20021120 Netscape/7.01 X-Accept-Language: en-us, en References: <001d01c2f854$bdf9a0f0$3b8506c1@cthulhu> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: 4cpa Date: Wed, 02 Apr 2003 10:46:50 +0100 To: rasmol@lists.umass.edu Any news on this entry? Can we expect it to change? Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: A little help with Rasmol and Protein Explorerer Date: Fri, 11 Apr 2003 11:41:41 -0400 To: Scott Pendley Cc: rasmol@lists.umass.edu At 4/11/03, Scott Pendley wrote:
Eric,
 
I have been playing around with Rasmol for a little while but am new to PE.  I was wondering if you could tell me if there is a command that will list that atoms that are currently selected.  To put this in context I am working on very large protein-protein interaction and am looking for hydrogen between the complexes using the select within.  Trying to find the bonded residues based on color alone is a little difficult.  Do you know of any commands that will help eithor with listing selected atoms or determining hbonds on quaternary structures?
 
Thank you,
 
Scott

Dear Scott:

There are three shortcuts for visualizing noncovalent bonds in PE. The resulting selected residues, atoms, or chains can easily be listed. In each case, the scripts employed are displayed in the message box so you can see how much of a shortcut these are.

1. In QuickViews, select e.g. one chain (or any moiety), then DISPLAY Contacts.
After doing this, at the very bottom of the long explanation in the middle help window are instructions for listing the contacting atoms. In addition to "show residue" you can also "show atom" or "show chain". These Chime commands are not implemented in RasMol 2.6; I don't know about RasMol 2.7.

2. In Advanced Explorer, Contact Surfaces, you have more control. For example if you "generate the surface on" ":a and not carbon" you will unclutter the display by excluding putative van der Waals interactions. The same commands can be used for listing residues or atoms.

3. In Advanced Explorer, use the NonCovalent Bond Finder. Again the "show" commands can be used to list the current shell. Click on the "Instruction" button and look under "Selectable terms defined by NCBF". For example, you can "select found" (all atoms found to date in all shells), then "show residue". Here, there are slots for "don't find" or "find only", so "don't find carbon" will find mostly hydrogen bonds or salt bridges.

"show atom" lists only atom serial numbers. You could inspect the PDB file to find out the complete information about each serial number listed. "show atom identify" lists only the element and position. These lists are not as useful as they could be since they don't show the residues containing the atoms. "show residue" lists only the residues containing selected atoms, but not the individual atoms selected. Of course you can click on any atom (in the graphic) for a full identification of that one atom, including its residue.

I have copied this to the email list because it may be of interest to some subscribers.
-Eric

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Protein Explorer - 3D Visualization: http://proteinexplorer.org
Workshops: http://www.umass.edu/molvis/workshop
World Index of Molecular Visualization Resources: http://molvisindex.org
ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
PDB Lite Macromolecule Finder: http://pdblite.org
Molecular Visualization EMail List:
      http://www.umass.edu/microbio/rasmol/raslist.htm

Eric Martz, Professor (Immunology), Dept Microbiology
U Mass, Amherst MA US  413-545-2325/FAX 413-545-2532
              http://www.umass.edu/molvis/martz
- - - - - - - - - - - - - - - - - - - - - - - - - - - */
----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 boundary="Boundary_(ID_EQTYqBZrIpx/8TtfXmG67Q)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Helios Chen Subject: help command can not work Date: Tue, 29 Apr 2003 21:56:42 +0800 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_EQTYqBZrIpx/8TtfXmG67Q) Hi, The message " Unable to find RasMol help file "occurs when I enter the "help" in the RasMol Command Line, could you tell me what's wrong or any path need to be set? Thanks a lot. --Boundary_(ID_EQTYqBZrIpx/8TtfXmG67Q)

Hi,
 
The message " Unable to find RasMol help file "occurs when I enter the "help" in the RasMol Command Line, could you tell me what's wrong or any path need to be set?  Thanks a lot.
--Boundary_(ID_EQTYqBZrIpx/8TtfXmG67Q)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Assessment of Protein Explorer by Classes Date: Wed, 30 Apr 2003 09:29:24 -0400 To: rasmol@lists.umass.edu, pdb-l@rcsb.org To All Educators Who Are Using Protein Explorer in Classes: As the semester wraps up, please hand out the short one-page Student Assessment of Learning Gains (SALG) form available at http://molvis.sdsc.edu/protexpl/evalppr.htm This will only take about 5 minutes of class time and the results will be useful for future funding and development priorities for Protein Explorer. This will be useful even if you used Protein Explorer only in lectures, or only for a single computer laboratory class or homework assignment. For those interested in electronic assessment, you can set up the SALG website for your students to fill out the above form in a web browser, and you can also use the SALG mechanism for evaluation of your entire course, including questions that you formulate or modify from the generic template available. Details at http://molvis.sdsc.edu/protexpl/eval.htm Thanks, -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: pdb-l: Assessment of Protein Explorer by Classes Date: Wed, 30 Apr 2003 11:02:26 -0400 (EDT) To: rasmol@lists.umass.edu, pdb-l@rcsb.org Please do not confuse the use of Protein Explorer with the use of RasMol. Please send reports of your classroom and research experience with RasMol to reports@rasmol.org Such reports will help us in setting priorities for RasMol development. Our thanks to the community for the continuing interest in RasMol and the steady stream of downloads. -- H. J. Bernstein ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Wed, 30 Apr 2003, Eric Martz wrote: > To All Educators Who Are Using Protein Explorer in Classes: > > As the semester wraps up, please hand out the short one-page Student > Assessment of Learning Gains (SALG) form available at > http://molvis.sdsc.edu/protexpl/evalppr.htm > > This will only take about 5 minutes of class time and the results will be > useful for future funding and development priorities for Protein Explorer. > > This will be useful even if you used Protein Explorer only in lectures, or > only for a single computer laboratory class or homework assignment. > > For those interested in electronic assessment, you can set up the SALG > website for your students to fill out the above form in a web browser, and > you can also use the SALG mechanism for evaluation of your entire course, > including questions that you formulate or modify from the generic template > available. Details at http://molvis.sdsc.edu/protexpl/eval.htm > > Thanks, -Eric Martz > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > > TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see > https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l . > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Brian Foley Subject: Multiple windows open? Prevent duplicate names of same object. Date: Thu, 01 May 2003 09:52:50 -0500 To: rasmol@lists.umass.edu Dear RasMol/CHIME users, Last night, as I was debugging some HTML/CHIME scripting used to make an online macromolecular "museum exhibit" (such as those at David Marcey's OMM http://www.clunet.edu/BioDev/omm/gallery.htm) I found out that if I have two windows open in my www browser that are both running CHIME and accessing the same (or even related) pages, CHIME can be confused by dealing with two object with the same name. Scripts called from one www browser window will operate on the object in to other window that has the same name as the "target" of the CHIME script. Eric Martz uses a nice technique to avoid this in Protein Explorer: --------- from Eric ---------- The solution to this, Brian, is to give the Chime's in each window different names. In Protein Explorer, concurrent sessions are possible because the parent window assigns a number to each new session, and uses that number as part of the Chime names to make each unique. You can see this by viewing the source of the Chime frame. In Netscape, it is sufficient if each window has a different name, even if the Chime's don't. However in IE, each Chime must have a different name to avoid the problem you describe. ---------------------------------- Brian Foley, PhD HIV Genetic Sequences and Immunology Databases btf@lanl.gov (505) 665-1970 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Darrell Brooks Subject: Chime & Windows XP Date: Wed, 07 May 2003 17:32:28 +0100 To: rasmol A naive question Our network is going over to Windows XP. This won't affect Chime will it? Darrell ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Chip Coward Subject: RE: Chime & Windows XP Date: Wed, 07 May 2003 12:51:37 -0400 To: rasmol@lists.umass.edu Darrell, We have just set up Protein Explorer on a Dell Workstation and Dell Laptop using Windows XP Professional and all I had to do was to download the latest version of Chime. Chip -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Darrell Brooks Sent: Wednesday, May 07, 2003 12:32 PM From: owner-rasmol@lists.umass.edu Subject: Chime & Windows XP To: rasmol A naive question Our network is going over to Windows XP. This won't affect Chime will it? Darrell ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: "Paul I. Reisberg" Subject: Chime & OSX Date: Wed, 07 May 2003 14:58:42 -0400 To: rasmol@lists.umass.edu Is using Netscape 4.79 in classic mode still the best option for those using OSX? Anyone have any success with an OSX browser, Safari or Opera perhaps? ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Chime & OSX Date: Wed, 07 May 2003 16:04:44 -0400 To: rasmol@lists.umass.edu Chime only works under OS X running netscape 4.x in Classic mode. It does not work in any native OS X browser. that being said, Chime still works just fine in Classic NS4. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest at 2:58 PM EDT on (Wednesday) 7 May 2003 Paul I. Reisberg said: > Is using Netscape 4.79 in classic mode still the best option for those > using OSX? > Anyone have any success with an OSX browser, Safari or Opera perhaps? > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 boundary="Boundary_(ID_genbFwy6DrIQZrPIOkwgWQ)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Helios Chen Subject: Chime script Date: Sat, 10 May 2003 09:38:16 +0800 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_genbFwy6DrIQZrPIOkwgWQ) Dear Sir, The rotation command "spin on" in the Chime is too fast, could any script command adjust the speed? Best Regards. Helios Chen --Boundary_(ID_genbFwy6DrIQZrPIOkwgWQ)
Dear Sir, The rotation command "spin on" in the Chime is too fast, could any script command adjust the speed?  Best Regards.
 
Helios Chen
--Boundary_(ID_genbFwy6DrIQZrPIOkwgWQ)-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Chime script Date: Fri, 09 May 2003 22:02:02 -0400 To: rasmol@lists.umass.edu at 9:38 AM EDT on Saturday, May 10, 2003 Helios Chen said: > Dear Sir, The rotation command "spin on" in the Chime is too fast, could any > script command adjust the speed? Best Regards. > > Helios Chen from the Chime site at mdli: " Tag name: set spin fps Description: Sets the spin frames per second. This is equivalent to the spinfps embed tag Syntax: set spin fps ### ------------------------------------------------------------------------ Tag name: set spin x|y|z Description: Sets the speed of spin along the x, y, or z axis, in degrees per second. This is equivalent to the spinX, spinY, and spinZ embed tags. Syntax: set spin {x|y|z} ### ------------------------------------------------------------------------ " hope that helps! regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Chime in OSX Date: Fri, 09 May 2003 22:10:06 -0400 To: LIST rasmol those of us "waiting" for an OSX-friendly version of Chime may do well to read the mdl faq: " When will you have a version of Chime for Macintosh OS-X or Linux? We don't have any current plans for an OS-X version of Macintosh or a Linux version. " I believe that means there is no X-friendly version of Chime forthcoming. how sad. :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Helios Chen Subject: Re: Chime script Date: Sat, 10 May 2003 10:55:03 +0800 To: rasmol@lists.umass.edu Thanks for your help, colud any script command get the "spin" function in Rasmol?? I command the "spin on" on the Rasmol Command Line, but it can't work? If the first question could execute, are ther any command adjust the speed in Rasmol? ----- Original Message ----- Sent: Saturday, May 10, 2003 10:02 AM From: "timothy driscoll" Subject: Re: Chime script To: > > at 9:38 AM EDT on Saturday, May 10, 2003 Helios Chen said: > > > Dear Sir, The rotation command "spin on" in the Chime is too fast, could any > > script command adjust the speed? Best Regards. > > > > Helios Chen > > > from the Chime site at mdli: > > " > Tag name: set spin fps > Description: Sets the spin frames per second. This is equivalent to the > spinfps embed tag > Syntax: set spin fps ### > > ------------------------------------------------------------------------ > > Tag name: set spin x|y|z > Description: Sets the speed of spin along the x, y, or z axis, in degrees per > second. This is equivalent to the spinX, spinY, and spinZ embed tags. > Syntax: set spin {x|y|z} ### > > ------------------------------------------------------------------------ > " > > > hope that helps! > > > regards, > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Info: This message was accepted for relay by smtp02.mrf.mail.rcn.net as the sender used SMTP authentication X-Trace: UmFuZG9tSVbu7tfnfi9UNHMnFEicc/lc+eVdLm1FJfG18Eew5CEMXKUs4mKtPDU+ ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Masi Subject: Re: Chime in OSX Date: Fri, 09 May 2003 23:06:23 -0400 To: rasmol@lists.umass.edu That makes me sad. I am guessing that it would not be trivial to convert the Rasmol source to a plug-in. So, is there a cross platform way of creating web pages that can display molecules? I have used Chemical Applet but this page seems to have _recently_ disappeared. The developer, John Purvis, was associated with the CAChe molecular modeling system, and the Applet displayed molecules and surfaces generated by the CAChe molecular modeling system. I have also created QuickTIme Virtual Reality Objects of molecules and orbital surfaces, but QTVR Objects are limited in options and large in size. Thanks, Chris On Friday, May 9, 2003, at 10:10 PM, timothy driscoll wrote: > those of us "waiting" for an OSX-friendly version of Chime may do well > to read > the mdl faq: > > " > When will you have a version of Chime for Macintosh OS-X or Linux? > > We don't have any current plans for an OS-X version of Macintosh or a > Linux > version. > " > > > I believe that means there is no X-friendly version of Chime > forthcoming. how > sad. > > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Chime script Date: Sat, 10 May 2003 13:32:57 -0400 To: rasmol@lists.umass.edu At 5/10/03, Helios Chen wrote: >Thanks for your help, colud any script command get the "spin" function in >Rasmol?? I command the "spin on" on the Rasmol Command Line, but it can't >work? If the first question could execute, are ther any command adjust the >speed in Rasmol? The 'spin', 'move', and 'delay' commands are some of the many that Tim Maffett (of MDL) added to Chime that are not implemented in RasMol, at least in RasMol 2.6 beta-2a. I'm not sure about RasMol 2.7. Maffett spent a lot of time making movements in Chime be relatively independent of the hardware computer speed. In RasMol 2.6, there is no way to do that. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: ChimeShim "pbd" bug in Chime 2.6 SP4 Installer Date: Mon, 12 May 2003 17:10:55 -0400 To: rasmol@lists.umass.edu Cc: chime-team@mdli.com There is a bug in the Chime 2.6 SP4 installer as follows. In Internet Explorer (but not Netscape) when trying to display a PDB file directly in Chime (e.g. http://www.umass.edu/microbio/chime/atp.pdb) you sometimes get this spurious file download dialog: File Download: File Name: atp.pbd [NOTE THE TYPO, SHOULD BE .pdb] File Type: ChimeShimLibrary Object (open or save?) Clicking Open fails to invoke Chime. The bug is the typographical error "pbd" instead of "pdb" in the Windows Registry, put there by the Chime installer. The Chime 2.6 SP3 installer does not insert the incorrect ".pbd" extension in the registry, so the bug seems to be new with SP4. This bug was reported on this email list by Robley Light on January 24, but none of the responses identified the problem in the registry. Robert Lancashire recently told me about the typo in the registry, and said that MDL is aware of the problem. Shortly after that, it happened on my computer for the first time, and I investigated further. I have seen the spurious ChimeShim message occur in Internet Explorer 6.0 in Win98 and Win2000, but not consistently, even on the same machine (different boots). So far I have no explanation for why it occurs sometimes and not others. I have seen the error in the registry on WinXP but in my limited tests, the spurious ChimeShim message did not occur (the ATP molecule loaded correctly). However, since it occurs inconsistently in Win98 and Win2000, it won't surprise me if it sometimes occurs on WinXP also. If you need to correct this problem, Start, Run, RegEdit. In the left panel of the Registry Editor, be sure to highlight the top entry, My Computer, so your search will start at the top. Searching the Registry for "pbd" (the wrong spelling) finds two instances. The first is the one that needs fixing. The second involves "MSPBDE40.DLL" which must not be changed. Specifically, the incorrect registry entry is under My Computer HKEY_CLASSES_ROOT MIME Database Content Type chemical/x-pdb Extension ".pbd" ["chemical/x-pdb" occurs 13 times in my registry. ".pdb" occurs close to 30 times.] To correct the incorrect Extension ".pbd": right click, Modify, change to ".pdb", and exit (careful! the registry is automatically saved when you change it in RegEdit). This appears to fix the problem. You don't have to reboot, but you have to close IE and re-open it for the registry change to take effect in IE. I also tried uninstalling Chime 2.6 SP4 (from both IE 6 and Netscape 4) on Windows 2000, and then installing Chime 2.6 SP3. This did not fix the problem. Instead, Chime 2.6 SP3 failed to work at all in IE 6 (but worked in Netscape 4). -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: SYBYL on LINUX? Date: Wed, 14 May 2003 21:20:12 +0200 To: rasmol@lists.umass.edu The most recent issue of Biosilico magazine (www.drugdiscoverytoday.com) has an advertisement saying that Tripos Inc. (www.tripos.com) has made Sybil available on the Linux platform. I was curious how many people on this mailing list use Sybyl or have access to it via their respective institutions? Any feedback would be appreciated. Next, one of the reasons I mention Biosilico in terms of the question listed above is due to an article in this issue written by Brian Donnelly, "Data integration technologies: an unfulfilled revolution in the drug discovery process?" pp. 59-63 ... The plug for his own company on page 60 made me immediately think "infomercial", but as I read on much of what was said paralleled my own thoughts developing in the years since first hearing the term "bioinformatics" in 1998. Does Brian Donnelly know about this list? Does he subscribe? How much interaction is there between commercial software developers and those using the technology? The Verity House group comes to mind when I think about software manufacturers with both biomedical skills and programming skills under the same roof. Is there a distance between the "bio" and the "informatic" still? What level of cooperation do each of you see between your research/educational group and commercial software developers? Is there any central developmental organization concerning integration of services for the bioinformatics industry? I subscribe to an IBM software developer's list. I subscribe to databank and cluster-server tech lists. I get info regularly from Cisco, Sun Microsystems, etc. I cannot do more than just dip my finger in any particular pie, because I am a hardware specialist that just happened to get a medical core curriculum in a program that was cancelled about the time I finished the bachelor's level prerequisites. My interest in computer hardware drove my interest in other disciplines because one needs to have a finger on the pulse of various industries in order to anticipate the next shift in hardwar demands. While this reader list is focused on a particular software, I find so many different issues being brought up concerning how to do this, or that, as to feel that most persons on this list would be interested in the Biosilico magazine and in software using open-code operating systems. If any of you know of a user list or shared-topic discussion group where these questions would be more appropriate, I would appreciate that information. Lewis Edgel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- charset=us-ascii X-Accept-Language: en X-OriginalArrivalTime: 19 May 2003 14:11:34.0700 (UTC) FILETIME=[8DFD3EC0:01C31E10] ++++------+------+------+------+------+------+------+------+------+------+ From: Brian White Subject: Open-source chime project? Date: Mon, 19 May 2003 10:20:05 -0400 To: "rasmol@lists.umass.edu" With all this talk of 'no plans for an OS-X chime' and other platform issues, it seemes to me that what we _really_ need is an open-source chime. I don't know about the software or legal issues, but I'd be willing to look into grant funding posibilities - it seems like it would be very useful. Does anyone out there know whether this is possible or not? Has anyone tried? Is anyone interested in working with me to get the grant? Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://intro.bio.umb.edu/BW/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 11:07:09 -0400 To: rasmol@lists.umass.edu hi Brian, Rob Lue at Harvard and I have initiated an ambitious project to create a modern mol vis authoring environment; we should have a demo ready by the end of this summer. it is not a browser plug-in, though it will be fully compatible with Chime. instead, our software tool will be a platform to develop mol vis animations and figures and combine them with other media types. it will provide a lot of mol vis tools, all based on sound scientific principles, but very little true modeling. OTOH, you will be able to import various types of media (2D and 3D) created in other software and merge everything into a single module. We thought a lot about making a plug-in "viewer" to go with it, ala the Flash model (stand-alone authoring tool, plug-in viewer). we decided against it for various reasons, opting instead to make our tool Internet-savvy on its own. of course, it is still pre-demo so YNK... ;-) anyway, our software will be free, open-source, and aimed primarily at educators. if you (or anyone) are interested in contributing, drop me a line. currently, we are especially interested in lining up mol vis users to provide feedback on our demo once it comes out. we plan to use the demo (and the accompanying tech specs) to apply for significant grant money to acutally build, distribute, and support the thing. anyone who wants to be part of this project, feel free to email me offlist and I can provide more details. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest at 10:20 AM EDT on Monday, May 19, 2003 Brian White said: > With all this talk of 'no plans for an OS-X chime' and other platform > issues, it seemes to me that what we _really_ need is an open-source > chime. I don't know about the software or legal issues, but I'd be > willing to look into grant funding posibilities - it seems like it would > be very useful. Does anyone out there know whether this is possible or > not? Has anyone tried? Is anyone interested in working with me to get > the grant? > > Brian > > -- > Prof. Brian White > Biology Department > University of Massachusetts, Boston > 100 Morrissey Blvd > Boston MA 02125 > (617) 287-6630 > fax:(617) 287-6650 > brian.white@umb.edu > http://intro.bio.umb.edu/BW/ > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 11:13:59 -0400 (EDT) To: brian.white@umb.edu, rasmol@lists.umass.edu Dear Prof. White, I am all in favor of an open source Chime project, and, as the maintainer of RasMol, would be happy to collaborate in a funding proposal for such a project. It would be best if MDL were to release the source for this purpose, but if they will not do so, then the safest approach to avoid legal tangles is a "clean-room" project in which a person who has never used chime works from the RasMol source and a set of external specifications to produce the desired functionality. Regards, Herbert J. Bernstein ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 19 May 2003, Brian White wrote: > With all this talk of 'no plans for an OS-X chime' and other platform > issues, it seemes to me that what we _really_ need is an open-source > chime. I don't know about the software or legal issues, but I'd be > willing to look into grant funding posibilities - it seems like it would > be very useful. Does anyone out there know whether this is possible or > not? Has anyone tried? Is anyone interested in working with me to get > the grant? > > Brian > > -- > Prof. Brian White > Biology Department > University of Massachusetts, Boston > 100 Morrissey Blvd > Boston MA 02125 > (617) 287-6630 > fax:(617) 287-6650 > brian.white@umb.edu > http://intro.bio.umb.edu/BW/ > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_kFyeyPxHH9snEVJg946Cbg)" ++++------+------+------+------+------+------+------+------+------+------+ From: "A.Malcolm Campbell" Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 11:23:06 -0400 To: rasmol@lists.umass.edu --Boundary_(ID_kFyeyPxHH9snEVJg946Cbg) Oh yeah, one other thing. CrystalEyes now works with OSX. I bet you can get the drivers so your new program could project in stereo. Malcolm On Monday, May 19, 2003, at 11:07 AM, timothy driscoll wrote: > hi Brian, > > Rob Lue at Harvard and I have initiated an ambitious project to create > a > modern mol vis authoring environment; we should have a demo ready by > the end > of this summer. it is not a browser plug-in, though it will be fully > compatible with Chime. instead, our software tool will be a platform > to > develop mol vis animations and figures and combine them with other > media > types. it will provide a lot of mol vis tools, all based on sound > scientific > principles, but very little true modeling. OTOH, you will be able to > import > various types of media (2D and 3D) created in other software and merge > everything into a single module. > > We thought a lot about making a plug-in "viewer" to go with it, ala > the Flash > model (stand-alone authoring tool, plug-in viewer). we decided > against it for > various reasons, opting instead to make our tool Internet-savvy on its > own. > of course, it is still pre-demo so YNK... ;-) > > anyway, our software will be free, open-source, and aimed primarily at > educators. if you (or anyone) are interested in contributing, drop me > a line. > currently, we are especially interested in lining up mol vis users to > provide > feedback on our demo once it comes out. we plan to use the demo (and > the > accompanying tech specs) to apply for significant grant money to > acutally > build, distribute, and support the thing. > > anyone who wants to be part of this project, feel free to email me > offlist and > I can provide more details. > > > regards, > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > > > > at 10:20 AM EDT on Monday, May 19, 2003 Brian White said: > >> With all this talk of 'no plans for an OS-X chime' and other platform >> issues, it seemes to me that what we _really_ need is an open-source >> chime. I don't know about the software or legal issues, but I'd be >> willing to look into grant funding posibilities - it seems like it >> would >> be very useful. Does anyone out there know whether this is possible >> or >> not? Has anyone tried? Is anyone interested in working with me to get >> the grant? >> >> Brian >> >> -- >> Prof. Brian White >> Biology Department >> University of Massachusetts, Boston >> 100 Morrissey Blvd >> Boston MA 02125 >> (617) 287-6630 >> fax:(617) 287-6650 >> brian.white@umb.edu >> http://intro.bio.umb.edu/BW/ >> >> >> >> > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > > ________________________________________________________ A. Malcolm Campbell, Ph.D. Associate Professor of Biology Davidson College Director of GCAT (www.bio.davidson.edu/GCAT) Co-Editor-In-Chief Cell Biology Education (www.cellbioed.org) PO Box 7118 (US Mail) 209 Ridge Road (shipping) Davidson College Davidson, NC 28035 704-894-2692 (phone) 704-894-2512 (fax) www.bio.davidson.edu/campbell --Boundary_(ID_kFyeyPxHH9snEVJg946Cbg) Oh yeah, one other thing. CrystalEyes now works with OSX. I bet you can get the drivers so your new program could project in stereo. Malcolm On Monday, May 19, 2003, at 11:07 AM, timothy driscoll wrote: hi Brian, Rob Lue at Harvard and I have initiated an ambitious project to create a modern mol vis authoring environment; we should have a demo ready by the end of this summer. it is not a browser plug-in, though it will be fully compatible with Chime. instead, our software tool will be a platform to develop mol vis animations and figures and combine them with other media types. it will provide a lot of mol vis tools, all based on sound scientific principles, but very little true modeling. OTOH, you will be able to import various types of media (2D and 3D) created in other software and merge everything into a single module. We thought a lot about making a plug-in "viewer" to go with it, ala the Flash model (stand-alone authoring tool, plug-in viewer). we decided against it for various reasons, opting instead to make our tool Internet-savvy on its own. of course, it is still pre-demo so YNK... ;-) anyway, our software will be free, open-source, and aimed primarily at educators. if you (or anyone) are interested in contributing, drop me a line. currently, we are especially interested in lining up mol vis users to provide feedback on our demo once it comes out. we plan to use the demo (and the accompanying tech specs) to apply for significant grant money to acutally build, distribute, and support the thing. anyone who wants to be part of this project, feel free to email me offlist and I can provide more details. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization < usa:north carolina:wake forest at 10:20 AM EDT on Monday, May 19, 2003 Brian White said: With all this talk of 'no plans for an OS-X chime' and other platform issues, it seemes to me that what we _really_ need is an open-source chime. I don't know about the software or legal issues, but I'd be willing to look into grant funding posibilities - it seems like it would be very useful. Does anyone out there know whether this is possible or not? Has anyone tried? Is anyone interested in working with me to get the grant? Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://intro.bio.umb.edu/BW/ Helvetica ________________________________________________________ A. Malcolm Campbell, Ph.D. Associate Professor of Biology Davidson College Director of GCAT (www.bio.davidson.edu/GCAT) Co-Editor-In-Chief Cell Biology Education (www.cellbioed.org) PO Box 7118 (US Mail) 209 Ridge Road (shipping) Davidson College Davidson, NC 28035 704-894-2692 (phone) 704-894-2512 (fax) www.bio.davidson.edu/campbell --Boundary_(ID_kFyeyPxHH9snEVJg946Cbg)-- Importance: Normal References: <3EC8E810.1631FF46@umb.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 17:27:38 +0200 (CEST) To: rasmol@lists.umass.edu Cc: brian.white@umb.edu, jmol-developers@lists.sourceforge.net Brian, The good news ------------- The newest version of Jmol (http://jmol.sourceforge.net) offers support for RasMol/Chime scripts in both the java application and the applet. I encourage all RasMol/Chime users to take a look at Jmol, tell us what you think, tell us where it falls short of your needs, and help us make it better. The bad news ------------ Jmol currently has performance problems with larger molecules ... like the protein molecules that most of you are probably interested in :( The Jmol rendering engine is currently unable to support isosurfaces, cartoons, ribbons, and other protein-visualization methods ... the kind of thing that most of you are probably interested in :( Detail ------ I only subscribed to this mailing list last week, so I am not familiar with a lot of the discussions which have gone on in the past. I am one of the contributing developers on the Jmol project, a java based open-source viewer based at http://jmol.sourceforge.net My plan was to make an announcement next week, but since you raised this question I felt I should respond a little earlier :) We are in the process of releasing Jmol v6, and will have the packaging done this week. I joined the Jmol project explicitly to write an open-source RasMol/Chime interpreter. I have worked on it for for the past 6 months, and believe that the interpreter engine is very solid. It now supports most RasMol/Chime scripting commands and atom expressions. Unfortunately, it *does* fall short in some important protein-specific areas. The rendering engine currently does not support intersecting shapes nor any protein-specific visualization shapes, like cartoons, ribbons, etc. However, some development prototyping has been done in this area. In addition, the core chemistry classes are quite heavy-weight and somewhat sluggish for larger molecules. More than 1K atoms and things start to slow down. The code is now ready for some 'real world' testing ... that is why I joined this mailing list :) So, if you have some scripts that work on smaller molecules, we would very much like to work with you. I would very much like for the readership to take a look at jmol (http://jmol.sourceforge.net), tell us what you think, tell us where it falls short of your needs, and help us make it better. Miguel > With all this talk of 'no plans for an OS-X chime' and other platform > issues, it seemes to me that what we _really_ need is an open-source > chime. I don't know about the software or legal issues, but I'd be > willing to look into grant funding posibilities - it seems like it would > be very useful. Does anyone out there know whether this is possible or > not? Has anyone tried? Is anyone interested in working with me to get > the grant? > > Brian > > -- > Prof. Brian White > Biology Department > University of Massachusetts, Boston > 100 Morrissey Blvd > Boston MA 02125 > (617) 287-6630 > fax:(617) 287-6650 > brian.white@umb.edu > http://intro.bio.umb.edu/BW/ > > -------------------------------------------------- Miguel Howard miguel@howards.org c/Peña Primera 11-13 esc dcha 6B 37002 Salamanca España Spain -------------------------------------------------- telefono casa 923 27 10 82 movil 650 52 54 58 -------------------------------------------------- To call from the US dial 9:00 am Pacific US = home 011 34 923 27 10 82 12:00 noon Eastern US = cell 011 34 650 52 54 58 6:00 pm Spain -------------------------------------------------- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 11:35:34 -0400 To: rasmol@lists.umass.edu a clarification on my last post: full compatibility with Chime means not only the command language, but also as mnay existing Chime resources as possible. this includes javascript-based buttons, interfaces, and the like. my goal is to have our software tool accept full web sites without a hiccup, if you want to incoporate them in a module. it was 11:07 am EDT on (Monday) 19 May 2003 when timothy driscoll said: >hi Brian, > >Rob Lue at Harvard and I have initiated an ambitious project to create >a modern mol vis authoring environment; we should have a demo ready by >the end of this summer. it is not a browser plug-in, though it will >be fully compatible with Chime. instead, our software tool will be a >platform to develop mol vis animations and figures and combine them >with other media types. it will provide a lot of mol vis tools, all >based on sound scientific principles, but very little true modeling. >OTOH, you will be able to import various types of media (2D and 3D) >created in other software and merge everything into a single module. > >We thought a lot about making a plug-in "viewer" to go with it, ala >the Flash model (stand-alone authoring tool, plug-in viewer). we >decided against it for various reasons, opting instead to make our >tool Internet-savvy on its own. of course, it is still pre-demo so >YNK... ;-) > >anyway, our software will be free, open-source, and aimed primarily at >educators. if you (or anyone) are interested in contributing, drop me >a line. currently, we are especially interested in lining up mol vis >users to provide feedback on our demo once it comes out. we plan to >use the demo (and the accompanying tech specs) to apply for >significant grant money to acutally build, distribute, and support the >thing. > >anyone who wants to be part of this project, feel free to email me >offlist and I can provide more details. > > >regards, > >:tim > >-- timothy driscoll molvisions - molecular graphics & visualization > usa:north carolina:wake forest > > > >at 10:20 AM EDT on Monday, May 19, 2003 Brian White said: > >> With all this talk of 'no plans for an OS-X chime' and other >> platform issues, it seemes to me that what we _really_ need is an >> open-source chime. I don't know about the software or legal issues, >> but I'd be willing to look into grant funding posibilities - it >> seems like it would be very useful. Does anyone out there know >> whether this is possible or not? Has anyone tried? Is anyone >> interested in working with me to get the grant? >> >> Brian >> >> -- Prof. Brian White Biology Department University of Massachusetts, >> Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) >> 287-6650 brian.white@umb.edu http://intro.bio.umb.edu/BW/ >> >> >> >> > >----------------------------------------------------------------rasmol >-+ > >To change your address, unsubscribe, view previous messages/history, >receive messages as weekly digests, or for any other information about >the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > >----------------------------------------------------------------rasmol >-- > > :tim - timothy driscoll molvisions molecular graphics and visualization ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 11:39:13 -0400 To: rasmol@lists.umass.edu in all deference to Rasmol, and to Roger Sayle, I have also been impressed with John Moreland's Java-based Molecular Biology Toolkit. I saw him demo a simple viewer app that took just a few lines of Java on top of his MBT core, and looked very promising. worth considering... it was 11:13 am EDT on (Monday) 19 May 2003 when Herbert J. Bernstein said: >Dear Prof. White, > > I am all in favor of an open source Chime project, and, as the >maintainer of RasMol, would be happy to collaborate in a funding proposal >for such a project. It would be best if MDL were to release the source >for this purpose, but if they will not do so, then the safest approach >to avoid legal tangles is a "clean-room" project in which a person >who has never used chime works from the RasMol source and a set of >external specifications to produce the desired functionality. > > Regards, > Herbert J. Bernstein >===================================================== > Herbert J. Bernstein, Professor of Computer Science > Dowling College, Kramer Science Center, KSC 020 > Idle Hour Blvd, Oakdale, NY, 11769 > > +1-631-244-3035 > yaya@dowling.edu >===================================================== > >On Mon, 19 May 2003, Brian White wrote: > >> With all this talk of 'no plans for an OS-X chime' and other platform >> issues, it seemes to me that what we _really_ need is an open-source >> chime. I don't know about the software or legal issues, but I'd be >> willing to look into grant funding posibilities - it seems like it would >> be very useful. Does anyone out there know whether this is possible or >> not? Has anyone tried? Is anyone interested in working with me to get >> the grant? >> >> Brian >> >> -- >> Prof. Brian White >> Biology Department >> University of Massachusetts, Boston >> 100 Morrissey Blvd >> Boston MA 02125 >> (617) 287-6630 >> fax:(617) 287-6650 >> brian.white@umb.edu >> http://intro.bio.umb.edu/BW/ >> >> >> >> > > > :tim - timothy driscoll molvisions molecular graphics and visualization ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 11:39:54 -0400 To: rasmol@lists.umass.edu it was 11:23 am EDT on (Monday) 19 May 2003 when A.Malcolm Campbell said: >Oh yeah, one other thing. CrystalEyes now works with OSX. I bet you can >get the drivers so your new program could project in stereo. > >Malcolm > :tim - timothy driscoll molvisions molecular graphics and visualization ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6249.0 boundary="Boundary_(ID_7r5ljpJUU1yq6PR0g+bUeQ)" Thread-Topic: Open-source chime project? Thread-Index: AcMeGzY9VnrssKEeQvO3/ebbjeuhSAAAOPEw content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: David Cassinelli Subject: RE: Open-source chime project? Date: Mon, 19 May 2003 11:34:53 -0400 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_7r5ljpJUU1yq6PR0g+bUeQ) James River Technical has a Passive Stereo 3D visualization system that Robert Lue at Harvard has seen personally. For more information go to www.jrti.com/vew Sorry about the commercial but this is a fantastic affordable solution perfect for education and research. David Cassinelli James River Technical 120 Quarry Dr Milford, MA 01757 508-381-6311 Office 508-667-3311 Cell 508-381-6981 Fax www.jrti.com -----Original Message----- Sent: Monday, May 19, 2003 11:23 AM From: A.Malcolm Campbell [mailto:macampbell@davidson.edu] Subject: Re: Open-source chime project? To: rasmol@lists.umass.edu Oh yeah, one other thing. CrystalEyes now works with OSX. I bet you can get the drivers so your new program could project in stereo. Malcolm On Monday, May 19, 2003, at 11:07 AM, timothy driscoll wrote: hi Brian, Rob Lue at Harvard and I have initiated an ambitious project to create a modern mol vis authoring environment; we should have a demo ready by the end of this summer. it is not a browser plug-in, though it will be fully compatible with Chime. instead, our software tool will be a platform to develop mol vis animations and figures and combine them with other media types. it will provide a lot of mol vis tools, all based on sound scientific principles, but very little true modeling. OTOH, you will be able to import various types of media (2D and 3D) created in other software and merge everything into a single module. We thought a lot about making a plug-in "viewer" to go with it, ala the Flash model (stand-alone authoring tool, plug-in viewer). we decided against it for various reasons, opting instead to make our tool Internet-savvy on its own. of course, it is still pre-demo so YNK... ;-) anyway, our software will be free, open-source, and aimed primarily at educators. if you (or anyone) are interested in contributing, drop me a line. currently, we are especially interested in lining up mol vis users to provide feedback on our demo once it comes out. we plan to use the demo (and the accompanying tech specs) to apply for significant grant money to acutally build, distribute, and support the thing. anyone who wants to be part of this project, feel free to email me offlist and I can provide more details. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest at 10:20 AM EDT on Monday, May 19, 2003 Brian White said: With all this talk of 'no plans for an OS-X chime' and other platform issues, it seemes to me that what we _really_ need is an open-source chime. I don't know about the software or legal issues, but I'd be willing to look into grant funding posibilities - it seems like it would be very useful. Does anyone out there know whether this is possible or not? Has anyone tried? Is anyone interested in working with me to get the grant? Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://intro.bio.umb.edu/BW/ ________________________________________________________ A. Malcolm Campbell, Ph.D. Associate Professor of Biology Davidson College Director of GCAT (www.bio.davidson.edu/GCAT) Co-Editor-In-Chief Cell Biology Education (www.cellbioed.org) PO Box 7118 (US Mail) 209 Ridge Road (shipping) Davidson College Davidson, NC 28035 704-894-2692 (phone) 704-894-2512 (fax) www.bio.davidson.edu/campbell --Boundary_(ID_7r5ljpJUU1yq6PR0g+bUeQ)
James River Technical has a Passive Stereo 3D visualization system that Robert Lue at Harvard has seen personally.  For more information go to www.jrti.com/vew
Sorry about the commercial but this is a fantastic affordable solution perfect for education and research.
 

David Cassinelli
James River Technical
120 Quarry Dr
Milford, MA  01757

508-381-6311 Office
508-667-3311 Cell
508-381-6981 Fax
www.jrti.com

-----Original Message-----
From: A.Malcolm Campbell [mailto:macampbell@davidson.edu]
Sent: Monday, May 19, 2003 11:23 AM
To: rasmol@lists.umass.edu
Subject: Re: Open-source chime project?

Oh yeah, one other thing. CrystalEyes now works with OSX. I bet you can get the drivers so your new program could project in stereo.

Malcolm

On Monday, May 19, 2003, at 11:07 AM, timothy driscoll wrote:

hi Brian,

Rob Lue at Harvard and I have initiated an ambitious project to create a
modern mol vis authoring environment; we should have a demo ready by the end
of this summer. it is not a browser plug-in, though it will be fully
compatible with Chime. instead, our software tool will be a platform to
develop mol vis animations and figures and combine them with other media
types. it will provide a lot of mol vis tools, all based on sound scientific
principles, but very little true modeling. OTOH, you will be able to import
various types of media (2D and 3D) created in other software and merge
everything into a single module.

We thought a lot about making a plug-in "viewer" to go with it, ala the Flash
model (stand-alone authoring tool, plug-in viewer). we decided against it for
various reasons, opting instead to make our tool Internet-savvy on its own.
of course, it is still pre-demo so YNK... ;-)

anyway, our software will be free, open-source, and aimed primarily at
educators. if you (or anyone) are interested in contributing, drop me a line.
currently, we are especially interested in lining up mol vis users to provide
feedback on our demo once it comes out. we plan to use the demo (and the
accompanying tech specs) to apply for significant grant money to acutally
build, distribute, and support the thing.

anyone who wants to be part of this project, feel free to email me offlist and
I can provide more details.


regards,

:tim

--
timothy driscoll
molvisions - molecular graphics & visualization
<http://www.molvisions.com/>
usa:north carolina:wake forest



at 10:20 AM EDT on Monday, May 19, 2003 Brian White said:

With all this talk of 'no plans for an OS-X chime' and other platform
issues, it seemes to me that what we _really_ need is an open-source
chime. I don't know about the software or legal issues, but I'd be
willing to look into grant funding posibilities - it seems like it would
be very useful. Does anyone out there know whether this is possible or
not? Has anyone tried? Is anyone interested in working with me to get
the grant?

Brian

--
Prof. Brian White
Biology Department
University of Massachusetts, Boston
100 Morrissey Blvd
Boston MA 02125
(617) 287-6630
fax:(617) 287-6650
brian.white@umb.edu
http://intro.bio.umb.edu/BW/








________________________________________________________
A. Malcolm Campbell, Ph.D.
Associate Professor of Biology
Davidson College
Director of GCAT (www.bio.davidson.edu/GCAT)
Co-Editor-In-Chief Cell Biology Education (www.cellbioed.org)

PO Box 7118 (US Mail)
209 Ridge Road (shipping)
Davidson College
Davidson, NC 28035
704-894-2692 (phone)
704-894-2512 (fax)
www.bio.davidson.edu/campbell
--Boundary_(ID_7r5ljpJUU1yq6PR0g+bUeQ)-- User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3) Gecko/20030312 X-Accept-Language: es-ar, es, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Fernando Gabriel Ranea Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 13:18:48 -0300 To: rasmol@lists.umass.edu Hello, I'm glad because you bring forward a Open Source Chime project. Months ago, this subject received treatment. But, I think that "a Open Chime project" needs evolution like everything in the life. A hard work will be necesary to build a open source software "full compatible" with Chime. To walk a road we need to take a first step. Andrej Sali from Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University has developed the SkyMol plug-in, but it works only with Netscape 4.X under Linux (http://salilab.org/modview/news.shtml). A Open Source Chime software could be builded with other programming others language like tk/tcl, etc. Regards, timothy driscoll wrote: > a clarification on my last post: > > full compatibility with Chime means not only the command language, but also as > mnay existing Chime resources as possible. this includes javascript-based > buttons, interfaces, and the like. my goal is to have our software tool accept > full web sites without a hiccup, if you want to incoporate them in a module. > > Fernando Gabriel Ranea fernandoranea@microbiologia.org.ar http://www.microbiologia.org.ar ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 13:05:17 -0500 (CDT) To: rasmol@lists.umass.edu Hi, Has anybody officially contacted MDL regarding this? Or know how MDL actually stands on this (officially or unofficially)? I think that is best to directly include MDL in any discussions. Since Chime is currently a 'free' download then it would be nice to hear their side. Clearly based on the Rasmol situation there are numerous problems involved that need to be clarified. There are many forms of 'Open Source' that can be used that may not conflict with their commercial interests and intellectual property. The General Public License of GNU is probably not suitable but www.opensource.org lists a number of examples. (However it is NOT my right to determine the 'fate' of code that I didn't write.) As only a suggestion (I do have some understanding of what is involved), perhaps those who are creating 'Open Source' should try to see if they can combine their projects. Just my thoughts, Bruce ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_He60lACWscc7MOoxTIYt4A)" ++++------+------+------+------+------+------+------+------+------+------+ From: Barry E Rowe Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 22:22:37 -0500 To: rasmol@lists.umass.edu --Boundary_(ID_He60lACWscc7MOoxTIYt4A) I'm interested. I am a consultant at NCSA in Champaign Urbana Il. I'll see if we can find a programmer who would be interested. Is the source of chime public domain? barry On Monday, May 19, 2003, at 09:20 AM, Brian White wrote: > With all this talk of 'no plans for an OS-X chime' and other platform > issues, it seemes to me that what we _really_ need is an open-source > chime. I don't know about the software or legal issues, but I'd be > willing to look into grant funding posibilities - it seems like it > would > be very useful. Does anyone out there know whether this is possible or > not? Has anyone tried? Is anyone interested in working with me to get > the grant? > > Brian > > -- > Prof. Brian White > Biology Department > University of Massachusetts, Boston > 100 Morrissey Blvd > Boston MA 02125 > (617) 287-6630 > fax:(617) 287-6650 > brian.white@umb.edu > http://intro.bio.umb.edu/BW/ > > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > > Barry Rowe O- farquasi@mac.com Chemistry / Physics Teacher http://roweba.com Champaign Centennial High School NCSA ChemViz Team "War may sometimes be a necessary evil, but no matter how necessary, it is always evil, never good. We will not learn how to live together in peace by killing each other's children." Nobel Peace Prize Laureate Jimmy Carter --Boundary_(ID_He60lACWscc7MOoxTIYt4A) I'm interested. I am a consultant at NCSA in Champaign Urbana Il. I'll see if we can find a programmer who would be interested. Is the source of chime public domain? barry On Monday, May 19, 2003, at 09:20 AM, Brian White wrote: With all this talk of 'no plans for an OS-X chime' and other platform issues, it seemes to me that what we _really_ need is an open-source chime. I don't know about the software or legal issues, but I'd be willing to look into grant funding posibilities - it seems like it would be very useful. Does anyone out there know whether this is possible or not? Has anyone tried? Is anyone interested in working with me to get the grant? Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://intro.bio.umb.edu/BW/ Barry Rowe O- farquasi@mac.com Chemistry / Physics Teacher http://roweba.com Champaign Centennial High School NCSA ChemViz Team Lucida Grande "War may sometimes be a necessary evil, but no matter how necessary, it is always evil, never good. We will not learn how to live together in peace by killing each other's children." Nobel Peace Prize Laureate Jimmy Carter --Boundary_(ID_He60lACWscc7MOoxTIYt4A)-- User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3) Gecko/20030312 X-Accept-Language: es-ar, es, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Fernando Gabriel Ranea Subject: Re: Open-source chime project? Date: Tue, 20 May 2003 02:21:30 -0300 To: rasmol@lists.umass.edu Hi, When I think in Open Source Chime I think in a General Public License for Chime. It's my opinion. I believe that is the best way to make a educational software for any OS. Obviously, if MDL make not free the source code to scientific comunity, we will to need starting from zero using the RasMol algorithms and the Pluging Tutorial from Netscape or Mozilla web site. If anybody wants read about GNU Licenses: http://www.gnu.org/licenses/licenses.html Regards, southey@ux1.cso.uiuc.edu wrote: > Hi, > Has anybody officially contacted MDL regarding this? Or know how MDL > actually stands on this (officially or unofficially)? > > I think that is best to directly include MDL in any discussions. Since > Chime is currently a 'free' download then it would be nice to hear their > side. Clearly based on the Rasmol situation there are numerous problems > involved that need to be clarified. There are many forms of 'Open Source' > that can be used that may not conflict with their commercial interests and > intellectual property. The General Public License of GNU is probably not > suitable but www.opensource.org lists a number of examples. (However it is > NOT my right to determine the 'fate' of code that I didn't write.) > > As only a suggestion (I do have some understanding of what is involved), > perhaps those who are creating 'Open Source' should try to see if they can > combine their projects. > > Just my thoughts, > Bruce > > > -- Fernando Gabriel Ranea fernandoranea@microbiologia.org.ar http://www.microbiologia.org.ar ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 23:43:05 -0700 To: rasmol@lists.umass.edu I agree with you Bruce and I suggested some times ago in a private discussion that we should release the central part of RasMol code under the LGPL. But before all, it is important to give to RasMol all the means to be a project where everybody wants to contribute. In that regards, I am surprised that RasMol be still under an exotic license and not under the GPL. I think it is time for the contributors to take position so that we could move forward quickly. Personnally, I authorize the release of RasMol derivative works containing code contributed by myself under the GPL. Of course, all contributors must agree before any change can occur. Philippe Valadon ----- Original Message ----- Sent: Monday, May 19, 2003 11:05 AM From: Subject: Re: Open-source chime project? To: > Hi, > Has anybody officially contacted MDL regarding this? Or know how MDL > actually stands on this (officially or unofficially)? > > I think that is best to directly include MDL in any discussions. Since > Chime is currently a 'free' download then it would be nice to hear their > side. Clearly based on the Rasmol situation there are numerous problems > involved that need to be clarified. There are many forms of 'Open Source' > that can be used that may not conflict with their commercial interests and > intellectual property. The General Public License of GNU is probably not > suitable but www.opensource.org lists a number of examples. (However it is > NOT my right to determine the 'fate' of code that I didn't write.) > > As only a suggestion (I do have some understanding of what is involved), > perhaps those who are creating 'Open Source' should try to see if they can > combine their projects. > > Just my thoughts, > Bruce > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: MDL/Biosilico/open source solutions for 3D molecular visualization Date: Tue, 20 May 2003 11:30:07 +0200 To: rasmol@lists.umass.edu I still have not gotten any positive feedback concerning the issues discussed in Biosilico magazine. I would encourage all persons interested in projects such as this topic most recently being kicked around this user list avail themselves of this publication. For those of you who do not keep up with corporate structures, MDL is a subsidiary of Elsevier Science Company. Biosilico is a publication from the same source. Complaints concerning the nature of the Chime licensing, etc. turn into conversation on this list regularly suggesting alternative platforms. Want to tap into the motherload (?) or do as Mr. Bernstein, et al, suggest and find a virgin programmer in terms of the current software subjected to debate and thus capable of re-inventing the wheel without anyone claiming contamination from the MDL (etc.) world. It seems to me that is something akin to looking for the immaculate conception. I seem to recall that certain lower forms of like can accomplish this, but they don't make good programmers. The persons agreeing to take responsibility for the editorial board of Biosilico include Craig Vetter and a host of other high-profile specialists with the reputation of getting things done. A goldmine of contact information is available via this magazine. Two readers of this user-list responded privately to my last email query and neither commented on the magazine, so I assume that the readers of this list are quite busy - hence responding to something like my query is a low priority. Still leaves me wondering how many people found the time to go the the website and ask for a free copy of the journal. Of that number, who actually had the time to read an issue, and does the number of persons reading the material correspond to a smaller number actually understanding the implications of the material discussed? So why am I pushing this magazine so hard? There are issues to consider like establishing rules for processing before creation of the 3D generator, establishing rules for structural attachments based on chemistry/physics, etc. The basic information is the bear and not the actual programming. I can give you an analogy that I think is appropriate for the sort of responses I see in this group. This concerns MIDI files, which are a means of making musical information logical to a computer. While one person would think, "well yes, this is a no brainer", in terms of the process of evolving a solution for presenting a 3D representation of a molecule or a MIDI representation of J. S. Bach's Imprivisation #9, another person would not understand this sort of analytical process until a explanation like: "A MIDI file allows a computer to use a well defined functional set and parameters for the audible presentation of data related to instrument dynamics, timing, etc. allowing a very small input of data to be translated into audible output, which by comparison recording a directly digital expression of the analog when compared to MIDI information is a logarithmically multiplied output in terms of space occupied on the storage medium." Yet another person would need an explanation like: "I just finished encoding a 45 minute CD album in MIDI format. The program running the MIDI to audio output conversion fits on a 1.44MB floppy disk. 650MB of data corresponds to 74 minutes of audio in standard format as read by your audio CD player. The entire 45 minutes consisted of 343KB of data in MIDI format." At this point most people would want to know why the format used for consumer audio CD takes the space-hungry format it does. Then the brain kicks in... hmmm 45 minutes is 343kb in MIDI, perhaps my whole record collection could be put on one CD-ROM. Next synaptic burst would (hopefully) come up with the marketing nightmare of selling an entire musical collection on a single CD-ROM disk with the corresponding price compared to conventional formatting. ECONOMICS! Asleep yet? OK, back to contacts with persons who know what your up against in reinventing the wheel - as it would be a non-MDL wheel that everyone could take for a spin at the same time and would work on everything from the baby-buggy to the space shuttle. IF anyone is still with me, I suggest you look for a 3D programmer ala Duke Nuke-um or Wolfenstein. I can recall when these were freebie programs written when the biggest question was, programming's done - now can we make it run on a 286? Those same guys that pioneered the 3D gaming phenomenon are still out there. Are any of you guys reading this user list? If so, have you absolutely no idea what MDL was up to (wink, wink, nod) when they constructed the MDL Chime? We have an offer not unlike Uncle Sam when he says, "Join the Navy and see the world!" Now I have to do some real work. (Make lunch) Lewis Edgel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: MDL/Biosilico/open source solutions for 3D molecular visualization Date: Tue, 20 May 2003 10:59:48 +0100 To: rasmol@lists.umass.edu I tried to get a free copy, but I don't know if my subscription will be accepted as I am a lowly phd student. I too am interested in developing open source systems for 'open science'. I feel like I am banging my head against a wall when I talk about integrated systems. My idea is based around an integrated database a la SRS (only better, as I have a better understanding of what data modeling in the biological domain really means). I have not found any comfort in the vast array of different licenses that different db's use, nor the willingness of the biological community to work together on standards for data integration. It is getting better, but the committee road is a hard one to walk. Can you post the relevant article in its entirety? Cheers, Dan. Lewis Edgel wrote: >I still have not gotten any positive feedback concerning the issues >discussed in Biosilico magazine. I would encourage all persons interested in >projects such as this topic most recently being kicked around this user list >avail themselves of this publication. For those of you who do not keep up >with corporate structures, MDL is a subsidiary of Elsevier Science Company. >Biosilico is a publication from the same source. Complaints concerning the >nature of the Chime licensing, etc. turn into conversation on this list >regularly suggesting alternative platforms. Want to tap into the motherload >(?) or do as Mr. Bernstein, et al, suggest and find a virgin programmer in >terms of the current software subjected to debate and thus capable of >re-inventing the wheel without anyone claiming contamination from the MDL >(etc.) world. It seems to me that is something akin to looking for the >immaculate conception. I seem to recall that certain lower forms of like can >accomplish this, but they don't make good programmers. > >The persons agreeing to take responsibility for the editorial board of >Biosilico include Craig Vetter and a host of other high-profile specialists >with the reputation of getting things done. A goldmine of contact >information is available via this magazine. Two readers of this user-list >responded privately to my last email query and neither commented on the >magazine, so I assume that the readers of this list are quite busy - hence >responding to something like my query is a low priority. Still leaves me >wondering how many people found the time to go the the website and ask for a >free copy of the journal. Of that number, who actually had the time to read >an issue, and does the number of persons reading the material correspond to >a smaller number actually understanding the implications of the material >discussed? > >So why am I pushing this magazine so hard? There are issues to consider like >establishing rules for processing before creation of the 3D generator, >establishing rules for structural attachments based on chemistry/physics, >etc. The basic information is the bear and not the actual programming. I can >give you an analogy that I think is appropriate for the sort of responses I >see in this group. This concerns MIDI files, which are a means of making >musical information logical to a computer. While one person would think, >"well yes, this is a no brainer", in terms of the process of evolving a >solution for presenting a 3D representation of a molecule or a MIDI >representation of J. S. Bach's Imprivisation #9, another person would not >understand this sort of analytical process until a explanation like: "A MIDI >file allows a computer to use a well defined functional set and parameters >for the audible presentation of data related to instrument dynamics, timing, >etc. allowing a very small input of data to be translated into audible >output, which by comparison recording a directly digital expression of the >analog when compared to MIDI information is a logarithmically multiplied >output in terms of space occupied on the storage medium." > >Yet another person would need an explanation like: "I just finished encoding >a 45 minute CD album in MIDI format. The program running the MIDI to audio >output conversion fits on a 1.44MB floppy disk. 650MB of data corresponds to >74 minutes of audio in standard format as read by your audio CD player. The >entire 45 minutes consisted of 343KB of data in MIDI format." At this point >most people would want to know why the format used for consumer audio CD >takes the space-hungry format it does. Then the brain kicks in... hmmm 45 >minutes is 343kb in MIDI, perhaps my whole record collection could be put on >one CD-ROM. Next synaptic burst would (hopefully) come up with the marketing >nightmare of selling an entire musical collection on a single CD-ROM disk >with the corresponding price compared to conventional formatting. ECONOMICS! > >Asleep yet? OK, back to contacts with persons who know what your up against >in reinventing the wheel - as it would be a non-MDL wheel that everyone >could take for a spin at the same time and would work on everything from the >baby-buggy to the space shuttle. IF anyone is still with me, I suggest you >look for a 3D programmer ala Duke Nuke-um or Wolfenstein. I can recall when >these were freebie programs written when the biggest question was, >programming's done - now can we make it run on a 286? Those same guys that >pioneered the 3D gaming phenomenon are still out there. Are any of you guys >reading this user list? If so, have you absolutely no idea what MDL was up >to (wink, wink, nod) when they constructed the MDL Chime? We have an offer >not unlike Uncle Sam when he says, "Join the Navy and see the world!" > >Now I have to do some real work. (Make lunch) > >Lewis Edgel > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.5762.3 Thread-Topic: MDL/Biosilico/open source solutions for 3D molecular visualization Thread-Index: AcMes0Xo9kjDlyNsT1OF2Ui6ToVq1gAEpLvg content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Robin Forder Subject: RE: MDL/Biosilico/open source solutions for 3D molecular visualization Date: Tue, 20 May 2003 12:51:49 +0100 To: rasmol@lists.umass.edu Dear Lewis Edgel, Re. the motherload (?): motherlode, probably. >From Robin Forder. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: Jmol offers RasMol/Chime scripting Date: Tue, 20 May 2003 13:53:32 +0200 (CEST) To: rasmol@lists.umass.edu Cc: egonw@sci.kun.nl Forwarded to this mailing list on behalf of egonw@sci.kun.nl > The good news > ------------- > The newest version of Jmol (http://jmol.sourceforge.net) offers support > for RasMol/Chime scripts in both the java application and the applet. I > encourage all RasMol/Chime users to take a look at Jmol, tell us what you > think, tell us where it falls short of your needs, and help us make it > better. I would like to add this to it: More good news ------------- Jmol works on all browsers going back and including IE5.0 and Netscape4.5 on a number of platforms, including several GNU/Linux, Windows95/98, and SunOS. In addition, the Jmol applet does not require anythings else than a Java plugin, i.e. no Java3D required. kind regards, Egon Willighagen jmol.sf.net ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by marlin.bio.umass.edu id h4L47Fj27492 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Open-source chime project? Date: Tue, 20 May 2003 09:11:02 -0400 (EDT) To: rasmol@lists.umass.edu Cc: brian.white@umb.edu, jmol-developers@lists.sourceforge.net Jmol is a very nice program and the feature/performance issues for macromolecules can be solved. While applets are not a perfect solution, they now cause far less grief in multi-platform porting than do plug-ins. I am all in favor achieving full RasMol functionality and better in a java environment. -- HJB ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 19 May 2003, Miguel wrote: > Brian, > > The good news > ------------- > The newest version of Jmol (http://jmol.sourceforge.net) offers support > for RasMol/Chime scripts in both the java application and the applet. I > encourage all RasMol/Chime users to take a look at Jmol, tell us what you > think, tell us where it falls short of your needs, and help us make it > better. > > > The bad news > ------------ > Jmol currently has performance problems with larger molecules ... like the > protein molecules that most of you are probably interested in :( > The Jmol rendering engine is currently unable to support isosurfaces, > cartoons, ribbons, and other protein-visualization methods ... the kind of > thing that most of you are probably interested in :( > > > Detail > ------ > I only subscribed to this mailing list last week, so I am not familiar > with a lot of the discussions which have gone on in the past. > > I am one of the contributing developers on the Jmol project, a java based > open-source viewer based at http://jmol.sourceforge.net > > My plan was to make an announcement next week, but since you raised this > question I felt I should respond a little earlier :) > > We are in the process of releasing Jmol v6, and will have the packaging > done this week. > > I joined the Jmol project explicitly to write an open-source RasMol/Chime > interpreter. I have worked on it for for the past 6 months, and believe > that the interpreter engine is very solid. It now supports most > RasMol/Chime scripting commands and atom expressions. > > Unfortunately, it *does* fall short in some important protein-specific areas. > > The rendering engine currently does not support intersecting shapes nor > any protein-specific visualization shapes, like cartoons, ribbons, etc. > However, some development prototyping has been done in this area. > > In addition, the core chemistry classes are quite heavy-weight and > somewhat sluggish for larger molecules. More than 1K atoms and things > start to slow down. > > The code is now ready for some 'real world' testing ... that is why I > joined this mailing list :) > > So, if you have some scripts that work on smaller molecules, we would very > much like to work with you. > > I would very much like for the readership to take a look at jmol > (http://jmol.sourceforge.net), tell us what you think, tell us where it > falls short of your needs, and help us make it better. > > Miguel > > > With all this talk of 'no plans for an OS-X chime' and other platform > > issues, it seemes to me that what we _really_ need is an open-source > > chime. I don't know about the software or legal issues, but I'd be > > willing to look into grant funding posibilities - it seems like it would > > be very useful. Does anyone out there know whether this is possible or > > not? Has anyone tried? Is anyone interested in working with me to get > > the grant? > > > > Brian > > > > -- > > Prof. Brian White > > Biology Department > > University of Massachusetts, Boston > > 100 Morrissey Blvd > > Boston MA 02125 > > (617) 287-6630 > > fax:(617) 287-6650 > > brian.white@umb.edu > > http://intro.bio.umb.edu/BW/ > > > > > > > -------------------------------------------------- > Miguel Howard miguel@howards.org > c/Peña Primera 11-13 esc dcha 6B > 37002 Salamanca > España Spain > -------------------------------------------------- > telefono casa 923 27 10 82 movil 650 52 54 58 > -------------------------------------------------- > To call from the US dial 9:00 am Pacific US = > home 011 34 923 27 10 82 12:00 noon Eastern US = > cell 011 34 650 52 54 58 6:00 pm Spain > -------------------------------------------------- > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Open-source chime project? Date: Tue, 20 May 2003 08:22:55 -0400 (EDT) To: rasmol@lists.umass.edu With respect to licenses: The current RasMol license is GPL-like (not LGPL-like). A future version of RasMol _will_ be released under the the GPL. We have approval from Richard Stallman in our handling of the conflict between using the GPL and dealing with code that involves software patents. However, in order to prevent a repeat of the problems with Chime (which is a closed-source derivative of RasMol), please note that the current license and the GPL are infectious. All code derived from RasMol is and will be covered by the same infectious open-source license. Some people feel that this inhibits commercial development, and hope for some sort of license that will allow then to develop a closed-source derivative of RasMol. I disagree. You are free to develop commercial open-source derivatives of RasMol. Doing science with closed-source software leaves its users with a serious gap in their understanding of how they have obtained their results, making closed-source software of questionable value for scientific applications. For those who are interested in statistics, please note that RasMol enjoys a steady stream of downloads of the latest releases of RasMol (i.e. RasWin, RasMac and Rasmol) -- more than 1000 a week from the primary site alone. The current license does not seem to be inhibiting the widespread use of RasMol. Regards, Herbert J. Bernstein ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 19 May 2003, Philippe wrote: > I agree with you Bruce and I suggested some times ago in a private > discussion that we should release the central part of RasMol code under the > LGPL. But before all, it is important to give to RasMol all the means to be > a project where everybody wants to contribute. In that regards, I am > surprised that RasMol be still under an exotic license and not under the > GPL. I think it is time for the contributors to take position so that we > could move forward quickly. Personnally, I authorize the release of RasMol > derivative works containing code contributed by myself under the GPL. Of > course, all contributors must agree before any change can occur. > > Philippe Valadon > > > ----- Original Message ----- > From: > To: > Sent: Monday, May 19, 2003 11:05 AM > Subject: Re: Open-source chime project? > > > > Hi, > > Has anybody officially contacted MDL regarding this? Or know how MDL > > actually stands on this (officially or unofficially)? > > > > I think that is best to directly include MDL in any discussions. Since > > Chime is currently a 'free' download then it would be nice to hear their > > side. Clearly based on the Rasmol situation there are numerous problems > > involved that need to be clarified. There are many forms of 'Open Source' > > that can be used that may not conflict with their commercial interests and > > intellectual property. The General Public License of GNU is probably not > > suitable but www.opensource.org lists a number of examples. (However it is > > NOT my right to determine the 'fate' of code that I didn't write.) > > > > As only a suggestion (I do have some understanding of what is involved), > > perhaps those who are creating 'Open Source' should try to see if they can > > combine their projects. > > > > Just my thoughts, > > Bruce > > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- charset=us-ascii X-Accept-Language: en X-OriginalArrivalTime: 20 May 2003 15:09:27.0164 (UTC) FILETIME=[CE26F3C0:01C31EE1] References: <4E92C217-8A72-11D7-A7B4-000502931696@mac.com> ++++------+------+------+------+------+------+------+------+------+------+ From: Brian White Subject: Re: Open-source chime project? Date: Tue, 20 May 2003 11:18:10 -0400 To: rasmol@lists.umass.edu Barry - No, it is not public domain - RasMol is. Many people have responded with various info on the legal issues. I need to contact MDL to see what 's up. I'll be in touch if it looks like I can work something out. Brian Barry E Rowe wrote: > I'm interested. I am a consultant at NCSA in Champaign Urbana Il. I'll see if we can find a programmer who would be interested. > > Is the source of chime public domain? > > barry > On Monday, May 19, 2003, at 09:20 AM, Brian White wrote: > > With all this talk of 'no plans for an OS-X chime' and other platform > issues, it seemes to me that what we _really_ need is an open-source > chime. I don't know about the software or legal issues, but I'd be > willing to look into grant funding posibilities - it seems like it would > be very useful. Does anyone out there know whether this is possible or > not? Has anyone tried? Is anyone interested in working with me to get > the grant? > > Brian > > -- > Prof. Brian White > Biology Department > University of Massachusetts, Boston > 100 Morrissey Blvd > Boston MA 02125 > (617) 287-6630 > fax:(617) 287-6650 > brian.white@umb.edu > http://intro.bio.umb.edu/BW/ > > Barry Rowe O- farquasi@mac.com > Chemistry / Physics Teacher http://roweba.com Champaign Centennial High School NCSA ChemViz Team > > "War may sometimes be a necessary evil, but no matter how necessary, it is always evil, never good. We will not learn how to live together in peace by killing each other's children." > Nobel Peace Prize Laureate Jimmy Carter -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://intro.bio.umb.edu/BW/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: RE: MDL/Biosilico/open source solutions for 3D molecular visualization Date: Tue, 20 May 2003 23:39:38 +0200 To: rasmol@lists.umass.edu Perhaps I could have been more succinct in offering my viewpoint. MDL is not the devil incarnate. When others have tried to replicate the MDL product the results have been rather inferior in comparison. While people talk of funding a "me-too" product, I think it would be better to raise money and fund MDL to produce the various flavours of Chime, etc. meeting user's needs. The MDL product is a mature technology. MY earlier reference to MIDI relates to an industry-wide concensus about how to proceed with digital music processes and based on this agreed framework standardization became possible. One has to decide - Am I, and my coworkers the end-user (consumer)? The end-user for commercial music products do not get the same quality of product as a person with sufficient training to access a more "geek-chic" product. An industry needs to have a certifying body. That body assumes responsibility for standardization for the benefit of all members in the industry. MDL Chime has been the de facto standard for many years for educational 3D molecular representation AND that product is free of charge. Dissatisfaction with that product should not result in conversation to replace the MDL product until it is clear that a progressive relationship with the patent-holder for this de facto product cannot be developed. If funding can be arranged, I think those funds would get the most "bang for the buck" in the hands of MDL. Biosilico magazine can be a platform for informed discussion in the subject of standardization within the industry. Biosilico is free at this point. Elsevier is in the business of making money, so if you can put two and two together, you get: MDL + Biosilico = moving toward standardization within an industry. It might not be too hard to understand YOUR benefits from taking part in the standardization process. I use Free/OpenBSD for a lot of things. These UNIX type operating systems have been around for a long long time. Myriad free programs are available to run on this OS. Still, people insist on spending money when free alternatives have been in place since the infancy of computer science. Why? Imagine this scenario: You have a problem with the free lunch I just gave you. Perhaps, the meat was cooked too little or too much for your liking. Compare that to a lunch you paid good money for - dissatisfaction can be remedied via the legal process. I say where the issue is: MDL or not to MDL - I say the money is better spent continuing the MDL relationship and providing concerted maintenance-funding for this mature technology. I apologise to anyone who could not follow my obtuse opinions as presented in the previous message to the Chime/Rasmol user-group list Lewis Edgel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: rasmol@lists.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: RE: Open-source chime project? Date: Wed, 21 May 2003 10:33:03 +0200 To: rasmol@lists.umass.edu Cc: jmol-developers@lists.sourceforge.net I agree with Mr. Bersteins comments concerning Java applets' future role in providing a solution to Internet-based problems when an educator wishes to place a 3D generator inside an HTML application. I tried several different applets over the years and as standardization in web-browsers' interpretation of the java code came into being - so also came JS as an effective solution. I also think that careful consideration of the form licensing takes in any project as being currently suggested is a very important topic. Comparison between the MDL approach to an Internet based interface and Rasmol's does provide one with some insight into the future one can expect if there is a divergence between the technologies. I wonder how compatible is a product specifically written for Rasmol when it is placed in the Chime environment? As I understand it there are just minor timing issues that come up. As I understand some of the past comments in this user's group discussion, several people began documenting problems related to cross-platform compatibility issues, etc. It might be a good idea for a central collection site for all pertinent information on the subject to be established, before the project feasibility study is begun. A third point Mr. Bernstein made concerns the problems arising when a macromolecule is attempted in Jmol. Has anyone tried consecutively more complex molecules in the Jmol environment with the intent of forming a body of information that can be used to categorize the relationship between molecule complexity and the problems in manipulating such inside the Jmol environment? Such a project would go far in allowing one to suggest solutions to that problem. I found from personal use, that JS is great for "passing off" information to another programming body and then returning the completed product back to the HTML-GUI. It sometimes happens that JS consumes too much time in internal processes and that results in some timing problems. My gut-feeling is that might be a structural limitation in JS, but I am far from an authority on any programming subject. Most of what I know of programming is a result of being the poor slob that is stuck with the task of proving that an issue is NOT a hardware problem. What I know of programming is an evolution of the need to route problems to those who could provide a solution. Too many times I had software problems sent to me because the end-user had experienced past problems that WERE hardware related and based on the user's level of expertise the new problem had the same characteristics. Other than that, my experience with programming is "hobby-class". A close friend was working on a project that required a flexible transfer medium. He found that the "C" programming language was best for certain parts of his project while Fortran accomplished a solution to other parts of the problem fastest. His nightmare arose when he reached a point where he needed to integrate the various functions. He had to shelve the project for a time. When JS finally was sorted out, he was able to construct the interface required to pass information back and forth within the prescribed time limits. My conclusion is that if it becomes a concensus that MDL cannot respond to user needs, the most viable solution in terms of cross-platform compatibility is the use of Java scripting. I still think at this point that offering to fund MDL to develop more flexible and user friendly products ala Chime is the most reasonable because it is already here, and already effective. Oh, and thanks to Robin Forder for pointing out my spelling error... I got a good laugh out of that! My wife would say I had made a Freudian slip as she often views my commentary as being a "load". I hope this message to which he (or she) refers was not viewed by the majority of readers as being the "mother of all loads." (grin) Lewis Edgel -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Herbert J. Bernstein Sent: Tuesday, May 20, 2003 3:11 PM From: owner-rasmol@lists.umass.edu Subject: Re: Open-source chime project? To: rasmol@lists.umass.edu Cc: brian.white@umb.edu; jmol-developers@lists.sourceforge.net Jmol is a very nice program and the feature/performance issues for macromolecules can be solved. While applets are not a perfect solution, they now cause far less grief in multi-platform porting than do plug-ins. I am all in favor achieving full RasMol functionality and better in a java environment. -- HJB ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 19 May 2003, Miguel wrote: > Brian, > > The good news > ------------- > The newest version of Jmol (http://jmol.sourceforge.net) offers support > for RasMol/Chime scripts in both the java application and the applet. I > encourage all RasMol/Chime users to take a look at Jmol, tell us what you > think, tell us where it falls short of your needs, and help us make it > better. > > > The bad news > ------------ > Jmol currently has performance problems with larger molecules ... like the > protein molecules that most of you are probably interested in :( > The Jmol rendering engine is currently unable to support isosurfaces, > cartoons, ribbons, and other protein-visualization methods ... the kind of > thing that most of you are probably interested in :( > > > Detail > ------ > I only subscribed to this mailing list last week, so I am not familiar > with a lot of the discussions which have gone on in the past. > > I am one of the contributing developers on the Jmol project, a java based > open-source viewer based at http://jmol.sourceforge.net > > My plan was to make an announcement next week, but since you raised this > question I felt I should respond a little earlier :) > > We are in the process of releasing Jmol v6, and will have the packaging > done this week. > > I joined the Jmol project explicitly to write an open-source RasMol/Chime > interpreter. I have worked on it for for the past 6 months, and believe > that the interpreter engine is very solid. It now supports most > RasMol/Chime scripting commands and atom expressions. > > Unfortunately, it *does* fall short in some important protein-specific areas. > > The rendering engine currently does not support intersecting shapes nor > any protein-specific visualization shapes, like cartoons, ribbons, etc. > However, some development prototyping has been done in this area. > > In addition, the core chemistry classes are quite heavy-weight and > somewhat sluggish for larger molecules. More than 1K atoms and things > start to slow down. > > The code is now ready for some 'real world' testing ... that is why I > joined this mailing list :) > > So, if you have some scripts that work on smaller molecules, we would very > much like to work with you. > > I would very much like for the readership to take a look at jmol > (http://jmol.sourceforge.net), tell us what you think, tell us where it > falls short of your needs, and help us make it better. > > Miguel > > > With all this talk of 'no plans for an OS-X chime' and other platform > > issues, it seemes to me that what we _really_ need is an open-source > > chime. I don't know about the software or legal issues, but I'd be > > willing to look into grant funding posibilities - it seems like it would > > be very useful. Does anyone out there know whether this is possible or > > not? Has anyone tried? Is anyone interested in working with me to get > > the grant? > > > > Brian > > > > -- > > Prof. Brian White > > Biology Department > > University of Massachusetts, Boston > > 100 Morrissey Blvd > > Boston MA 02125 > > (617) 287-6630 > > fax:(617) 287-6650 > > brian.white@umb.edu > > http://intro.bio.umb.edu/BW/ > > > > > > > -------------------------------------------------- > Miguel Howard miguel@howards.org > c/Peña Primera 11-13 esc dcha 6B > 37002 Salamanca > España Spain > -------------------------------------------------- > telefono casa 923 27 10 82 movil 650 52 54 58 > -------------------------------------------------- > To call from the US dial 9:00 am Pacific US = > home 011 34 923 27 10 82 12:00 noon Eastern US = > cell 011 34 650 52 54 58 6:00 pm Spain > -------------------------------------------------- > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: RE: MDL/Biosilico/open source solutions for 3D molecular visualization Date: Wed, 21 May 2003 06:31:49 -0400 To: rasmol@lists.umass.edu hi Lewis, thanks for your comments. may I suggest that you post the link to biosilico again? some of us (esp new subscribers) may not have your earlier message. at 11:39 PM EDT on Tuesday, May 20, 2003 Lewis Edgel said: > Perhaps I could have been more succinct in offering my viewpoint. MDL is not > the devil incarnate. When others have tried to replicate the MDL product the > results have been rather inferior in comparison. While people talk of > funding a "me-too" product, I think it would be better to raise money and > fund MDL to produce the various flavours of Chime, etc. meeting user's > needs. The MDL product is a mature technology. > the free version of Chime is not a mature product at all, just underdeveloped and undersupported. look around the video game industry and see the possibilities for 3D molecular visualization. also check out "mainstream" 3D modelers like Amapi 3D, Maya, 3ds max, etc. Director now has a 3D component, too, although I have never seen it in action. MDL has its own agenda regarding Chime development. it is wonderful when this runs in conjunction with (or at least does not oppose) the needs of the educational community. it sucks when the two apparently diverge. we are not MDL's user base. this does not make them the devil incarnate. (I am allowed to complain loudly about them, however, since this is an open forum.) > MY earlier reference to MIDI relates to an industry-wide concensus about how > to proceed with digital music processes and based on this agreed framework > standardization became possible. One has to decide - Am I, and my coworkers > the end-user (consumer)? The end-user for commercial music products do not > get the same quality of product as a person with sufficient training to > access a more "geek-chic" product. An industry needs to have a certifying > body. That body assumes responsibility for standardization for the benefit > of all members in the industry. > are you suggesting that MDL be a certifying body for mol vis? certainly the Protein Data Bank does most, if not all, of that work now, and is in a better position to handle it. in any case, there are standards already in place, and being refined. isn't pdb is a standard file format? your ref to MIDI is apt. it may reflect a consensus, but it is certainly not the only type of music file in widespread use. and it does not include a definition of what software to use, or who can develop that software. you may prefer Media Player or Real Audio; I like iTunes. no standardization body should tell either of us to use a specific software product. > MDL Chime has been the de facto standard for many years for educational 3D > molecular representation AND that product is free of charge. Dissatisfaction > with that product should not result in conversation to replace the MDL > product until it is clear that a progressive relationship with the > patent-holder for this de facto product cannot be developed. If funding can > be arranged, I think those funds would get the most "bang for the buck" in > the hands of MDL. > there have been many efforts to develop a "public" relationship between MDL and the edu mol vis community. I have not seen any positive results. there has always been some level of behind-the-scenes communication with individual programmers at MDL, but my general impression is that the entity that is MDL has no official policy of supporting Chime development for emv. and frankly, I doubt we could gather enough funding to divert MDL from its customer base even if we wanted to. I can't see that grant proposal sailing through the NSF ;-) as far as complaining about Chime, well, if my healthcare is free, but they're still using leeches, don't I have a right to speak up? I think the dissatisfaction is not with Chime per se, but rather with the lack of development, support, and open communication about it from MDL - again, from the perspective of the emv community. at least, that is my complaint. others may differ. > Biosilico magazine can be a platform for informed discussion in the subject > of standardization within the industry. Biosilico is free at this point. > Elsevier is in the business of making money, so if you can put two and two > together, you get: MDL + Biosilico = moving toward standardization within an > industry. It might not be too hard to understand YOUR benefits from taking > part in the standardization process. > again, standardization of what? the software to use for mol vis? Elsevier, to be more specific, is in the business of making money by selling scientific materials (i.e., textbooks). so Elsevier + Chime + control over standards in mol vis = monopoly. > I use Free/OpenBSD for a lot of things. These UNIX type operating systems > have been around for a long long time. Myriad free programs are available to > run on this OS. Still, people insist on spending money when free > alternatives have been in place since the infancy of computer science. Why? > you have to ask? ease of use. comfort level. ease of use. advertising. ease of use. wider base of general programs. my mom likes it. it has a cool color. ease of use. etc. I could go out in my yard, catch a rabbit, clean it, cook it over an open fire, and eat it, but honestly - I'd rather pay a couple bucks and buy a hamburger. for one thing, I could spend the extra hours with my family, or working - and I'll make more money working those hours than I'll save by killing my own dinner. one of the wonderful aspects about computers is that I can find what I want, and you can find what you want. I use a lot of free software, and a lot of commercial stuff. it lets me tinker with things when I want, and not spend time trying to learn everything about everything just to use my computer. > Imagine this scenario: You have a problem with the free lunch I just gave > you. Perhaps, the meat was cooked too little or too much for your liking. > Compare that to a lunch you paid good money for - dissatisfaction can be > remedied via the legal process. I say where the issue is: MDL or not to > MDL - I say the money is better spent continuing the MDL relationship and > providing concerted maintenance-funding for this mature technology. I > apologise to anyone who could not follow my obtuse opinions as presented in > the previous message to the Chime/Rasmol user-group list > 1. the relationship between MDL and the emv is one-sided, publicly at least, and IMHO it has become a lodestone on progress in the field. 2. I am not aware of any successful precedent for suing a company because you paid for their software and didn't like it. 3. Chime is not mature; it is going in a direction that does not seem to coincide with needs of the emv community. the time has come to provide software designed for this audience, by institutions that respond directly to feedback from this user base. besides, a group of us already tried throwing money at MDL to fix a bug in Chime, and nothing came of it. ;-) politics is a nasty business. I appreciate your comments; please continue to contribute to the list, and repost the link to biosilico. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > > Lewis Edgel > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Open-source chime project? Date: Wed, 21 May 2003 08:22:16 -0400 (EDT) To: rasmol@lists.umass.edu The RasMol 2.7 series is _not_ public domain, it is open source. There is an important difference -- you can make copies and base new programs on RasMol, but the copies you make and the programs you derive are also covered by the same license and are open source as well. This hopefully will keep us from ever getting into the difficulties we have now with MDL's derivative of RasMol ever again. There is an older version of RasMol which is in the public domain, but it is half a decade out of date. -- H. J. Bernstein ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Tue, 20 May 2003, Brian White wrote: > Barry - > No, it is not public domain - RasMol is. Many people have responded > with various info on the legal issues. I need to contact MDL to see > what 's up. I'll be in touch if it looks like I can work something out. > > Brian > > Barry E Rowe wrote: > > > I'm interested. I am a consultant at NCSA in Champaign Urbana Il. I'll > > see if we can find a programmer who would be interested. > > > > Is the source of chime public domain? > > > > barry > > On Monday, May 19, 2003, at 09:20 AM, Brian White wrote: > > > > With all this talk of 'no plans for an OS-X chime' and other platform > > issues, it seemes to me that what we _really_ need is an open-source > > chime. I don't know about the software or legal issues, but I'd be > > willing to look into grant funding posibilities - it seems like it would > > be very useful. Does anyone out there know whether this is possible or > > not? Has anyone tried? Is anyone interested in working with me to get > > the grant? > > > > Brian > > > > -- > > Prof. Brian White > > Biology Department > > University of Massachusetts, Boston > > 100 Morrissey Blvd > > Boston MA 02125 > > (617) 287-6630 > > fax:(617) 287-6650 > > brian.white@umb.edu > > http://intro.bio.umb.edu/BW/ > > > > Barry Rowe O- farquasi@mac.com > > Chemistry / Physics Teacher http://roweba.com Champaign Centennial High School NCSA ChemViz Team > > > > "War may sometimes be a necessary evil, but no matter how necessary, it is always evil, never good. We will not learn how to live together in peace by killing each other's children." > > Nobel Peace Prize Laureate Jimmy Carter > > -- > Prof. Brian White > Biology Department > University of Massachusetts, Boston > 100 Morrissey Blvd > Boston MA 02125 > (617) 287-6630 > fax:(617) 287-6650 > brian.white@umb.edu > http://intro.bio.umb.edu/BW/ > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: computer virus warning Date: Wed, 21 May 2003 14:31:13 +0200 To: rasmol@lists.umass.edu I received an email to my in-box supposedly from support@microsoft.com having the subject "Approved (Ref: 38406-263)" With the body holding a statement: "All necessary information is contained in the attachment." The attachment was labeled "approved.pif". I checked the attachment characteristics to see if it had the proper author ID such as a legit file from Microsoft would have. It did not have this. I searched the "known virus" database and found it is a variant worm of the "W32/palyh". If you have received something like this and opened it, do a system search for files named "msccn32.exe", "hnks.ini", and "mdbrr.ini". If any of these are found, you have been infected with a computer virus that can potentially steal password and credit card information. As well, my firewall has been taking hits all day. (but that is normal...) Lucky me, I crushed the little worm before it could wiggle into my system (grin). I'm sending this message to everyone with addresses in my mailer. If such is not appreciated, I apologise in advance. I do not have time to prune my mailer tree at the moment. Lewis Edgel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: RE: MDL/Biosilico/open source solutions for 3D molecular visualization Date: Wed, 21 May 2003 08:52:43 -0400 (EDT) To: rasmol@lists.umass.edu Actually, one could just as well claim that RasMol been the de facto "standard", of which Chime is just one of many variants. Fortunately for the progress of science there is no body which attempts to stifle the creativity of the community in exploring new and useful ways to approach molecular visualization, and there are many powerful and useful programs available. It is unfortunate that there are now problems for the potential users of Chime that MDL has not yet effectively addressed. There is no reason why we cannot have a robust competition of ideas, with MDL doing what they can to make Chime attractive to users and the open source proponents doing what they can to provide alternatives, whether creating something from scratch or making something based on RasMol, Jmol, or some other program. -- HJB ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Tue, 20 May 2003, Lewis Edgel wrote: > Perhaps I could have been more succinct in offering my viewpoint. MDL is not > the devil incarnate. When others have tried to replicate the MDL product the > results have been rather inferior in comparison. While people talk of > funding a "me-too" product, I think it would be better to raise money and > fund MDL to produce the various flavours of Chime, etc. meeting user's > needs. The MDL product is a mature technology. > > MY earlier reference to MIDI relates to an industry-wide concensus about how > to proceed with digital music processes and based on this agreed framework > standardization became possible. One has to decide - Am I, and my coworkers > the end-user (consumer)? The end-user for commercial music products do not > get the same quality of product as a person with sufficient training to > access a more "geek-chic" product. An industry needs to have a certifying > body. That body assumes responsibility for standardization for the benefit > of all members in the industry. > > MDL Chime has been the de facto standard for many years for educational 3D > molecular representation AND that product is free of charge. Dissatisfaction > with that product should not result in conversation to replace the MDL > product until it is clear that a progressive relationship with the > patent-holder for this de facto product cannot be developed. If funding can > be arranged, I think those funds would get the most "bang for the buck" in > the hands of MDL. > > Biosilico magazine can be a platform for informed discussion in the subject > of standardization within the industry. Biosilico is free at this point. > Elsevier is in the business of making money, so if you can put two and two > together, you get: MDL + Biosilico = moving toward standardization within an > industry. It might not be too hard to understand YOUR benefits from taking > part in the standardization process. > > I use Free/OpenBSD for a lot of things. These UNIX type operating systems > have been around for a long long time. Myriad free programs are available to > run on this OS. Still, people insist on spending money when free > alternatives have been in place since the infancy of computer science. Why? > > Imagine this scenario: You have a problem with the free lunch I just gave > you. Perhaps, the meat was cooked too little or too much for your liking. > Compare that to a lunch you paid good money for - dissatisfaction can be > remedied via the legal process. I say where the issue is: MDL or not to > MDL - I say the money is better spent continuing the MDL relationship and > providing concerted maintenance-funding for this mature technology. I > apologise to anyone who could not follow my obtuse opinions as presented in > the previous message to the Chime/Rasmol user-group list > > > Lewis Edgel > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: On having choices.... (etc.) Date: Thu, 22 May 2003 10:11:44 +0200 To: rasmol@lists.umass.edu First, for those who might have missed the link for Biosilico, it is: www.drugdiscoverytoday.com (the last time I looked)... I cannot verify for today, as my direct link to the Internet is not available. On to next items for debate. Some time ago I endorsed the idea of using a java-scripted solution for 3D modeling internal to HTML because of the cross-platform functionality Java has to offer. People reading this list might wonder if I have "flip-flopped" in supporting the idea that funding be offered to MDL to continue the development of the Chime Internet-based interface. As Mr. Bernstein points out these options are not mutually exclusive. Just as competition in the natural world ensures robust species, so does populating every available niche in the world of technology produce a comparably healthy working environment for users of the technology. Again, Mr. Berstein has made clear the importance of formulating a policy dictating what may or may not be done with the charitable products variously called freeware, GNU, etc. I have not researched the matter, but as Mr. Bernstein infers - the change of status concerning Rasmol from public domain to such as it exists today, could well be directly related to the evolving relationship as seen in how Chime used the technology without seeming to endorse the spirit of sharing inherent in the milieu from which came Rasmol. When a public-domain product does not have a legally-binding statement of use dictating how that product may be adapted for other uses, etc., the result can be a limiting of the open-sharing of ideas. After looking at the evolution of the debate over some months, I began to see that the immediate solution to the problem of cross-platform compatibility was well on the way of being addressed. It was at this point that I began to see a parallel between the biological evolution in our natural world and that taking place in the world of computer-based technologies. Since so many of you are struggling with genomic research and need to look at myriad complex molecules, I began to think of this biological model in terms of computer science. The "standardization" of the DNA-RNA complex should be considered as a model for the standardization of the technology used to study the material of life itself. There is bound to be a lot of nonsense-code carried along as baggage while we move forward, but just as it was eventually possible to conclude that there are mandatory base-pairs for functionality - the binary code of computer science has achieved a wonderful complexity based on the number pair (0,1). I think the same ethical concerns debated when it became possible to consider that patent-right for genetic material could eventually evolve into the legal right to own a life form similar to a human-being. Most people would not question the right to ownership of a pet cat, or for a farmer to own a herd of cattle. The essential matter that I think concerned bio-ethics specialists was the possibility that if an open-forum for debate was not initiated a legal decision could be made that was short-sighted with implications that could limit public access to information of great personal concern to all. After all, regardless of one's religious-ethical ideals - the role of DNA is at the core of all known life. Corresponding to this is the very real and finite function of how elements interact with one another. When the variety of ways a carbon atom can interact with other elements has been reduced to a mathematical formula and thus rendered accessible to a computer, the person or persons doing the work deserve payment for their analytic skills. But this formula does, in a sense, become public domain because the research is directly tied to the natural world. Imagine Pythagoras being alive today and arriving at the conclusion of his theorem, picking up his phone and calling a patent-attorney. I do not think this matter of reaching a concensus concerning how the basic research allowing 3D visualization is to go forward and how this research is to be shared has been discussed sufficiently. User groups are very important, but the platform for debate is by nature limited. The good people at U.Mass kindly support this forum, but without industry-wide funding it would not be possible for the finite facilities housing this debate to serve as a clearinghouse for this sort of issue. Are bioinformatics professionals ready for an international symposium dedicated to discussing standards? How long after the invention of the automobile before the Society of Automotive Engineers was formed? How much longer after that was the SAE standard for nuts and bolts established? I think it is overdue for bioinformatics professionals to consider the "nuts and bolts" of their industry. When I endorse Biosilico, it is because of the sort of concerns discussed within the bounds of the journal - the use of the silicon chip for the study of biology. I am not endorsing putting the public debate under the control of a private corporation. The issue of funding is never far away for any researcher. I would have to say that a large proportion of at-home crisis in my household are the product of a demanding work schedule followed by at- home work trying to write a grant-proposal at the same time as the teenager thinks it appropriate to test the limits of the speaker system attached to the home stereo. Every time basic research is assigned a price tag, there is the constant concern that the price will limit the possibility of future research. (Not to mention the cost in frayed nerves and un-paid overtime!) I was glad to see how many people offered services and funding for the development of visualization software. Can we ask U.Mass to provide some hard-drive space for a separate forum where people separated by physical distance can have a place to unite in cyberspace? I tend to spiral out into outerspace when a birdseye view would be sufficient, so to return to a functional level: Having a separate forum would allow this user group to remain focused on the immediate issues related to Rasmol. (Not to mention allowing debate that is not mediated by a corporate body.) Well, the morning "fika" is over... Lewis Edgel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: On having choices.... (etc.) Date: Thu, 22 May 2003 11:29:44 -0400 To: rasmol@lists.umass.edu it was 10:11 am EDT on (Thursday) 22 May 2003 when Lewis Edgel said: >First, for those who might have missed the link for Biosilico, it is: >www.drugdiscoverytoday.com (the last time I looked)... I cannot verify for >today, as my direct link to the Internet is not available. > yes, that link works. thanks, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en X-Cam-ScannerAdmin: mail-scanner-support@ucs.cam.ac.uk X-Cam-AntiVirus: Not scanned X-Cam-SpamDetails: References: ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: On having more choices.... (etc.) Date: Thu, 22 May 2003 17:49:00 +0100 To: rasmol@lists.umass.edu Just a quick question, Has anyone explored the possibility of using SVG (Scalable Vector Graphics) to build a molecular viewer? I like the idea of SVG, being a standard dialect of XML, images of molecules can easily be created by an apache web server with access to relational PDB DB and an appropriate XMLST. The beauty of such an image is that even though it is being rendered by your browser in all the ways you might want to render a molecule, it would also contain all the original molecular data for you to save / analyse separatly. I have heard that the RDB PDB is well under way, and this would seem like a natural extension to that project. Mozilla is developing an SVG viewer, as well as netscape and several other java iniatives, so soon it should be widely supported just like flash. The power of an XML 'flash like' language is that any well organized DB (such as a DB of molecular motions) could potentially be dumped using an appropriate XMLST to create an image with standard navigation / display features. SVG is about as open as a format can get, so, any plans? > I think it is overdue for bioinformatics >professionals to consider the "nuts and bolts" of their industry. > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: SVG annual developer's meeting Date: Thu, 22 May 2003 20:20:01 +0200 To: rasmol@lists.umass.edu http://www.svgopen.org/2003/registration.html SVG developer's meeting in Vancouver, Canada from July 13th to 18th, 2003. -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Dan Bolser Sent: Thursday, May 22, 2003 6:49 PM From: owner-rasmol@lists.umass.edu Subject: Re: On having more choices.... (etc.) To: rasmol@lists.umass.edu Just a quick question, Has anyone explored the possibility of using SVG (Scalable Vector Graphics) to build a molecular viewer? I like the idea of SVG, being a standard dialect of XML, images of molecules can easily be created by an apache web server with access to relational PDB DB and an appropriate XMLST. The beauty of such an image is that even though it is being rendered by your browser in all the ways you might want to render a molecule, it would also contain all the original molecular data for you to save / analyse separatly. I have heard that the RDB PDB is well under way, and this would seem like a natural extension to that project. Mozilla is developing an SVG viewer, as well as netscape and several other java iniatives, so soon it should be widely supported just like flash. The power of an XML 'flash like' language is that any well organized DB (such as a DB of molecular motions) could potentially be dumped using an appropriate XMLST to create an image with standard navigation / display features. SVG is about as open as a format can get, so, any plans? > I think it is overdue for bioinformatics >professionals to consider the "nuts and bolts" of their industry. > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_SnWbiB4XnpWP6dCBLUN3Eg)" ++++------+------+------+------+------+------+------+------+------+------+ From: Barry E Rowe Subject: Re: SVG annual developer's meeting Date: Thu, 22 May 2003 14:25:24 -0500 To: rasmol@lists.umass.edu --Boundary_(ID_SnWbiB4XnpWP6dCBLUN3Eg) Will it run on a mac? In OSX? barry On Thursday, May 22, 2003, at 01:20 PM, Lewis Edgel wrote: > http://www.svgopen.org/2003/registration.html > > SVG developer's meeting in Vancouver, Canada from July 13th to 18th, > 2003. > > > > -----Original Message----- > From: owner-rasmol@lists.umass.edu > [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Dan Bolser > Sent: Thursday, May 22, 2003 6:49 PM > To: rasmol@lists.umass.edu > Subject: Re: On having more choices.... (etc.) > > > Just a quick question, > > Has anyone explored the possibility of using SVG > (Scalable Vector Graphics) to build a molecular viewer? > > I like the idea of SVG, being a standard dialect of XML, > images of molecules can easily be created by an apache > web server with access to relational PDB DB and an > appropriate XMLST. > > The beauty of such an image is that even though it is being > rendered by your browser in all the ways you might want > to render a molecule, it would also contain all the original > molecular data for you to save / analyse separatly. > > I have heard that the RDB PDB is well under way, and this > would seem like a natural extension to that project. > > Mozilla is developing an SVG viewer, as well as netscape > and several other java iniatives, so soon it should be widely > supported just like flash. > > The power of an XML 'flash like' language is that any well > organized DB (such as a DB of molecular motions) could > potentially be dumped using an appropriate XMLST to create > an image with standard navigation / display features. > > SVG is about as open as a format can get, so, any plans? > >> I think it is overdue for bioinformatics >> professionals to consider the "nuts and bolts" of their industry. >> > > > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > > Barry Rowe O- farquasi@mac.com Chemistry / Physics Teacher http://roweba.com Champaign Centennial High School NCSA ChemViz Team "War may sometimes be a necessary evil, but no matter how necessary, it is always evil, never good. We will not learn how to live together in peace by killing each other's children." Nobel Peace Prize Laureate Jimmy Carter --Boundary_(ID_SnWbiB4XnpWP6dCBLUN3Eg) Will it run on a mac? In OSX? barry On Thursday, May 22, 2003, at 01:20 PM, Lewis Edgel wrote: http://www.svgopen.org/2003/registration.html SVG developer's meeting in Vancouver, Canada from July 13th to 18th, 2003. -----Original Message----- From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Dan Bolser Sent: Thursday, May 22, 2003 6:49 PM To: rasmol@lists.umass.edu Subject: Re: On having more choices.... (etc.) Just a quick question, Has anyone explored the possibility of using SVG (Scalable Vector Graphics) to build a molecular viewer? I like the idea of SVG, being a standard dialect of XML, images of molecules can easily be created by an apache web server with access to relational PDB DB and an appropriate XMLST. The beauty of such an image is that even though it is being rendered by your browser in all the ways you might want to render a molecule, it would also contain all the original molecular data for you to save / analyse separatly. I have heard that the RDB PDB is well under way, and this would seem like a natural extension to that project. Mozilla is developing an SVG viewer, as well as netscape and several other java iniatives, so soon it should be widely supported just like flash. The power of an XML 'flash like' language is that any well organized DB (such as a DB of molecular motions) could potentially be dumped using an appropriate XMLST to create an image with standard navigation / display features. SVG is about as open as a format can get, so, any plans? I think it is overdue for bioinformatics professionals to consider the "nuts and bolts" of their industry. Barry Rowe O- farquasi@mac.com Chemistry / Physics Teacher http://roweba.com Champaign Centennial High School NCSA ChemViz Team Lucida Grande "War may sometimes be a necessary evil, but no matter how necessary, it is always evil, never good. We will not learn how to live together in peace by killing each other's children." Nobel Peace Prize Laureate Jimmy Carter --Boundary_(ID_SnWbiB4XnpWP6dCBLUN3Eg)-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 boundary="Boundary_(ID_k2R4/mfpcBMxgPNFXfVS9Q)" Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: RE: SVG annual developer's meeting Date: Thu, 22 May 2003 22:00:26 +0200 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_k2R4/mfpcBMxgPNFXfVS9Q) Go to http://www.w3.org/ and you will find most of the pertinent information concerning current and future plans for the world wide web (hence the name). Specific information is in the collumn to the left. Scroll down to SVG - one mouse click, and PRESTO! All the basic need to know info (such as compatibility issues). Lewis Edgel -----Original Message----- From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Barry E Rowe Sent: Thursday, May 22, 2003 9:25 PM To: rasmol@lists.umass.edu Subject: Re: SVG annual developer's meeting Will it run on a mac? In OSX? barry On Thursday, May 22, 2003, at 01:20 PM, Lewis Edgel wrote: http://www.svgopen.org/2003/registration.html SVG developer's meeting in Vancouver, Canada from July 13th to 18th, 2003. -----Original Message----- From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Dan Bolser Sent: Thursday, May 22, 2003 6:49 PM To: rasmol@lists.umass.edu Subject: Re: On having more choices.... (etc.) Just a quick question, Has anyone explored the possibility of using SVG (Scalable Vector Graphics) to build a molecular viewer? I like the idea of SVG, being a standard dialect of XML, images of molecules can easily be created by an apache web server with access to relational PDB DB and an appropriate XMLST. The beauty of such an image is that even though it is being rendered by your browser in all the ways you might want to render a molecule, it would also contain all the original molecular data for you to save / analyse separatly. I have heard that the RDB PDB is well under way, and this would seem like a natural extension to that project. Mozilla is developing an SVG viewer, as well as netscape and several other java iniatives, so soon it should be widely supported just like flash. The power of an XML 'flash like' language is that any well organized DB (such as a DB of molecular motions) could potentially be dumped using an appropriate XMLST to create an image with standard navigation / display features. SVG is about as open as a format can get, so, any plans? I think it is overdue for bioinformatics professionals to consider the "nuts and bolts" of their industry. Barry Rowe O- farquasi@mac.com Chemistry / Physics Teacher http://roweba.com Champaign Centennial High School NCSA ChemViz Team "War may sometimes be a necessary evil, but no matter how necessary, it is always evil, never good. We will not learn how to live together in peace by killing each other's children." Nobel Peace Prize Laureate Jimmy Carter --Boundary_(ID_k2R4/mfpcBMxgPNFXfVS9Q)
Go to http://www.w3.org/ and you will find most of the pertinent information concerning current and future plans for the world wide web (hence the name). Specific information is in the collumn to the left. Scroll down to SVG - one mouse click, and PRESTO! All the basic need to know info (such as compatibility issues).
Lewis Edgel
-----Original Message-----
From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Barry E Rowe
Sent: Thursday, May 22, 2003 9:25 PM
To: rasmol@lists.umass.edu
Subject: Re: SVG annual developer's meeting

Will it run on a mac? In OSX?

barry
On Thursday, May 22, 2003, at 01:20 PM, Lewis Edgel wrote:

http://www.svgopen.org/2003/registration.html

SVG developer's meeting in Vancouver, Canada from July 13th to 18th, 2003.



-----Original Message-----
From: owner-rasmol@lists.umass.edu
[mailto:owner-rasmol@lists.umass.edu]On Behalf Of Dan Bolser
Sent: Thursday, May 22, 2003 6:49 PM
To: rasmol@lists.umass.edu
Subject: Re: On having more choices.... (etc.)


Just a quick question,

Has anyone explored the possibility of using SVG
(Scalable Vector Graphics) to build a molecular viewer?

I like the idea of SVG, being a standard dialect of XML,
images of molecules can easily be created by an apache
web server with access to relational PDB DB and an
appropriate XMLST.

The beauty of such an image is that even though it is being
rendered by your browser in all the ways you might want
to render a molecule, it would also contain all the original
molecular data for you to save / analyse separatly.

I have heard that the RDB PDB is well under way, and this
would seem like a natural extension to that project.

Mozilla is developing an SVG viewer, as well as netscape
and several other java iniatives, so soon it should be widely
supported just like flash.

The power of an XML 'flash like' language is that any well
organized DB (such as a DB of molecular motions) could
potentially be dumped using an appropriate XMLST to create
an image with standard navigation / display features.

SVG is about as open as a format can get, so, any plans?

I think it is overdue for bioinformatics
professionals to consider the "nuts and bolts" of their industry.







Barry Rowe O- farquasi@mac.com
Chemistry / Physics Teacher http://roweba.com Champaign Centennial High School NCSA ChemViz Team

"War may sometimes be a necessary evil, but no matter how necessary, it is always evil, never good. We will not learn how to live together in peace by killing each other's children."
Nobel Peace Prize Laureate Jimmy Carter
--Boundary_(ID_k2R4/mfpcBMxgPNFXfVS9Q)-- X-Info: This message was accepted for relay by smtp02.mrf.mail.rcn.net as the sender used SMTP authentication X-Trace: UmFuZG9tSVZ9t9UYpsmNRT4cz8GDOobr9lOIF2xQny5fomf87a5ZCSzqjDWCUpZ0 ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Masi Subject: Re: SVG annual developer's meeting Date: Thu, 22 May 2003 16:51:42 -0400 To: rasmol@lists.umass.edu Yes. Yes. There may be others, but here is one implementation of an SVG viewer for the Mac. http://www.adobe.com:80/svg/svgOSX.html http://www.adobe.com:80/support/downloads/ product.jsp?product=46&platform=Macintosh Chris On Thursday, May 22, 2003, at 03:25 PM, Barry E Rowe wrote: > Will it run on a mac? In OSX? > > barry > On Thursday, May 22, 2003, at 01:20 PM, Lewis Edgel wrote: > >> http://www.svgopen.org/2003/registration.html >> >> SVG developer's meeting in Vancouver, Canada from July 13th to 18th, >> 2003. >> >> >> >> -----Original Message----- >> From: owner-rasmol@lists.umass.edu >> [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Dan Bolser >> Sent: Thursday, May 22, 2003 6:49 PM >> To: rasmol@lists.umass.edu >> Subject: Re: On having more choices.... (etc.) >> >> >> Just a quick question, >> >> Has anyone explored the possibility of using SVG >> (Scalable Vector Graphics) to build a molecular viewer? >> >> I like the idea of SVG, being a standard dialect of XML, >> images of molecules can easily be created by an apache >> web server with access to relational PDB DB and an >> appropriate XMLST. >> >> The beauty of such an image is that even though it is being >> rendered by your browser in all the ways you might want >> to render a molecule, it would also contain all the original >> molecular data for you to save / analyse separatly. >> >> I have heard that the RDB PDB is well under way, and this >> would seem like a natural extension to that project. >> >> Mozilla is developing an SVG viewer, as well as netscape >> and several other java iniatives, so soon it should be widely >> supported just like flash. >> >> The power of an XML 'flash like' language is that any well >> organized DB (such as a DB of molecular motions) could >> potentially be dumped using an appropriate XMLST to create >> an image with standard navigation / display features. >> >> SVG is about as open as a format can get, so, any plans? >> >>> I think it is overdue for bioinformatics >>> professionals to consider the "nuts and bolts" of their industry. >>> >> >> >> >> >> >> > Barry Rowe O- > farquasi@mac.com > Chemistry / Physics Teacher > http://roweba.com Champaign Centennial High > School NCSA ChemViz Team > > "War may sometimes be a necessary evil, but no matter how necessary, > it is always evil, never good. We will not learn how to live together > in peace by killing each other's children." > Nobel Peace Prize Laureate Jimmy Carter ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerAdmin: mail-scanner-support@ucs.cam.ac.uk X-Cam-AntiVirus: Not scanned X-Cam-SpamDetails: References: <3ECCFF7C.6010902@mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: SVG annual developer's meeting Date: Thu, 22 May 2003 22:32:02 +0100 (BST) To: rasmol@lists.umass.edu ;) Lewis Edgel said: > http://www.svgopen.org/2003/registration.html > > SVG developer's meeting in Vancouver, Canada from July 13th to 18th, 2003. > > > > -----Original Message----- > From: owner-rasmol@lists.umass.edu > [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Dan Bolser > Sent: Thursday, May 22, 2003 6:49 PM > To: rasmol@lists.umass.edu > Subject: Re: On having more choices.... (etc.) > > > Just a quick question, > > Has anyone explored the possibility of using SVG > (Scalable Vector Graphics) to build a molecular viewer? > > I like the idea of SVG, being a standard dialect of XML, > images of molecules can easily be created by an apache > web server with access to relational PDB DB and an > appropriate XMLST. > > The beauty of such an image is that even though it is being > rendered by your browser in all the ways you might want > to render a molecule, it would also contain all the original > molecular data for you to save / analyse separatly. > > I have heard that the RDB PDB is well under way, and this > would seem like a natural extension to that project. > > Mozilla is developing an SVG viewer, as well as netscape > and several other java iniatives, so soon it should be widely > supported just like flash. > > The power of an XML 'flash like' language is that any well > organized DB (such as a DB of molecular motions) could > potentially be dumped using an appropriate XMLST to create > an image with standard navigation / display features. > > SVG is about as open as a format can get, so, any plans? > >> I think it is overdue for bioinformatics >>professionals to consider the "nuts and bolts" of their industry. >> > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: pymol question Date: Fri, 23 May 2003 09:07:02 -0400 To: LIST rasmol hi folks, anyone out there using PyMOL? I want to zoom, which is normally right-click. but I am on a powerbook with only one mouse button. I can't figure out the correct syntax for zoom from the cmd line. any PyMOL gurus that can help? thanks, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: ++++------+------+------+------+------+------+------+------+------+------+ From: David Fahrney Subject: Re: pymol question Date: Fri, 23 May 2003 07:58:58 -0600 To: rasmol@lists.umass.edu Zoom is a move command along the z axis. A positive argument zooms in. move z, +10 move z, -4 Dave Fahrney Professor of Biochemistry timothy driscoll wrote: > > hi folks, > > anyone out there using PyMOL? I want to zoom, which is normally right-click. > but I am on a powerbook with only one mouse button. I can't figure out the > correct syntax for zoom from the cmd line. any PyMOL gurus that can help? > > thanks, > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: pymol question Date: Fri, 23 May 2003 10:12:58 -0400 To: rasmol@lists.umass.edu at 7:58 AM EDT on Friday, May 23, 2003 David Fahrney said: > Zoom is a move command along the z axis. > A positive argument zooms in. > > move z, +10 > move z, -4 > > Dave Fahrney > Professor of Biochemistry > thanks Dave, and all offlist responders, too. (quick note - move in PyMOL is incremental and not absolute like Chime and RasMol.) :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > timothy driscoll wrote: > > > > hi folks, > > > > anyone out there using PyMOL? I want to zoom, which is normally > > right-click. but I am on a powerbook with only one mouse button. I > > can't figure out the correct syntax for zoom from the cmd line. any > > PyMOL gurus that can help? > > > > thanks, > > > > :tim > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: "Andrew W. Maverick" Subject: Re: RASMOL digest 282 Date: Sun, 25 May 2003 14:54:37 +0200 To: rasmol@lists.umass.edu Dear Colleagues, I wasn't going to send this, but now that we've had one comment on "motherlode": We have been reminded once again that, like immaculate conception and virgin birth, open source and public domain are not the same thing. Andy Maverick Andrew W. Maverick Department of Chemistry Louisiana State University Baton Rouge LA 70803-1804 USA (225)LSU-4415 (578-4415) Fax: (225)LSU-3458 (578-3458) maverick@lsu.edu ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3) Gecko/20030312 X-Accept-Language: es-ar, es, en References: <5.1.0.14.2.20030525144938.00b23218@mail031.lsu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Fernando Gabriel Ranea Subject: Re: RASMOL digest 282 Date: Sun, 25 May 2003 13:50:54 -0300 To: rasmol@lists.umass.edu Hi, It is obvious, if you know the licenses. You earn money developing open source applications: you sell the program and you have to give the source. I believe that the development of a Open Chime software have to be Open Source and GPL. Regards, Andrew W. Maverick wrote: > Dear Colleagues, > I wasn't going to send this, but now that we've had one comment on > "motherlode": > We have been reminded once again that, like immaculate conception and > virgin birth, open source and public domain are not the same thing. > Andy Maverick > > Andrew W. Maverick > Department of Chemistry > Louisiana State University > Baton Rouge LA 70803-1804 > USA > (225)LSU-4415 (578-4415) > Fax: (225)LSU-3458 (578-3458) > maverick@lsu.edu > > > -- Fernando Gabriel Ranea fernandoranea@microbiologia.org.ar http://www.microbiologia.org.ar ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Info: This message was accepted for relay by smtp02.mrf.mail.rcn.net as the sender used SMTP authentication X-Trace: UmFuZG9tSVYbpQVsYJKreCyUDsgjFxS4WnuhggcUK/52YdLUOst81tWOXNPsNLrk ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Masi Subject: Re: pymol question Date: Sun, 25 May 2003 20:23:57 -0400 To: rasmol@lists.umass.edu Tim, Did someone point out that zoom is a "command+up/down mouse drag". Chris On Friday, May 23, 2003, at 10:12 AM, timothy driscoll wrote: > at 7:58 AM EDT on Friday, May 23, 2003 David Fahrney said: > >> Zoom is a move command along the z axis. >> A positive argument zooms in. >> >> move z, +10 >> move z, -4 >> >> Dave Fahrney >> Professor of Biochemistry >> > > thanks Dave, and all offlist responders, too. (quick note - move in > PyMOL is > incremental and not absolute like Chime and RasMol.) > > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > > > > >> timothy driscoll wrote: >>> >>> hi folks, >>> >>> anyone out there using PyMOL? I want to zoom, which is normally >>> right-click. but I am on a powerbook with only one mouse button. I >>> can't figure out the correct syntax for zoom from the cmd line. any >>> PyMOL gurus that can help? >>> >>> thanks, >>> >>> :tim >>> > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: select element in chime Date: Mon, 26 May 2003 09:07:37 -0400 To: LIST rasmol greetings, regarding selection by element in Chime, is select *.[element symbol] the most consistent syntax? because as far as I can tell, support for select [element name] and select [element symbol] is inconsistent, and these are the only three variations that I know. for example, I can "select carbon" but I can not "select magnesium" (I can, however, "select mg"). before I test the various flavors of select, I thought someone might know the answer already. thanks! :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- RASter display of MOLecular structure X-Accept-Language: en,es-ES ++++------+------+------+------+------+------+------+------+------+------+ From: shalpine@earthlink.net Subject: Re: Open-source chime project? Date: Mon, 26 May 2003 12:27:32 -0700 To: Brian White Cc: timothy driscoll , Hello Brian: Thank you for the discussion on developing an Open Source version of Chime. I tried to initiate interest in this topic at the GRC at Mt Hollyoke two years ago, with little success. In fact, I had proposed a mini-grant to investigate a combination Flash animation-Chime-like package. I don't think anyone at NSF knew what Flash was (or was capable of) at the time, so the proposal was turned down. ( See p. 7 of IEEE Multimedia, 2001: http://home.earthlink.net/~shalpine/gallery/CGA/halpine.pdf) Tim Driscoll and Rob Lue's software sound very similar to my initial proposal. Tim - as you know, I am very interested in the development of this type of software. Please keep me in the loop. Some solution is long overdue. Susana Susana Maria Halpine Artist-Biochemist Candle Light Productions 239 Sunridge Street Playa del Rey, CA 90293 (310) 306-8399 shalpine@earthlink.net http://home.earthlink.net/~shalpine Women Chemists Committee Chair American Chemical Society, Southern California Section ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Originator-info: login-token=Mulberry:01WMHWp88uBhdqL14tn0IGBOshUdTj9U/FNgQMjkE=; token_authority=postmaster@andrew.cmu.edu Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: will mcclure Subject: Re: select element in chime Date: Mon, 26 May 2003 20:18:55 -0400 To: rasmol@lists.umass.edu Tim, 'select elemno=##' always works . . . but you may have to check a periodic table. 'symbol' works when the HETERO in the PDB file is defined that way (eg CA, MG, etc), but they often have other names (eg. MGO). -Will McClure --On Monday, May 26, 2003 9:07 AM -0400 timothy driscoll wrote: > greetings, > > regarding selection by element in Chime, is > > select *.[element symbol] > > the most consistent syntax? because as far as I can tell, support > for > > select [element name] > > and > > select [element symbol] > > is inconsistent, and these are the only three variations that I > know. for example, I can "select carbon" but I can not "select > magnesium" (I can, however, "select mg"). > > before I test the various flavors of select, I thought someone > might know the answer already. > > > thanks! > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > > > ----------------------------------------------------------------ras > mol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ----------------------------------------------------------------ras > mol-- > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: select element in chime Date: Mon, 26 May 2003 20:53:08 -0400 To: rasmol@lists.umass.edu at 8:18 PM EDT on Monday, May 26, 2003 will mcclure said: > Tim, > > 'select elemno=##' always works . . . but you may have to check a > periodic table. > > 'symbol' works when the HETERO in the PDB file is defined that way > (eg CA, MG, etc), but they often have other names (eg. MGO). > > -Will McClure > ah ha - forgot about elemno. thanks, Will! :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > --On Monday, May 26, 2003 9:07 AM -0400 timothy driscoll > wrote: > > > greetings, > > > > regarding selection by element in Chime, is > > > > select *.[element symbol] > > > > the most consistent syntax? because as far as I can tell, support > > for > > > > select [element name] > > > > and > > > > select [element symbol] > > > > is inconsistent, and these are the only three variations that I > > know. for example, I can "select carbon" but I can not "select > > magnesium" (I can, however, "select mg"). > > > > before I test the various flavors of select, I thought someone > > might know the answer already. > > > > > > thanks! > > > > :tim > > > > -- > > timothy driscoll > > molvisions - molecular graphics & visualization > > > > usa:north carolina:wake forest > > > > > > ----------------------------------------------------------------ras > > mol-+ > > > > To change your address, unsubscribe, view previous messages/history, > > receive messages as weekly digests, or for any other information > > about the RasMol EMail List, please go to > > http://www.umass.edu/microbio/rasmol/raslist.htm > > > > ----------------------------------------------------------------ras > > mol-- > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en X-Cam-ScannerAdmin: mail-scanner-support@ucs.cam.ac.uk X-Cam-AntiVirus: Not scanned X-Cam-SpamDetails: References: <3ECE0F9A.6080403@mrc-dunn.cam.ac.uk> <3ECFD8E2.3020207@mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Strange format for PDB 1cm4 Date: Tue, 27 May 2003 11:53:07 +0100 To: info@rcsb.org Cc: Wan Kyu Kim , rasmol The following atom line section for 1cm4 looks a little wrong, having a stray atom from residue 293 of chain F in between the TER and HETATM lines of chain E. I always asumed that all the atoms for a residue should be sequential. Is this correct? Cheers, Dan. ATOM 3641 N THR E 146 31.312 61.978 75.234 0.25 36.30 N ATOM 3642 CA THR E 146 32.587 61.624 75.853 0.25 38.50 C ATOM 3643 C THR E 146 32.984 62.653 76.912 0.25 39.10 C ATOM 3644 O THR E 146 32.170 62.973 77.780 0.25 38.90 O ATOM 3645 CB THR E 146 33.768 61.528 74.820 0.25 39.70 C ATOM 3646 OG1 THR E 146 33.927 62.815 74.234 0.25 41.30 O ATOM 3647 CG2 THR E 146 33.545 60.456 73.753 0.25 39.30 C TER 3648 THR E 146 ATOM 3649 CB PHE F 293 11.275 70.102 78.942 0.25 40.50 C <---- ?? HETATM 3650 CA CA E 401 8.040 46.688 78.529 0.25 18.20 CA HETATM 3651 CA CA E 402 14.450 40.835 85.677 0.25 28.00 CA HETATM 3652 CA CA E 403 22.542 69.262 59.236 0.25130.40 CA HETATM 3653 CA CA E 404 28.059 73.861 66.193 0.25 7.60 CA ATOM 3654 N PHE F 293 10.703 69.598 81.261 0.25 40.10 N ATOM 3655 CA PHE F 293 11.610 69.258 80.181 0.25 38.30 C ATOM 3656 C PHE F 293 13.054 69.496 80.591 0.25 36.70 C ATOM 3657 O PHE F 293 13.390 70.501 81.221 0.25 38.80 O ATOM 3658 CG PHE F 293 12.212 69.884 77.755 0.25 42.50 C ATOM 3659 CD1 PHE F 293 12.147 68.699 77.016 0.25 42.80 C ATOM 3660 CD2 PHE F 293 13.154 70.866 77.422 0.25 42.80 C ATOM 3661 CE1 PHE F 293 13.023 68.500 75.948 0.25 42.80 C ATOM 3662 CE2 PHE F 293 14.026 70.657 76.355 0.25 43.40 C ATOM 3663 CZ PHE F 293 13.963 69.475 75.619 0.25 43.20 C ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: KMail/1.4.1 X-Spam-Status: No, hits=-104.5 required=5.8 tests=BAYES_10,DATE_IN_FUTURE_12_24,USER_AGENT_KMAIL, USER_IN_WHITELIST version=2.55 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) ++++------+------+------+------+------+------+------+------+------+------+ From: Boris Gorelik Subject: saving in gif format Date: Wed, 28 May 2003 14:02:19 +0300 To: rasmol@lists.umass.edu Hello, Sorry, but I couldn't find anywere how to solve this problem: I have a linux version of Rasmol (on Redhat 7.3) that was compiled with 16 bit depth. When trying to save gif images, i get "Output Error: Only 8-bit GIF files supported!", When I try to run 8-bit version, on rasmol invoking I get: "No suitable display detected!" message So currently, I cannot use a single file for both viewing molecules and exporting images: for viewing I use rasmol (the 16 bit version), and for exporting I use "rasmol_8BIT -nodisplay". Is there any better way to perform these tasks? Thanks in advance Boris Gorelik ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <200305281402.19699.bgbg@pob.huji.ac.il> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: Re: saving in gif format Date: Tue, 27 May 2003 16:42:04 +0200 (CEST) To: rasmol@lists.umass.edu Cc: bgbg@pob.huji.ac.il Boris, I don't have a lot of rasmol experience ... so this may not be the best answer ... but, I would save the images in a format that works. Then convert them to .gif if necessary. Or, you can do screen captures of the rasmol window using xwd. Then convert to whatever format you want. For image conversion on linux/unix systems go to www.imagemagick.org. On RedHat install from the imagemagick rpm. Miguel > Hello, > Sorry, but I couldn't find anywere how to solve this problem: > I have a linux version of Rasmol (on Redhat 7.3) that was compiled > with 16 bit depth. > When trying to save gif images, i get > "Output Error: Only 8-bit GIF files supported!", > When I try to run 8-bit version, on rasmol invoking I get: > "No suitable display detected!" message > So currently, I cannot use a single file for both viewing molecules and > exporting images: for viewing I use rasmol (the 16 bit version), and for > exporting I use "rasmol_8BIT -nodisplay". > > Is there any better way to perform these tasks? > > Thanks in advance > Boris Gorelik > > ----------------------------------------------------------------rasmol-+ To change