This document has the following sections: INSTALLATION OF RASWIN SCRIPT OPERATION OF SCRIPT SCRIPT SPEED/PACING/TIMING SCRIPT REVISION HISTORY - - - - - - - - - - - - - - - - - - - - - - - - - - - INSTALLATION OF RASWIN SCRIPT 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 ANTIBOD2.TOP could be installed in C:\RASWIN\ANTIBOD2. To do this, copy the packed file AB2ZIP.EXE into the desired subdirectory, and then run it as a DOS program at the DOS prompt (which will unpack it). Now run Windows. 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 changing the 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 antibod2.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 antibod2.top' command in the command window, until this is fixed.] OPERATION OF SCRIPT ANTIBOD2.TOP is the top-level script. Start it by typing 'script antibod2.top' in the RasWin command line window, then pressing Enter. This script has frequent pauses. Press the spacebar to continue. During the initial portion of the script, prior to the display of the F(ab')2, you are encouraged to rotate each image with the mouse before proceeding. Once the F(ab')2 appears, it is best not to rotate the image manually as subsequent views make assumptions about the previous orientation of the molecule. After the all-magenta representation of lysozyme appears, it is OK to rotate manually again, as the 'discontinuous' and 'flat' views of the lysozyme epitope are re-oriented properly by the script. If you are projecting this script in a lecture, it is best to do a practice run without manual rotation (so you can see the intended views), then re-run the script and try rotating images. By such practice runs you can optimize your rotation strategy. If you need a shorter script for a lecture, sections can be omitted by editing the file ANTIBOD2.TOP. You can run each .SCR file manually (e.g. 'script igdomain.scr') to see what it does. Insert '#' at the beginning of each script line you wish to omit (this converts it to a comment). SCRIPT SPEED/PACING/TIMING 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 execution speed is affected by the speed of your computer, 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 1024 x 768 to 800 x 600 to 640 x 480 pixels. 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. REVISIONS OF SCRIPT 1/29/96: (ANTIBODY.TOP, the original version which preceded ANTIBOD2.TOP.) To work around a bug identified by Roger Sayle, reduced ssbonds commands in S-S.SCR and IGG1-A.SCR from 300 to 200. This should prevent the 'Unhandled exception' crash observed by several people. If anyone still experiences this problem, try reducing the 200's to 150's. 3/3/96: Completed revisions and released ANTIBOD2. This revision includes the whole IgG1 molecule structure provided by Eduardo Padlan, and shows the carbohydrates and their linkages to the protein. Additional small rotations were inserted at frequent points; thus, manual rotation is less necessary during lecture projections. This version is likely to be too slow with the 16-bit version of RasWin; use the 32-bit version! -Eric Martz emartz@microbio.umass.edu