VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Tue Jun 28 2016 - 20:38:47 CDT

Hi Qasim,

You could check this link

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/11074.html

The variable "selstruct" will be a list containing 1-letter code of the
secondary structure. Once you write that to a file, you can easily plot it
in any way you want.

Hope this helps,
Chitrak.

On Tue, Jun 28, 2016 at 8:31 PM, Qasim Pars <qasimpars_at_gmail.com> wrote:

> Dear users,
>
> I wanted to get the secondary structure graph of a trajectory file (.xtc)
> using VMD. For that I used VMD timeline
> (Extensions-Analysis-Timeline-Caculate-Calc.Sec.Struct.) but it was very
> complex and couldn't get what I wanted
>
> As a matter of fact, I would like to get the secondary structure graph of
> SOME residues (not all of them in protein structure) but it is not easy
> with VMD timeline. Does anyone have a VMD or any script to get the
> secondary structure graph of SOME residues in the trajectory file (.xtc) as
> a function time?
>
> Any helps will be appreciated.
>
> --
> Qasim Pars
>