On Aug 28, 2008, at 3:33 PM, E. Merkley wrote:

Hello chimera team,

I am trying to evaluate which regions of (chi1,chi2) space for a particular tryptophan residue create steric clashes with a bound ligand. I see from the archives that findclash can be called from the command line, but I have been unable to find a way to use the "adjust torsions" feature from the command line. Is this possible? If not, any other suggestions?

I worked on a command-line implementation of this (the "turn" command from Midas) three years ago, got part way finished, then things came up and I have never gotten back to it. I'll try to get to it again. I've attached a script that, if you've selected a TYR residue, will run through the chi1 and chi2 angles in 10-degree increments and call the findclash command for each, saving the info into files named clashes.chi1.chi2. Keep in mind that the chi1/chi2 values are deltas from the starting chi1/chi2, so the evaluation at chi1==0 and chi2==0 is really the starting chi1/chi2 in the structure. If you want it to start at the "real" chi1/chi2 of zero, you will have to adjust the torsions yourself before running the script (make sure to "deactivate" the torsions after adjusting them so that the script gets the adjusted values as its starting point). Run the script with "open changeChis.py" or by opening it with File-

Open.

--Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu