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

[Eric Pettersen]

Hi Chinh,
	If you are able to write a Python script, you could use the info in the Chimera Programmer's Guide

http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide

to write a script to get the values.  There is a programmer's example specifically about atomic-level measurements such as angles and distances:

http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_AtomMeasure.html

Also, Python is reasonably easy to learn, especially if you already know how to program in another language.  There are links to Python tutorials in the Programmer's Guide.

--Eric

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

On Mar 8, 2013, at 9:08 AM, Elaine Meng wrote:

> 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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