VMD-L Mailing List

From: Mert Gür (gurmert_at_gmail.com)
Date: Thu Aug 18 2011 - 12:20:30 CDT

Dear John,

Is there no way to trick VMD so that it can do it ?

Best,

Mert

On Thu, Aug 18, 2011 at 12:48 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> VMD needs more than just the C-alpha atoms in order to draw
> either Cartoon or Ribbons representations, because it looks for
> oxygen atoms to determine the orientation of the ribbon cross section.
> Without this information, VMD can only draw a tube representation.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Aug 18, 2011 at 11:01:00AM -0400, Mert Gür 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
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>