This document has the following sections: INSTALLATION OF RASMOL SCRIPT OPERATION OF SCRIPT SCRIPT SPEED/PACING/TIMING SCRIPT REVISION HISTORY This script is distributed from the RasMol Home Page, http://www.umass.edu/microbio/rasmol. Look there for updates and other scripts. Most scripts are available in two versions. One runs unattended, continuously. The other contains pauses ('press any key to continue') and is intended to illustrate a lecture. 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. - - - - - - - - - - - - - - - - - - - - - - - - - - - INSTALLATION OF RASMOL SCRIPT MACINTOSH, UNIX Detailed, optimized installation instructions for these operating systems are not available at this time. If you can provide such instructions, please send them to emartz@microbio.umass.edu. For the MacIntosh, you can either download the self-extracting archive BILAYER1.SEA.HQX (if available), or use ftp to 'mget *' all the files of the script. (Precede the ftp command 'mget *' with 'prompt' to toggle off interactive prompting; that is, so ftp won't ask you to confirm the transfer of each and every script file.) If the script files are put in the same folder as the RasMac program, the script will run. This works, but may not be ideal because multiple scripts will mix hundreds of files on one folder. If you know how to get RasMac to run a script in a different folder, please email details to emartz@microbio.umass.edu. WINDOWS/DOS 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 BILAYER1 could be installed in C:\RASWIN\BILAYER1. To do this, copy the packed file BIL1ZIP.EXE into the desired subdirectory, and then 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 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. If you wish, you can even configure the Properties to run the script automatically when the icon is double-clicked. To do this, put '-script bilayer1.top' after RASWIN.EXE in the Command Line slot of the Properties box. [WARNING: there is a bug in RasWin beta 2.6. Scripts started in this way terminate at the first pause, returning the RasMol> prompt. Therefore, scripts will have to be run manually, with a 'script bilayer1.top' command in the command window, until this is fixed.] - - - - - - - - - - - - - - - - - - - - - - - - - - - OPERATION OF SCRIPT If you can provide details for Macintosh or Unix, please send them to emartz@microbio.umass.edu. However, the principles are very similar in all operating systems. Run RasMol. (Under Windows, double-click on the RasWin icon.) If the black RasMol graphics window extends to the bottom of the screen, move and reshape it so that it fills the top 5/6 of the screen, leaving the bottom 1/6 uncovered. 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, Options, Export, Help. This is the graphics window. (For a tutorial on how to use RasMol, see the web site http://www.umass.edu/microbio/rasmol, and look under classroom/education.) A separate, second 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, move it so that its bottom lines up with the bottom of the screen. Press Enter until the 'RasMol>' prompt is repeated all the way to the bottom of the Command Line Window. Arrange the two RasMol windows so that when the black graphics window is in the foreground, exactly seven lines of 'RasMol>' prompt are visible in the portion of the white Command Line Window which shows below the black graphics window. These 7 lines will display the script captions when the script is running. (The 7th line will always be blank, so there are actually a maximum of 6 lines of caption text.) BILAYER1.TOP is the top-level script. Start it by typing 'script bilayer1.top' in the RasMol command line window, then pressing Enter/Return. This script is designed to run unattended. See below for tips on how to adjust the speed/timing. - - - - - - - - - - - - - - - - - - - - - - - - - - - SCRIPT SPEED/PACING/TIMING Script execution speed is affected by the speed of your computer, the speed of your graphics card, the screen resolution, and the size of the RasMol graphics window. Starting with a full-screen graphics window, you can speed up execution by reducing the resolution from 1024 x 768 to 800 x 600 to 640 x 480 pixels. Under Windows, this is usually done with a SetRes (or related) icon in the Windows Control Panel. 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. This script was designed to run unattended. Since RasMol does not yet have a delay command, it took a while to hit upon a mechanism to insert delays (see file delay1.scr). Unfortunately the lengths of these delays are entirely dependent on the speed of the computer running the script. The delays work well on an 80486DX/66 megaherz PC running RasWin-32bit 2.6-beta, using a 640 x 480 pixel screen resolution. On faster or slower computers the delays may need to be tinkered with by editing the script files (but also consider the strategies mentioned above for fine tuning the overall pace). Windows: RasWin32 beta 2.6 (the 32 bit program) is several times faster than RasWin 2.6 (the 16 bit program). To run RASWIN32 you may need a Windows accessory package which is provided free by MicroSoft. For details see: http://www.umass.edu/microbio/rasmol/getras.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - SCRIPT REVISION HISTORY BILAYER1.TOP first released April 11, 1996. - - - - - - - - - - - - - - - - - - - - - - - - - - - -Eric Martz emartz@microbio.umass.edu