VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 06 2008 - 11:33:28 CDT
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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
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