VMD-L Mailing List

From: daniel aguayo (bioquimico_at_gmail.com)
Date: Tue Mar 06 2007 - 14:28:24 CST

That is the solution i'm using.
but.. anyone know a way to calculate the best axis of a pore
Tks a lot.

On 3/6/07, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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
> 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/ Fax: 217-244-6078
> 

-- 
saludos desde el fin del mundo