VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 18 2011 - 12:36:30 CDT

Hi,
  You can't "trick" VMD, the information is either there, or it's not.
You could make "fake" oxygens, and then VMD could use them, but I don't
see how you would get very far with this, since you also don't have
anywhere near enough information for STRIDE to be able to compute
the secondary structure either. You could provide the seconary
structure assignment manually using some atom selections, and that
would get you closer, but you still need the "O" atoms to get the
correct ribbon orientation for the alpha helices, beta sheets, etc..

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 18, 2011 at 01:20:30PM -0400, Mert Gür wrote:
> 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 Gu:r 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 

-- 
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