[Chimera-users] automating/scripting bond rotation

Eric Pettersen pett at cgl.ucsf.edu
Fri Aug 29 15:43:29 PDT 2008

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- 


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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