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

Eric Pettersen pett at cgl.ucsf.edu
Fri Mar 8 10:01:14 PST 2013

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


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


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 Pettersen
                        UCSF Computer Graphics Lab

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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