From: Iman Salehinia (isalehinia_at_gmail.com)
Date: Thu Jan 22 2009 - 18:21:59 CST

Dear John,

One of my friends using VMD had a problem for his modeling. The number of
atoms in his model is about 1000000 and VMD didn't work with this amount of
atoms (his memory is 4 GB). Will this problem be solved in the new version
of VMD? AtomEye doesn't have this problem, so this problem really forces
anyone to not to work with VMD, actually when the number of atoms is big!

Regards,
Iman.

On Thu, Jan 22, 2009 at 9:33 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> These aren't accessible via the scripting interface in existing
> versions of VMD, because VMD versions 1.8.6 and earlier did not
> store this information internally. The next version of VMD,
> version 1.8.7 (currently in development), stores this information,
> and will add new query routines for this purpose. I haven't yet added
> the query routines but will let you know when this feature has been
> added to a test version. I'm completing the upgrade to Tcl 8.5.x at
> present, and will likely add the new query routines for
> angles/dihedrals/etc
> shortly thereafter.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Jan 21, 2009 at 04:29:54PM -0500, Maxim Paliy wrote:
> > Dear VMD experts
> > I want to access the lists of bonds angles dihedrals etc,
> > i.e. the information normally contained in the PSF file,
> > after the PSF file has been read into VMD.
> >
> > Sorry if this question is dumb, but I cannot find
> > what variables all these data are stored in..
> >
> > Thanks a lot in advance for any suggestions,
> > Maxim
>
> --
> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>