VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 27 2005 - 16:39:24 CST

Daniel,
  Thanks for the note. I fixed a couple of memory leaks that used
to exist in the old versions of VMD, can you try the same selection
on one of the VMD 1.8.3 test builds and let me know if you experience
the same problem still?:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 26, 2005 at 07:53:55PM -0500, Daniel Han wrote:
>
> Hello VMDers,
> I am running a script that counts the number of contacts a residue has.
> I wanted to limit the contacts, to only those that were near the
> sidechain and not the backbone.
>
> While the two commands below, produce the same results:
> set nearby [atomselect $mol "$seltext2 and within $dist of ((resid
> $residue and not hydrogen) and (not backbone))" frame $i]
> set nearby [atomselect $mol "$seltext2 and within $dist of ((resid
> $residue and not hydrogen) and (sidechain))" frame $i]
>
> The second command uses up a large amount of memory, and the memory
> usage will stay high even after the script is complete.
> On the other hand, the first command uses a small to no amount of memory
> at all, but takes much longer for the script to complete.
>
> I imagine it has to do something with short circuiting of commands ...
> any ideas?
>
> Danny.
>
> 

-- 
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              
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