VMD-L Mailing List

From: Tim Travers (tstravers_at_gmail.com)
Date: Thu Aug 18 2011 - 12:26:14 CDT

Hi Mert,

I think VMD uses STRIDE to generate secondary structure assignments for New
Cartoon (and maybe also New
Ribbon) representations. Apparently STRIDE uses backbone dihedral angles to
make these assignments, so I'm
guessing that you'll at least need the backbone atoms to get the
representations you want.

If you have the full trajectories, then maybe you could extract the backbone
atom coordinates (similar perhaps to
how you extracted the alpha-C coordinates), and use this for viewing in VMD.

HTH,
Tim

On Thu, Aug 18, 2011 at 11:01 AM, Mert Gür <gurmert_at_gmail.com> wrote:

> Dear all,
> I only have the carbon alpha coordinates of an adenylate kinase MD
> trajectory.
> I would like to draw/depict the trajectory in VMD with New Ribbons or New
> Carton representation so that I can see the secondary structures visually.
> However, this seems not to be possible. The closest I get to what I want is
> to select the tube representation.
> Does anyone have a solution for this?
> I have the starting full atomistic pdb and psf files of the trajectory.
> Best,
> Mert
>