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

[Chinh Su Tran To]

Dear all,

Thank you very much for your help. I am coding it in python and will run in
batch mode.
I think it will work.

Chinh

On Sat, Mar 9, 2013 at 2:01 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> 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
>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20130309/61e031ac/attachment.html>