VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 06 2008 - 13:38:00 CDT

Cesar,
  In your case for 1Q71, the easiest solution is to use the
Extensions->Modeling->Automatic PSF Builder tool
(just click the "I'm feeling lucky" button at the bottom)
to build a complete structure. This cures the problem for me
with both VMD 1.8.6, and also with the the current test builds
of VMD 1.8.7. I'll have to investigate what it is that's upsetting
the structure analyzer in VMD, but given that you can use the
autopsf plugin to build a complete structure that displays correctly,
you've got a short-term solution to use in the mean time. I suspect
this may be an atom naming issue of some sort.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 06, 2008 at 02:01:49PM -0300, Cesar Luis Avila wrote:
> Dear John,
> Thanks for your fast and detailed reply. As you suggested, vmd is not
> recognizing the fragment as a protein while loading
> Fragments: 1 Protein:0 Nucleic:0
> How may I indicate vmd that this fragment is a protein? The structure
> that is giving me problems is 1Q71 from PDB.
> Best Regards
> Cesar
>
> John Stone escribió:
> >Cesar,
> > There's more involved in rendering secondary structure representations
> >than just the classification performed by STRIDE. Beyond that, the
> >structure must be recognized by VMD as either a "protein" or
> >"nucleic acid" according to the structure analysis VMD does when
> >the file is first loaded. You can determine what's going on with
> >that by looking at the output VMD prints when the file is loaded,
> >of particular interest is this line (a typical example):
> > Fragments: 1 Protein: 1 Nucleic: 0
> >
> >If you see a line that looks like this on the other hand, it
> >would indicate that VMD doesn't recognize the fragment as either
> >protein or nucleic acid, so it would not be drawable in any of
> >the ribbons or cartoon representations:
> > Fragments: 1 Protein: 0 Nucleic: 0
> >
> >Going further, in order to draw ribbons or cartoon representations,
> >VMD needs to be able to identify certain atoms within each residue
> >in order to compute the backbone spline and orientation vectors.
> >If VMD doesn't recognize or can't find the necessary atoms, it
> >may bail out and issue a warning that it can't draw the structure
> >for this reason.
> >
> >Last, VMD uses the secondary structure codes provided by STRIDE to
> >determine which cross-section shape to use when rendering the
> >backbone spline. VMD will still be able to render a ribbon
> >even if STRIDE aborts or is otherwise unable to assign secondary
> >structure codes.
> >
> >Since you're having trouble with both the ribbon and cartoon
> >representations, I suspect the cause of your problem is one of the
> >items I listed above, independent of what STRIDE says.
> >
> >If you send me the structure that's giving you trouble, I'd be
> >happy to take a look at it.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Wed, Aug 06, 2008 at 01:17:58PM -0300, Cesar Luis Avila wrote:
> >
> >>Hi all,
> >>I have a short peptide of 21 aminoacids for which I am trying to get a
> >>New cartoon representation. Even though STRIDE seems to work without
> >>problems, as seen from running the command on Tk console
> >>
> >>[atomselect top "name CA"] get structure
> >>C C C C C C E E E E E T T T E E E E E C C
> >>
> >>Nevertheless when I try to use any of the drawing methods Ribbons,
> >>NewRibbons, Cartoon or NewCartoon, I don't see anything rendered (empty
> >>screen). Which might be the problem? I am using vmd 1.8.6 on linux with
> >>Nvidia drivers.
> >>
> >>In line with the above question, is it possible to use this drawing
> >>representations with custom secondary structure information other than
> >>STRIDE? (perhaps derived from other tools).
> >>
> >>Thanks
> >>Cesar Avila
> >>
> >
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078