VMD-L Mailing List

From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Fri Jul 27 2012 - 12:41:51 CDT

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