NOTE: RasMol's built-in help, and the RasMol Manual, document the last full-release, version 2.5. To have all documented changes since then, you need the present document for 2.6beta2 (26beta2.txt) plus the document for 2.6beta1 (formerly release.txt, now renamed at the RasMol Home Page to 26beta1.txt, 26beta1.doc, or 26beta1.ps). All are available from http://www.umass.edu/microbio/rasmol. If anyone discovers undocumented changes (see Roger's disclaimer below) please describe them to the RasMol email list (rasmol@lists.umass.edu) or, if you don't wish to subscribe, to me, emartz@microbio.umass.edu. -Eric Martz - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Date: Thu, 18 Apr 1996 From: Sayle Dr R A Subject: Re: RasMol v2.6beta2 To: rasmol@lists.umass.edu Dear Rasmolians, > I'm sure all of us on this list are looking forward with great > anticipation to 2.6 full release. I'd like to thank Eric for his many compliments, but as some of you will know the real reason that v2.6 hasn't appeared yet is that I'm incredibly easily distracted and I spend too little time fixing RasMol and too much reading e-mail and prototyping the next generation RasMol (please, no e-mails). Anyway to prove the political sway this mailing list has I've decided to release a rushed RasMol version 2.6beta2. This fixes many of the bugs and problems that people have encountered, adds some more functionality and increases performance. A complete list of changes is given below, but to summarise an acceptable side-by-side stereo is now working and the documentation still hasn't been updated. I'm still not happy with stereo and so this will probably change before v2.6final. The complete source code, RasMol26.tar.gz and a 32bit Windows executable "raswin32.exe" have been placed on the anonymous FTP site in Edinburgh (ftp://ftp.dcs.ed.ac.uk/pub/rasmol/v2.6beta) and I'll try to update the 16bit Windows and Macintosh versions before the end of next week. However, users with compilers should be able to compile from source before then. Changes between RasMol v2.6beta and RasMol v2.6beta2 o RasMol now allows a numeric parameter to the "trace" command that allows the specification of the width of the "backbone" worm. This both fixes a bug in machine generated scripts containing cartoons, but also allows functionality such as the new "trace temperature" command which displays the backbone as a wider cylinder at high temperature factors and thinner at lower. This representation should be useful to x-ray crystallographers and NMR spectroscopists. o Side-by-side stereo is now implemented as well as the "set stereo" command to control the separation between the left and right images. Note that stereo support is not implemented through out RasMol, for example, Vector PostScript probably shouldn't be generated whilst stereo is on, the RasMol "write script" command probably doesn't save the stereo state of the current image, turning stereo on and off doesn't reposition the center of the molecule and finally the performance isn't as good as it could be. o Significantly increased the performance of ribbons and cartoons on all platforms, but especially on Macintoshes and PCs without hardware accelleration. All floating point calculations have been removed from the RasMol polygon rendering code which is now integer only. o RasMol scripts can now be interrupted during a "pause" command by using either control-Z or control-D. Under VAX VMS, Control-Z can no longer be used to terminate RasMol whilst running a script, use Control-C (as before) instead. o Fixed compatability problems for UNIX interprocess communication between Tcl/Tk v3.x and Tcl/Tk 4.x. Both Tcl versions may now communicate with any of the running RasMols. o Inorder to allow RasMol to compile on IBM RS/6000 workstations running AIX, all references to the variables "hx", "hy" and "hz" have been renamed, as "hz" clashes with an AIX predefined macro. o The RasMol "write gif " command has been modified to allow generation of transparent GIFs. This may be controlled by the "set transparent on" and "set transparent off" commands. o RasMol will now display double and triple bonds automatically for any file containing bond order information, rather than require the user type "set bonds true". [Added by E. Martz 96/07/25: this version no longer requires that all bonds be given in CONECT records; it is sufficient to give only the double or triple bonds. See the FAQ at the RasMol Home Page for an example (http://www.umass.edu/microbio/rasmol/faq.htm).] o Strands, ribbons and cartoons can now be drawn through protein residues that are not standard amino acids (i.e. UNK) provided that the residues contain the appropriate N-CA-C-O atom backbone. o Vector PostScript output now also contains RasMol distance monitors. o The RasMol "write mdl " command to write out an MDL Mol file now only writes out the currently selected atoms. o RasMol can now perform shading to an arbitrary background colour, rather than just black. This is controlled by the commands "set backfade on" and "set backfade off". For example, this may be used to generate depth-cued wireframe images that fade to white, rather than black. o The RasMol PDB file parser has been modified to correctly handle the new "MOL_ID:" molecule names. o The RasMol "quit" and "exit" commands now behave differently when using Inter-process communication. The "exit" command closes the link between programs, but the "quit" command terminates RasMol. o The hardware dials box handling routines in RasMol have now been modified to correctly reset the state of Evans and Sutherland ESV dials when the program exits. And probably have a dozen other things that I've forgotten. Alas I've become very lazy at keeping the RasMol "ChangeLog" upto date. My apologies for all those features that were requested but didn't quite make it into this interim release. For example, I've just remembered that I've forgotten to integrate the patches mailed to this list that allow the initial window size to be specified on the UNIX command line! > I'm sure a FAQ would help but I don't feel I can spare the time to edit > it and keep it up to date (any volunteers?) -- actually the list > history serves that purpose to a large degree if people will just > search it. I must admit that I am at fault here and should have produced a RasMol FAQ many years ago. However in my defense I cite the RasMol user manual as proof positive that I'm incapable of writing clearly and concisely. A volunteer would have my life-long appreciation. I hope this'll keep a few people happy over the next few days. Roger -- Roger Sayle INTERNET: ras32425@ggr.co.uk Glaxo Wellcome Medicines Research Centre, rasmol@ggr.co.uk Gunnels Wood Road, Stevenage, Tel: +44 (0)1438 763246 (direct line) Hertfordshire, SG1 2NY, U.K. Fax: +44 (0)1438 763082