VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri Dec 26 2014 - 07:20:29 CST

Hi Rebecca,

There isn't a way of getting more detailed information beyond looking
into the source code.

rc |= draw_protein_ribbons_old(framepos, bres, brad, ribbon_width, use_cyl);
   rc |= draw_nucleic_ribbons(framepos, bres, brad, ribbon_width,
use_cyl, 0, 0);
   rc |= draw_base_sugar_rings(framepos, bres, brad, ribbon_width, use_cyl);

   // XXX put the more specific error messages back in here if we feel
   // that they are helpful to the user.
   if (rc != 0) {
     if (emitstructwarning())
       msgErr << "Warning: ribbons code encountered an unusual
structure, geometry may not look as expected." << sendmsg;
   }

What this means is that one of those three methods failed to draw
things, and as written, there is no way to determine which one. What is
in your system (ideally you could share a pdb code...)? Is it just
protein, or is it some combination of protein, DNA, or sugars? I've seen
many different reasons why these methods fail, so there isn't one
specific problem that causes this. Generally, non-sequential resids
cause problems, or if there are any negative resids (particularly in DNA).

-Josh Vermaas

On 12/25/14 11:15 PM, Rebecca Taylor wrote:
> Hello everyone, I'm converting multiple PDB files into ribbon models
> ('new ribbons') and thereafter generating triangular meshes. I've
> scoured the previous posts for this topic, but I can't find anything.
>
> I get the following error when a ribbon isn't completely rendered:
> "ERROR) Warning: ribbons code encountered an unusual structure,
> geometry may not look as expected."
>
> I'd love to know the residue ids for the residues NOT rendered.
> Basically I want to know where the gaps are, but this information
> isn't an output. Is there some command I can issue to get VMD to
> output more information about each error?
>
> Many thanks and happy holidays,
> -rebecca
>
> --
> Rebecca Taylor
> Post Doctoral Fellow
> Spudich Lab (spudlab.stanford.edu <http://spudlab.stanford.edu>)
> Biochemistry
> Stanford University
> 650-319-5534