This document has the following sections:


This script is distributed from the
RasMol Home Page. Look there for updates and other scripts as they become available. This document itself was revised 96/08/04. Check the web site to see if the version there is newer.

Scripts can be paused or unpaused; some are available in both forms. The filename of some scripts ends with p or u to indicate which form. Paused scripts pause frequently, meaning that a key must be pressed to continue. These are designed for projection in a lecture, or for individual study. Unpaused scripts run without stopping from beginning to end. These are intended to impress viewers with RasMol's movie script capability, for audiences for whom the scientific content of the script is of secondary importance.

Installing and running a script is really quite simple. However, the first time you do it, there are a few details which might not be obvious. This document will help to make your first script-running experience smooth and easy. Once you have run a script, you'll be able to re-run it or run other scripts quite easily.

Throughout these instructions, the script name dna3p will be used as an example. Wherever you see dna3p, substitute the name of the script you are installing.

Details specific to each script will be found in the specifications file which accompanies each script.



For the latest and most complete information, see
RasMol Script Installation and Operation at the web site.

Each script consists of a top level script plus many subscripts and some PDB files. It is therefore advisable to install each script in a separate subdirectory. For example, assuming you have installed the RasWin program files in C:\RASWIN, the script DNA3P could be installed in C:\RASWIN\DNA3P.

To do this, copy/move the self-unpacking script file, which will have a filename ending in .EXE (e.g. DNA3P.EXE) into the desired subdirectory, and then double-click on it in File Manager, or run it as a DOS program at the DOS prompt (which will unpack it).

Now, in Windows, with the RasWin icon selected, select File, Preferences, and change the Working Directory to the one containing the unpacked script files. (If you want access to RasWin's built-in help, you must also copy RASWIN.HLP and RASMOL.HLP into the working directory.)

If you have several scripts, you may wish to create a separate RasWin icon for each. This would enable you to change scripts smoothly during a lecture, without repeatedly reconfiguring one icon's working directory. With the RasWin icon highlighted, select File, Copy. Now use File, Properties to change the working directory to the one for the script, and the Description (which will appear under the icon) to the script name. Thus you will end up with a script-name-labeled RasWin icon for each script.


For the latest and most complete information, see RasMol Script Installation and Operation at the web site.

For the MacIntosh 68k or PPC, look for a self-extracting archive file (filename ending in .sea.hqx) or a Stuffit file (ending in .sit.hqx). Provided you have installed the freeware Stuffit Expander (available from, a folder containing the script will be created automatically, and can be moved to wherever you wish.

If the script has not been packaged specifically for the Mac use Fetch (available free for educational or non-profit use from, or use any other anonymous ftp utility) to get the script files. Connect to and look in /pub/shareware/rasmol/scripts. Once you are in the folder containing the many files for the desired script, they can all be selected at once by holding down the shift key while clicking and dragging. All script files can be gotten as text. Put them in a new folder named according to the name of the script.

In order to run the script, the RasMac application file must be dragged into the same folder as the script files themselves. IMPORTANT: It is recommended that you drag your original RasMac application file into the script folder, as this will always work. An alias will not work in most cases. A copy will work if you start the script by typing a command line (see below). However, a copy will not always run a script dragged and dropped onto it. In order for a script to run after dragging and dropping, it must have RasMol's signature, indicated by having a RasMol Script icon (scroll with 3 balls). Typically, unpackaged scripts gotten with Fetch will not have RasMol's signature. Technical information about Mac signatures is available for those interested, but is not necessary for script operation.


For the latest and most complete information, see Installing RasMol Scripts at the web site.

No further details were available to the author of this document. If you can provide detailed, optimized instructions, please send them to


For the latest and most complete information, see Installing RasMol Scripts at the web site.

No further details were available to the author of this document. If you can provide detailed, optimized instructions, please send them to


If you can provide details for unix, please send to

The following method works in all operating systems. Run RasMol. Find RasMol's Command Line Window. The major problem beginners have is not being able to find the RasMol Command Line window. When you run RasMol, a black window will open entitled "RasMol Version N.N", with pull-down menus named File, Edit, Display, Colours, etc. This is the graphics window. A separate, second, white window, the Command Line Window, is also opened when you run RasMol.

Under Windows, the Command Line Window starts out minimized to an icon near the bottom of the screen. If you can see the icon, click on it to open it. If you cannot see it, under Windows, use Alt-Tab to cycle through all the windows until you find one titled "RasMol Command Line" -- then release the Alt key to open the window. The Command Line Window is white.

Once you have the Command Line Window open, press Enter until the 'RasMol>' prompt is repeated all the way to the bottom of the Command Line Window. (The command line window accepts typed letters even when the graphics window is active for both Windows and Macintosh.) Arrange the two RasMol windows so that when the black graphics window is active in the foreground, exactly six lines of 'RasMol>' prompt in the white command line window are visible below the bottom edge of the black graphics window. These 6 lines will display the script captions when the script is running. For some scripts, the number of lines needed may differ from six; see the specifications file for the script in question.

To start the script running, type script followed by the name of the top level script file in the RasWin command line window, then pressing Enter. For example, script To find the top level script filename for the script in question, see its specifications file. In scripts downloaded as sea.hqx files for the Macintosh, the top level script will be labeled essential.

PAUSED SCRIPTS: You can tell when the script is paused because the mouse icon will change from busy/wait to the pointer. Press any key to continue. While standing at a pause, the image can be manipulated with the mouse or menus, and unless intentionally disabled by the script, atom identifications can be reported by clicking on them. However, many scripts do not restore the image orientation etc. after a pause, so manipulating the image may cause misoriented images later on. The best advice is to run the script first without any manual manipulation. Then you can try rotating the image at pauses and watch the later consequences. Some script specifications files state whether the image orientation is restored after pauses.


Script execution speed is affected by the speed of your computer, the presence or absence of floating point hardware, the speed of your graphics card, the screen resolution, and the size of the RasWin graphics window.

Starting with a full-screen graphics window, you can speed up execution by reducing the resolution from 1024x768 to 800x600 to 640x480 pixels. Under Windows, this is usually done with a SetRes (or related) icon in the Windows Control Panel. On a Macintosh, select Apple, Control Panels, Monitors, Options.

Further increases in speed can be obtained by reducing the size of the graphics window (to less than full-screen). Quick previewing of scripts can be done very quickly in a tiny graphics window.

The pacing of a script can be altered by changing the increments in rotations and the delays. This requires several hours of programming per script.

Windows: RasWin32 (the 32 bit program) is several times faster than RasWin (the 16 bit program). To run RASWIN32.EXE you may need a Windows accessory package which is provided free by MicroSoft. For details see the web site page on Getting and Installing RasWin.

Information on how to write new scripts is available at the web site.