[Chimera-users] internal coordinates (z-matrix) in chimera

Elaine Meng meng at cgl.ucsf.edu
Fri Mar 8 09:08:07 PST 2013


Hi Chinh,
For scripting measurements (distance, angle, torsion) you can use commands: distance, angle
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>

These measurements are specified individually.  Chimera does not have an option to write out a Z-matrix, sorry.

More info on writing Chimera scripts to process multiple data files:
<http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 8, 2013, at 12:01 AM, Chinh Su Tran To wrote:

> Hi,
> I have some results after running docking from DOCK.
> I'd like to obtain information of internal coordinates (bond, angle, torsion OR z-matrix).
> 
> Could anyone please give me any suggestion how to do that in Chimera? Or if possible, please suggest me some references that can help me find it out.
> 
> I have bunch of conformations, so I may not use the gui. 
> Thank you.
> Chinh




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