Frequently Asked Questions (FAQ) on RasMol and Chime

answered by Eric Martz -- see also Roger Sayle's FAQ.

If you don't find what you want here, explore Roger Sayle's FAQ, the RasMol Classic Main Page site and the RasMol Reference Manual, and search the past messages in the history files of the RasMol email discussion.

Why don't my Chime files work from my server? Why is Netscape asking me to find the plugin when I already have Chime installed and working? My files work perfectly from my PC hard disk!

Your server administrator needs to set the MIME types needed by Chime on the server, including at least these 3: If you are using any other types of files for Chime, such as XYZ files, those need to be set also. The complete list can be seen by pulling down the Help menu in a Netscape where Chime is installed: click About Plugins, and find the list under Chime. The details of how to set the MIME types depend on the details of the server and should be known by your server administrator. Details for some common servers are listed at MDLI's Chime FAQ.

Gzipping PDB files for Chime

You can skip this (rather technical) section unless you are putting a Chime-based presentation on a web server.

All PDB files placed on servers for use by Chime should be gzipped. (Note, however, that if the same copy of the file is to be used for RasMol, it should not be gzipped since only unix-RasMol can understand gzipped PDB files -- RasWin and RasMac cannot!)

Chime will automatically decompress and display PDB files compressed with the gzip method. Such compression reduces the sizes of PDB files by about 3.5-fold, and reduces the time required to transfer the files through the Internet by a similar amount. When Chime's "File, Save Molecule As" menu option is used, the file will be saved decompressed (as plain text), even if Chime received the file gzipped.

Gzip is a freeware program available for a wide variety of computer platforms. Gzip originates from the Free Software Foundation, but they do not provide the application program directly. To download gzip, see the paragraph below for Windows or Macintosh.

Gzipping on Windows: Download gzip.exe (which is also available on most shareware/freeware web sites). To gzip, for example, 1d66.pdb, open a DOS window, and type the command "gzip 1d66.pdb". This will produce the file 1d66.pdz which you should probably rename to 1d66.pdb (see below).
To decompress a gzipped PDB file: If you run gzip with no parameters, just "gzip", it will reply "For help, type: gzip -h". From the help, you will learn that to decompress a file, the command is "gzip -d <filename>". However, the filename must end in "z", so before decompressing, you'll need to rename, for example, 1d66.pdb back to 1d66.pdz. Then after you "gzip -d 1d66.pdz" it will produce 1d66.pd, which you'll have to rename back to 1d66.pdb.

Gzipping on Macintosh: The source of the application is MacGzip Home Page (Spain).

Serving gzipped PDB files: In most cases, after gzipping a PDB file for use on a web server, you will need to rename the gzipped file back to a name ending in .pdb. This is because typically the server will be configured to serve files ending in .pdb as MIME type chemical/x-pdb, which directs the browser to hand these files to the Chime plug-in for display. Unless you can get the server administrator to reconfigure the server to serve other types of files (for example ending .pdb.gz or .pdz) as chemical/x-pdb, other file types won't be displayed in Chime.

If using ftp to transfer the gzipped PDB file to the server, make sure you force binary mode! Although unzipped PDB files are plain ASCII text, transferring a gzipped file in ASCII mode will corrupt it. Test your gzipped PDB files by viewing in Chime from the server after transferring them!

Is Chime Y2K complaint? Where do I get technical support for Chime?

All questions concerning support for Chime, Y2K compliance, etc. should be directed to the source of Chime, namely MDLI at chime-feedback@mdli.com. Eric Martz authored neither RasMol nor Chime.

Chime for SGI, linux, unix (not!)

MDLI has no plans to develop Chime for linux or any other flavor of unix. They did provide Chime 0.9 for SGI (still available and works fine as far as it goes) but decided not to bring that up to version 1 or 2. MDLI is continuing to develop and support Chime for Windows 95/98/NT and Macintosh PPC. This information is current as of mid-1999. The source code for Chime is of course proprietary and not available outside of MDLI. If you wish to contact MDLI and express your interest in Chime for linux, or in having them complete the documentation on Chime 2 at their website, send email to chime-feedback@mdli.com.

Double and triple bonds

Beginning with RasMol 2.6 beta-2 (and also in Chime 2) the PDB file needs to specify CONECT records only for the double or triple bonds (not for all bonds in the entire molecule as in the previous version of RasMol), and the default is to display double bonds (set bonds on). Beware that if the sticks get too large, the double bonds will disappear (reduce the size of your graphics window, or zoom to smaller size). Here is a sample PDB file with three double bonds, fumarate.pdb. The heavily commented contents of this file may be viewed as fumarate.txt, which may be used as an example for constructing your own such file. A stereo image showing double bonds is provided for the drug Alprazolam.

For purposes of showing delocalized double bonds (as in COO-) it would be ideal to draw the second bond in each pair as a broken line, but neither RasMol nor Chime can presently do this. The command wireframe dash draws the selected bonds as dashed (dotted) lines, but is presently incapable of showing double bonds, and the dashed bonds cannot be thick (sticks).

For historic details, use your browser's Find capability to search the RasMol email discussion history for February and July 1996 for the phrase "double bond".

Mouse Control Summary

These click-and-drag controls work similarly for RasMol and for Chime. In RasMol, the set mouse command mode defaults to set mouse rasmol, which gives the controls summarized below. However, there are also set mouse insight and set mouse quanta modes (not shown below).

Action Windows Macintosh
Rotate X,Y Left Unmodified
Translate X,Y Right Command*
Rotate Z Shift-Right Shift-Command*
Zoom Shift-Left Shift
Slab Plane Ctrl-Left Ctrl
*On some Macs, the Option (Alt) key has the same effect on RasMol as the Command key.

If you use unix, send your mouse information to me for inclusion in the above table.

Retaining RasMol's window sizes/positions

Windows 95: Retaining window sizes/positions. Get Deskey from Softarts (www.spiresoft.com). The shareware version runs for 1 hr at a time. Registration is $15. (I sent mine but never received any response, so I have to restart Deskey when I need it more than an hour after it was last started -- easy enough.)

When you run Deskey's SETUP.EXE, nothing seems to happen. However, at one end of the Taskbar (the bar with Start on it), you will now see a gold key. Click on this for Deskey's menu. Start RasMol and arrange the graphics window as you want it. Now select Window Placements on Deskey's menu, Add, select Capture from window, and OK the Add Window Placement Dialog (no further changes are necessary; be sure to leave the Auto-apply option checked).

Now arrange the RasMol Command Line window and do the same sequence to add a window placement in Deskey.

Close RasMol, restart it, and voila! Your window arrangement is automatically restored for both windows. If you have multiple icons for multiple RasMol working folders ("Start in" directories under Properties, Shortcut), you do not have to add window placements for each icon. Deskey recognizes RasMol as such regardless of which icon you use to start it. You can, however, have multiple placements stored simultaneously in Deskey for RasMol's windows. Whichever pair you move to the top of the Windows Placements list in Deskey become the active placements.

Enjoy! (Thanks to Rod Levine, NIH, for calling Deskey to my attention.)

Windows 3.1x: Retaining window sizes/positions. For Windows 3.1 (ONLY, not Win95), a shareware program called FreezeFrame makes RasMol (or most other programs) startup with the same windows sizes and positions (both windows!) as when you last closed it. Get the FreezeFrame file ff.zip from any shareware site (http://www.shareware.com, http://www.filepile.com).

Unzip the file (http://www.winzip.com). Now use Windows' File menu, New, to create an icon for ff.exe. Double click the icon and a minimized FF icon will appear at the bottom of your screen. Startup RasMol, resize/reposition the windows, and close RasMol. Now start it up again and Voila! FF remembers the window settings between sessions. Just start it up before RasMol and you get the same window sizes/positions every time. (You can include ff.exe in your autoexec.bat file to startup FF at boot time.) Oh what a relief it is!!

Use Write to view the help file ff.wri if you wish.

Please send the author the $5 he asks for! Send your check payable to Ronald Crane to: 

FreezeFrame Registration
c/o Ronald Crane
758 Vasona St.
Milpitas, California    95035-4316

Macintosh: Retaining window sizes/positions. Sorry, we don't know a solution for the Macintosh. If you know one, please let us know!

Printing in High Resolution

If you select "File, Print" from RasMol's menus, the image will be printed at screen resolution. This will appear jagged and of poor quality since most inkjet or laserjet printers print at least 300 dots/inch (120 per cm), while even at 1024 pixels wide by 768 pixels high, a 15-inch (38-cm) screen has less than 100 dpi (40 dpc). Below are outlined several alternative strategies for printing high-resolution images.

One solution is to use the highest screen resolution available to you (perhaps 1280 x 1024), and resize RasMol's graphics window to full-screen. Particularly if you print the result at less than screen-size (e.g. in portrait rather than landscape mode and/or xerographically reduce the image), it may have acceptable resolution. A similar result will be achieved if you select "Export, GIF" from RasMol's menus and save an image file (same resolution as screen). Such a GIF file can be used on a web page or printed with a shareware graphics editor such as LviewPro for Windows (what is good for Macs?). LviewPro is also good for combining several RasMol images, annotating them with good-looking text, cropping, changing the background color or making the background transparent (save as GIF89a), etc.

If you have a postscript printer, the RasMol command write vectps filename creates a postscript file at printer resolution, which can then be sent to your printer. (This command is not on RasMol's Export menu nor is it documented in the on-line help. The command write ps filename writes raster postscript at screen resolution.) The disadvantage of vector postscript is that at present it does not support ribbons, cartoons, strands, or traces. Note that the set vectps on command adds outlines to cylinder bonds or spheres. However, it presently does not work for spheres intersecting more than one other sphere. Thus, it works well for stick or ball-and-stick images but not for most spacefilling images.

A final solution is to recompile RasMol's source code after inserting modifications which facilitate making higher-resolution images. Details can be found by searching for "resolution" in the RasMol email discussion history for January, March and July 1996.

How do I see RasMol's stereo pairs in 3D?

See Gale Rhodes' excellent guide to viewing stereo image pairs, Stereo Viewing.

Modifying existing PDB files

Would you like to remove or extract some of the atoms from a PDB file? Both RasMol and WebLab can do this, but each with some limitations. Details are provided under PDB Tools.

This page is maintained by emartz@microbio.umass.edu