VMD-L Mailing List

From: Peter C. Lai (pcl_at_uab.edu)
Date: Wed Feb 22 2012 - 00:31:39 CST

VMD doesn't read HELIX, etc. from pdb either, afaik.

By default it tries to call STRIDE to compute secondary structure.
http://webclu.bio.wzw.tum.de/stride/

On 2012-02-21 10:24:14PM -0500, Zhuyi Xue wrote:
> Hi, there,
>
> If my input is a gro file, which just contains atom coordinates (I mean
> no secondary structure information). When I do Newcartoon representation
> and there comes out to be alpha helix and beta sheets. I am wondering
> how vmd calculates those secondary structures. Whether it follows the
> same way dssp does or only based on dihedral angles (those areas that
> belong to a particular secondary structure shown in Ramachandran map)?
> Pymol can also assign secondary structures, but the result sometimes
> differ from that of vmd, I am not sure how pymol does the calculation,
> either.
>
> Thank you for any explanation or suggestion in advance.
>
> Regards,
> Zhuyi 

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