VMD-L Mailing List

From: sajad falsafi (sajad.falsafi_at_yahoo.com)
Date: Wed Feb 22 2012 - 01:39:07 CST

Hi,

VMD uses the program STRIDE to compute the secondary structure.

vmd > Info) In any publication of scientific results based in part or
Info) completely on the use of the program STRIDE, please reference:
Info) Frishman,D & Argos,P. (1995) Knowledge-based secondary structure
Info) assignment. Proteins: structure, function and genetics, 23, 566-579.

also the Ramaplot plug-in measure the phi and psi angles of residues.

Best of luck,
Sajad Falsafi
Dept. of Genetics, Shahid Chamran University of Ahvaz
Toxicology Research Center, Jondi-Shapour University of Medical Sciences

--- On Wed, 2/22/12, Zhuyi Xue <alfred532008_at_gmail.com> wrote:

> From: Zhuyi Xue <alfred532008_at_gmail.com>
> Subject: vmd-l: Secondary structure assignment
> To: vmd-l_at_ks.uiuc.edu
> Date: Wednesday, February 22, 2012, 6:54 AM
> 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
>