VMD-L Mailing List

From: Jan Saam (saam_at_charite.de)
Date: Tue Feb 01 2005 - 00:01:29 CST

Paul,

I'm not sure, if I di understand you correctly, but I think the answer
is quite easy:
If you have an atomselection $sel then you can retrieve the indexes
either with
set myindexes [$sel list]
or
set myindexes [$sel get index]

if you want them for a specific residue than you have to select
something like this:

set psiindexes [atomselect top "protein and resid 5 and name N CA"]
set phiindexes [atomselect top "protein and resid 5 and name CA C"]

Note that vmd outputs the indexxes in ascending order, not in the order
you typed the atom names. If you need to identify individual indexes
with atom names you have to select single atoms.

Regards,
                Jan

Paul R Brenner wrote:
> Is it possible to use VMD to output index information for the dihedrals of a
> molecule. I see that I can use the get function within atomselect to get the
> angle values (phi,psi) but what I am looking for is an index.
>
> (I then plan to align these indexes with those assigned by a molecular dynamics
> program to selectively restrict their variation.)
>
> Thanks for any pointers,
>
> Paul R Brenner
> Graduate Research Associate
> Computer Science and Engineering
> The University of Notre Dame
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