[Chimera-users] Adjust torsion angles
meng at cgl.ucsf.edu
Fri May 7 08:20:49 PDT 2021
The Adjust Torsions graphical interface is meant for interactively changing torsion angles when you do not know what angle value that you want without moving it there by hand and viewing the result. So it does not have any way to attach a single control to multiple torsions (although you can of course have controls for multiple torsions shown in the dialog at the same time, as shown in the figure).
There is also a "rotation" command for activating and changing a torsion. Again it just does one at a time, but may be easier to script this repetitive task than to do it in the graphical interface.
For changing at the same time: if the angle is one of the clearly defined peptide angles psi, phi, omega, chi1, chi2, etc. and you know the value that you want, you can change multiple amino acids to that value at the same time using the Selection Inspector. First select all of the amino acids you want to change, then click the green magnifying glass icon near the bottom right of the Chimera window to open the Selection Inspector, then in that dialog Inspect "Residue" ... it will list "phi angle" "psi angle" and the chi angles, and you can enter the new value that you want.
For scripting, the above is the same as using the setattr command, e.g. if you have amino acid residue 58 in both chains A and B, then this would change psi to -60 degrees in both of them at the same time:
setattr r psi -60 :58.A:58.B
You have to be careful, though. There is no "undo" of this change.
I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On May 6, 2021, at 10:58 PM, Moradkhan, Tiglath A <tmoradkhan at csus.edu> wrote:
> I'm using the adjust torsions tool in Chimera. I was wondering whether there is an easier way of selecting several amino acids at once and adjusting their torsion angles rather than selecting them individually. I'm working with dimers and trying to select individual amino acids would take a very long time.
> Thank you
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