During detailed exploration of an unfamiliar model, you my want to put your work aside, and come back later to start with your current view. Sometimes you can invest much time and thought in producing a particularly revealing view of a model. RasMol provides a way to preserve your work. This is a great feature for illustrating lectures, because you can make vivid classroom views and bring them to the screen immediately. At any time during operation of RasMol, you can write a "script" that RasMol can use to recover the current view. You will now write a script to save the view of antibody CDRs that you made in the previous section.
First, rotate, translate, and zoom your model into a position that shows the CDRs clearly, and that fills the screen nicely.
RasMol > write script CDRs.spt <
return >
After a brief pause, RasMol writes the script. This new file will
appear in the same location as the RasMol program icon. If you have
been working, as instructed, with RasMol on your Macintosh desktop,
the file will appear there. Its icon is a little scroll. The file
ending .spt (for script) helps to distinguish a
script file from a coordinate file, which usually ends in .pdb
or .ent. After one more exercise, you will try out your
script.
Look back at the commands you have used with this file, and notice the syntax of atom expressions that designate the chain. Observe that just as .ca means atom CA (an alpha carbon), :Y means chain Y (if you prefer, you can use *Y). In a select or restrict command, you must specify the chain unless you want the command to apply to all chains. As an example of the select syntax, select gly40:L.ca selects one atom: the alpha carbon of glycine 40 in the L chain. To test yourself on this syntax, try this: restrict the display to aspartic acid 48 of the antigen chain, display it as ball and stick, center on the alpha carbon, select the gamma carbon of this residue, and color it green.
Next, exit from RasMol.
File: Quit
This commands stops RasMol, and its windows disappear, revealing
the desktop.
Find your script file (CDRs.spt) and double click on it. RasMol appears, and after a pause (perhaps a long pause!), presents the same view you were displaying when you wrote the script file.
There are some restrictions to your use of the RasMol scripts. In their original form, they can only be used from the same location (in this case, the desktop) into which RasMol saved them. This means that RasMol, the PDB file, and the script must all be exactly where they were at the time the script was prepared. Fortunately, by editing the scripts in a word processor, they can be modified and made portable. In the exercise at the end of this tutorial, you will make and save several scripts, and then transfer them to a disk to hand in. I will be able to modify them so I can see your results. If you want to use your own scripts on another computer, see Making Scripts Portable.