VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jul 27 2012 - 12:50:45 CDT

Brian,
  Off the top of my head, I seem to remember that the breakage started
at something like 2,000 molecules. If you want I can do a test later
this afternoon after I'm done with meetings, but that's my recollection.

Cheers,
  John

On Fri, Jul 27, 2012 at 10:41:51AM -0700, Bennion, Brian wrote:
> Hello John
>
> Thanks for the info. Do you about how many molecules brakes the fltk pulldown menus?
>
> I can work around this by figuring out a way to load in each molecule in a separate vmd session, find the desired rotation, and then render that frame to tachyon file. After all the tachyon files are made I can run tachyon in embarrassingly parallel mode and finally get my movie.
>
> brian.
>
>
>
> ________________________________________
> From: John Stone [johns_at_ks.uiuc.edu]
> Sent: Friday, July 27, 2012 9:51 AM
> To: Bennion, Brian
> Cc: vmd_at_ks.uiuc.edu
> Subject: Re: possible problem with graphics rep gui under with large numbers of molecules
>
> Brian,
> This is a bug in FLTK. I'd been doing work on the VMD GUIs to
> make them usable for tens of thousands of molecules, but quickly discovered
> that FLTK itself essentially breaks when browsers or listboxes have more
> than a certain number of entries in them.
>
> My thought is that I could permanently fix this problem by
> redesigning the VMD graphical interface to display only a subset
> of them in the GUI controls at a time, and the user could essentially
> page-up/page-down (so to speak) through groupings of N molecules/selections,
> such that it would be below the number that causes problems for FLTK.
> Perhaps an even better approach for such large numbers of molecules would
> be to allow the user to apply "molecule selections" to them, so only the
> ones the user is interested in would show up in the GUI at any given time.
> This would let you load the entire PDB, for example, and then "search" for
> the molecules that matched some particular criteria, and only populate the
> GUIs with those. I'd be curious to hear your thoughts on this since its
> somewhat related to your current problem.
> I haven't had a chance to begin doing any work on this yet, but its on
> my long-term TODO list.
>
> The short-term avenue for addressing this problem would be to try out
> the latest FLTK revs and see if they've cured this bug/limitation, or
> if this is still a problem in the latest versions. I am willing to
> give that a spin and see if it gets us anywhere. Maybe I can try it
> mid-next-week.
>
> If you can tell me more about what you're doing, maybe there's some other
> approach I haven't already listed that would work for your case.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Jul 26, 2012 at 12:44:05PM -0700, Bennion, Brian wrote:
> > Hello John,
> >
> > It appears that the graphics representation gui become unresponsive with large numbers of molecules loaded.
> >
> > My example is the display and rendering of 3000 molecules of differing number of atoms.
> >
> > If I want to change a rep on one of those individual molecules (ie TOP) I would normally click on the Selected Molecule window and scroll to the molecule for which I would like to change the reps.
> >
> > This is not what happens, in fact nothing happens. It is just stuck on the very last molecule which happens to be the protein providing the backdrop for the other atoms I am rendering.
> >
> > The vmd version is 1.9.2a7
> >
> > Thanks
> > Brian
> >
> > Biosciences and Biotechnology Division
> > Lawrence Livermore National Laboratory
> > 7000 East Ave Livermore California 94550
> > phone:925-422-5722
> > fax:925-424-4334
> >
> >
>
> --
> 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