VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Dec 16 2008 - 04:41:47 CST

Hi Bernhard,

You should take a look at the STRIDE documentation, as VMD uses STRIDE
to predict the secondary structure:

http://webclu.bio.wzw.tum.de/stride/

and the corresponding paper describing the method:

Frishman D, Argos P. Knowledge-Based Protein Secondary Structure
Assignment Proteins: Structure, Function, and Genetics 23:566-579
(1995)

Cheers,
Michel

On Tue, Dec 16, 2008 at 10:30 AM, Bernhard Knapp
<bernhard.knapp_at_meduniwien.ac.at> wrote:
> Hi everyone
>
> Does anybody of you know how the alpha helix structure in new cartoon
> representation is defined in vmd? Which angles and distances are necessary
> between which atoms? I am asking because during a molecular dynamics
> simulation the alpha helical structure of a MHC gets destroyed and I am
> wondering at which threshold it is not represented as alpha helix anymore?
> Unfortunately I could not find the answer neither in vmd reference nor in
> the user documentation.
>
> cheers
>
> Bernhard