VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Aug 18 2011 - 13:27:42 CDT

On Thu, 2011-08-18 at 13:20 -0400, Mert Gür wrote:
> Dear John,
>
> Is there no way to trick VMD so that it can do it ?

if you have the relevant data available elsewhere,
you can assign the secondary structure information
through an atom selection using the "structure"
property. check out the sscache script in the
vmd script library for an example of how to use that.

cheers,
    axel.

>
> 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
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.