VMD-L Mailing List
From: Davide Provasi (davide.provasi_at_gmail.com)
Date: Thu Aug 18 2011 - 13:00:15 CDT
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Hi-
one possible solution is to rebuild the backbone from the calpha positions.
a number of tools are available to do that.
for example http://www.pirx.com/pulchra/index.shtml
hope this helps,
Davide
-- Davide Provasi Dept. of Structural and Chemical Biology Mount Sinai School of Medicine Icahn Medical Institute Building 1425 Madison Avenue, Box 1677 New York, NY 10029-6574 Tel.:212-659-8618 Fax: 212-849-2456 On Thu, Aug 18, 2011 at 7:20 PM, Mert Gür <gurmert_at_gmail.com> 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 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 >> > >
- Next message: Axel Kohlmeyer: "Re: How can I draw secondary structures if I only have the carbon alpha coordinates"
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