[Chimera-users] phi psi angles

Eric Pettersen pett at cgl.ucsf.edu
Mon Sep 12 14:19:03 PDT 2005

On Sep 12, 2005, at 8:41 AM, Zenon Grabarek wrote:

> Hello,
> I am looking for a script that would allow me to change the phi psi  
> angles in a selected residue (allowing the C-terminal part of the  
> chain to move) and output the coordinates. Chimera has a very nice  
> interactive tool to do that, but I need to do it systematically in  
> small increments over a specified range of angles. I would be  
> grateful for any help in this matter.

Hi Zenon,
     I've appended a script to do this.  It expects you to select a  
residue (really an atom or bond in the residue) and then run the  
script either with "open changePhiPsi.py" on Chimera's command line  
or by using File...Open and changing the file type to Python.  You  
will actually get an amusing little animation as the angles change,  
though the structure itself won't change -- you'll see.
     If you want to run it non-interactively, you should run Chimera  
from a command line with "chimera --nogui <your structure file>  
changePhiPsi.py".  You will also have to change how the script  
decides which residue to use, and there are comments in the script  
about that.
     Also, you will undoubtedly want to change the script for the phi/ 
psi increments you use and where the output files go.  I think the  
script and comments are fairly clear, but let me know if you have  

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

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