VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 03 2006 - 23:52:24 CDT

Mario,
  I'll have to look at this more closely, but to make a long story shorter,
VMD 1.8.5 is a bit pickier with nucleic acid structures than VMD 1.8.4 was,
as a result of changes I made that allow it to do a better job drawing
nucleic acid structures. A side effect of these changes is that structures
with unusual terminal residues that were accepted by the older versions of
VMD will not be marked as nucleic acid fragments, and will thus be skipped
when secondary structure representations such as tube/ribbon/cartoon etc are
drawn. This is essentially the same issue that occurs with some of the new
RNA structures, and I'm working on making VMD 1.8.6 more flexible so it will
do the right thing even when it encounters unusual residues.

  John

On Mon, Oct 02, 2006 at 09:59:08AM +0200, Mario Valle wrote:
> I'm trying to determine if the following error is due to VMD or is the data erroneous.
> To reproduce:
> 1) download PDB 1D66
> 2) load it in VMD (tried in 1.8.5 on Linux)
> 3) select: "chain D E"
> 4) select representation "New Tube". Nothing will be draw and the following error appears
> on the console:
>
> ERROR) Internal error in draw_tube for P atoms: last_resid = 1 but no first atom was added.
> ERROR) Tubes may be incomplete.
>
> Instead the tube appears correctly on Windows under 1.8.4
> I suspect the data contains some error that makes VMD misbehave. Prof. Eric Martz told me
> this file is a good example of erroneous data in a public repository, but my chemistry is
> not at the level to understand and find the error...
>
> Thanks for your help!
> mario
>
> --
> Ing. Mario Valle
> Visualization Group | http://www.cscs.ch/~mvalle
> Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60
> v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82 

-- 
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