Hi Ben, When creating a script or alias, the first thing is to try all the commands individually rather than generating the whole thing at once and then wondering which one has not performed as expected. It looks like you had a space after the colon, which would not select anything. For example, I have a file ala12.mol2, so I tried the following commands: open ala12.mol2 (it was in the same directory in which I started Chimera) sel :2-6 write selected 0 ala12.stuff.mol2 I could see the selection command selected something, and then I could look in the output file, which did indeed contain those residues. Having validated the process, I can then try alias ^dostuff open $1.mol2; sel :2-6; write selected 0 $1.stuff.mol2 dostuff ala12 This does not address your underscore issue; I haven't experimented with that yet, but you may need to rename your inputs at least for now. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Feb 7, 2008, at 9:32 AM, Ben Keshet wrote:
Hi Eric,
Thanks for the detailed answer. I think the .cmd script will be sufficient for my purpose, however I was unable to write it correctly. What I want to do is slightly more complex than I outlined – I need to: open a mol2 structure, select certain residues (say select: 69-70), save the selected residues as a mol2 file, and select different residues and save them several more times. The .cmd looks something like that:
alias ^process open $1.mol2; sel : 69-70; write selected 0 $1.his_CEGI.mol2;
process p2
However, I was unable to create a proper mol2 file (I tried different options but my guess is that I have a syntax error). In some cases I was able to write out a file, but it was never a proper mol2 file. Alternatively, I tried:
alias ^process open $1.mol2; sel : 69-70; select invert; del sel; write 0 $1.his_CEGI.mol2;
process p2
which generated p2.his_CEGI.mol2, but the file could not be viewed with Chimera, and when inspected it looked different (no charge column and extra 3 columns: 1.00, 0.00, atom name). The whole script should be able to save mol2 files of several subsequences of several different structures. I would appreciate if you could help me identify what missing in the script.
On a related note, the name of my structures have an underline in them (_), I noticed that Chimera puts a space instead. How do I make Chimera read, for example, p2_3.mol2 as it is (and not as p2 3.mol2)?
Thanks a lot for you help,
ben