VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 06 2006 - 18:06:51 CDT

Ravi,
  It's quite possible that it's the Biograf plugin doing something wrong,
if that's the only case when you observe trouble. If you've got some
Biograf files that you've worked on that exhibited the problem, I'd
be happy to run the Biograf plugin (and VMD itself) through valgrind/Purify
to see if there's anything weird going on there...

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Oct 06, 2006 at 03:57:57PM -0700, Ravinder Abrol wrote:
>
> Hi John,
> I am running it on Windows platform and since the problem is not
> reproducable, I don't have a test case yet. This has happenned to me with
> many files. I am loading bgf (Biograf) files. Could they be causing the
> problem inconsistently?
> Thanks,
> Ravi
>
>
> -------------------------------------
> On Fri, 6 Oct 2006, John Stone wrote:
>
> >
> > Ravi,
> > I've never seen or heard of this sort of problem before, to me that
> > sounds like some sort of memory corruption issue. Do you have a test
> > case that reproduces the problem with high probability? As you can imagine,
> > thousands of VMD users perform the operations you're describing. The only
> > question is what specific representations they use and what other things
> > they might be doing with their structures. Which platform are you running on?
> > I actually wonder if it's a system level runtime library issue of some kind.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Thu, Oct 05, 2006 at 01:20:28PM -0700, Ravinder Abrol wrote:
> > > Hi All,
> > > This problem doesn't occur consistently, so I don't know how to fix it.
> > >
> > > With a fresh VMD start, when I load a protein with helices, all helices
> > > are displayed correctly using all graphical representations. After a few
> > > interations of deleting molecules and loading new molecules, a few of the
> > > helices (not all) stop being displayed (almost randomly) in [Trace to
> > > NewCartoon] representations. [Line to Licorice] representations display
> > > fine. When I close VMD and start a fresh session, everything is ok again.
> > > I have encountered this problem in both VMD1.8.4 and VMD1.8.5. I haven't
> > > tried older versions for this.
> > >
> > > Any solutions will be appreciated.
> > > Thanks in advance,
> > > Ravi
> >
> >
>
> --
> ________________________________________________
>
> Ravinder Abrol
> 139-74, Beckman Institute
> Division of Chemistry and Chemical Engineering
> Caltech, Pasadena, CA 91125
> Phone: 1.626.395.8143
> Fax: 1.626.585.0917
> Email: abrol_at_wag.caltech.edu
> ________________________________________________
> 

-- 
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