From: Axel Kohlmeyer (
Date: Sun May 01 2011 - 12:12:09 CDT

On Sun, May 1, 2011 at 12:27 PM, ban arn <> wrote:
> Dear VMD Users
> I am working on G-protein coupled receptor simulations.
> I would like to analyse teh helical motions of the extracellular part of the
> protein.
> For that, I would like to collect the c-alpha co-ordinates of X & Y from the
> center of the extracellular part of the each helix (not from the center of
> the whole protein) by making Z as zero.
> Is there any script available in VMD to do the same or if anyone performed
> similar task kindly advice.

VMD allows you finegrained access to coordinate and other atomic properties
via the atomselect command. to get the results that you are after requires some
additional (vector) math that seems quite straightforward from your description.

you should read through the VMD scripting tutorials and some Tcl tutorial
on math and lists and then you should be able to write the script you desire
by yourself. this kind of analysis is typically very specific and thus nobody
writes scripts that can be easily transfered to other problems.


> Many Thanks
> Balaji

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.