VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat Feb 02 2008 - 08:42:40 CST

Hi Aneesh,
to calculate the secondary structure for a selection at a given
timestep, you should got to that timestep, and the use the command
mol reanalyze top
which runs that timestep through stride (among other things). Once this
is done, you can access the secondary structure of an atomselect object with
$sel get structure

This will return a string with a one letter description of the secondary
structure at each position in your atom selection (eg. 'H' for helix).
You can then calculate %helicity by counting the Hs.

Best,
Peter

aneesh cna wrote:
> hello,
> Alex,thank you for immediate reply.Is there any plug-in in VMD to
> calculate % helicity ? or is there any script to do such calculation
> ?. Any help is appreciable
>
> with regards
> Aneeh
>
> On Feb 1, 2008 11:07 AM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu
> <mailto:akohlmey_at_cmm.chem.upenn.edu>> wrote:
>
> On Jan 31, 2008 11:54 PM, aneesh cna <aneeshcna_at_gmail.com
> <mailto:aneeshcna_at_gmail.com>> wrote:
> > Hello VMD users,
> > Is it possible to calculate %helicity
> over time
> > using VMD ?.
>
> yes.
>
>
> >
> > Thanks in advance
> > Aneesh
> >
>
>
>