VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 06 2007 - 12:43:42 CST

Hi,
  You could try trimming your atom count by using VMD's atom selections
to slice off structure that's on the exterior (away from the pore),
if that would get you down below 50,000 atoms.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 06, 2007 at 01:11:23PM -0500, Subramanian Vaitheeswaran wrote:
> I am trying to identify and select the atoms lining the channel of a large (>60,000 atoms) PDB structure. The program hole seems well suited for this purpose, but the max. number of atoms it can handle appears to be 50,000. This is the error msg I get:
> ***ERROR***^G
> Have exeeded array bound ATMAX 50000
> (the maximum no. of atoms allowed)
> HOLE: normal completion
>
> The source code is not included in the distribution and emails to the host site have not got a response. Any ideas on how I can do this (locate channel-lining atoms)? Is there a different plugin or stand alone program for this task? Any help is much appreciated.
>
> S. Vaitheeswaran
> (Vaithee) 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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