VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Feb 13 2010 - 17:20:59 CST

On Sat, 2010-02-13 at 14:19 -0800, Marc Charendoff wrote:
> Hello,

hi marc,

it is not clear to me from your question whether you need
this for interactive use or just in general.

> I am looking to create a script (tcl? Python?) whereby I can
> retrieve and store coordinates of a few selected atoms of a protein so
> that I might perform various geometric calculations through an entire
> trajectory. Is there a specific script I might be able to use as a
> template? Specifically, I am looking at how to pick an atom and get
> its x,y,z coordinates as a starting point. VMD uses the QUERY radio
> button under the mouse selection to get this exact information. The
> code snippet for this feature seems an ideal place to start. Guidance
> appreciated.

this code is internal c++ code. you can monitor tcl text mode command
equivalents when you turn on the logging feature (in the File menu).

if it is just about retrieving data for some atoms, have a look
at the atomselect command and then the vmd user's guide, scripting
tutorials, script library and plugins (best in that order).

it is also possible to intercept mouse picking. perhaps the molefacture
plugin is an example for that.

cheers,
   axel.

>
>
> Regards, Marc
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.