VMD-L Mailing List

From: OZGE ENGIN (OZENGIN_at_KU.EDU.TR)
Date: Sat Feb 09 2008 - 06:39:27 CST

Hi,

Thank you Rui, it works. Is there any way of writing these strings that describe the secondary structure of each residue within a peptide into an output file? Is there any script?

Thanks in advance

-----Original Message-----
From: jrui_at_ci.uc.pt
To: OZGE ENGIN <OZENGIN_at_KU.EDU.TR>
Date: Sat, 9 Feb 2008 10:50:46 +0000
Subject: Re: vmd-l: output of the ssrecalc command

Hi,

After ssrecalc, you could make an atom selection and then get the secondary
structure for that selection:

set sel [atomselect top "protein and name CA"]
$sel get structure

This will give you a list of the secondary structure of each residue.

Hope this helps,
Rui Rodrigues

Quoting OZGE ENGIN <OZENGIN_at_KU.EDU.TR>:

> Hi all,
>
> I have a question about ssrecalc command. I want to calculate the
> secondary structures of each of the residue of my protein. This
> command gives any output file? Wnen I write it in the command line,
> it gives nothing.
>
> Thanks in advance
> Ozge Engin
> =================================
> Computational Science & Engineering
> Koc University
>
>

Ozge Engin
=================================
Computational Science & Engineering
Koc University