VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 18 2012 - 09:57:28 CDT

Hi,
  I don't know what that error message means, but it shows up in two places
in the STRIDE source code in the source file fillasn.c (see attached file)
I'm not familiar with the minutiae of the STRIDE source code and don't have
time to dig into this personally, but in principle the code is here and one
may be able to figure out what's going on in this specific case by looking
at the two places where that message can be generated.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 17, 2012 at 11:21:47AM -0400, Sarah Richards wrote:
> Dear Mr. Stone,
>
> I haven't been able to figure out why STRIDE behaves differently based on the chain names of each strand, but I did notice something else. When I change the Representation to Secondary Structure, VMD shows this:
>
> Info) Using plugin pdb for coordinates from file betasheet.pdb
> Info) Finished with coordinate file betasheet.pdb.
> Info) In any publication of scientific results based in part or
> Info) completely on the use of the program STRIDE, please reference:
> Info) Frishman,D & Argos,P. (1995) Knowledge-based secondary structure
> Info) assignment. Proteins: structure, function and genetics, 23, 566-579.
> Ne tot variant.. Par /var/tmp/tmp.1.pmQLzi
> Ne tot variant.. Par /var/tmp/tmp.1.pmQLzi
> Ne tot variant.. Par /var/tmp/tmp.1.pmQLzi
> Ne tot variant.. Par /var/tmp/tmp.1.pmQLzi
> Ne tot variant.. Par /var/tmp/tmp.1.pmQLzi
> Ne tot variant.. Par /var/tmp/tmp.1.pmQLzi
> Ne tot variant.. Par /var/tmp/tmp.1.pmQLzi
> Ne tot variant.. Par /var/tmp/tmp.1.pmQLzi
> Ne tot variant.. Par /var/tmp/tmp.1.pmQLzi
> Ne tot variant.. Par /var/tmp/tmp.1.pmQLzi
> Ne tot variant.. Par /var/tmp/tmp.1.pmQLzi
> Ne tot variant.. Par /var/tmp/tmp.1.pmQLzi
> Ne tot variant.. Par /var/tmp/tmp.1.pmQLzi
> Ne tot variant.. Par /var/tmp/tmp.1.pmQLzi
>
> I haven't been able to find any mention of "Ne tot variant" on the mailing list. Any help would be greatly appreciated.
>
> Thank you!
>
> Sarah Richards
>
>
>
> On Jul 12, 2012, at 11:24 AM, John Stone wrote:
>
> >
> > Sarah,
> > I believe the problem you're having is related to the chain name issue
> > you mentioned below. If I'm not mistaken, (I haven't had to look at the
> > STRIDE code for years, so this was after a quick reading of the code)
> > I believe VMD is writing a STRIDE input PDB file that doesn't reproduce
> > the original segment name or chain field as the chain field in the input PDB,
> > and this may be the reason for the behavior you see.
> > I would be curious to know why STRIDE decides to behave differently based on
> > whether the strands have the same chains or not.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Fri, Jul 06, 2012 at 09:16:04AM -0400, Sarah Richards wrote:
> >> Hello VMD users and developers,
> >>
> >> I am having a problem getting the correct secondary structure to show for a beta-sheet in VMD. I have arranged the beta-strands parallel and positioned the strands to allow for the correct hydrogen bonding. When I show the secondary structure in Representations, however, it does not show the yellow arrows for beta-sheet. When I built each strand (in MOE), I set the dihedrals for a parallel beta-sheet and I have double-checked that these are correct.
> >>
> >> I have previously built a beta-sheet with an antiparallel arrangement, and VMD displayed the correct beta-sheet secondary structure.
> >>
> >> I checked the secondary structure of the parallel beta-sheet in the Stride web interface (http://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py/) and found that the beta-sheet conformation is only shown when each strand has a different chain name. When I load this PDB in VMD, however, beta-sheet secondary structure is not shown. I have attached a PDB with a different chain name for each strand.
> >>
> >> I am using a VMD 1.9 for Mac (running Lion). I would greatly appreciate any help.
> >>
> >>
> >> Thank you,
> >>
> >> Sarah Richards
> >>
> >
> > --
> > 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
> 

-- 
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