VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 18 2011 - 11:48:01 CDT

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 

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