VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 07 2007 - 13:26:41 CST

Hi,
  You can use the volmap plugin to synthesize a density map. You can
then select atoms that correspond to a voxel with a certain range
of density values:
  http://www.ks.uiuc.edu/Research/vmd/minitutorials/selbyvox/

The problem in your case is that what you really need is a selection
method that allows you to select atoms that are within a certain
distance of a voxel with a particular density value/range, rather than only
atoms that are _on_ a voxel with that value/range. At present we don't
have an atom selection method that searches voxels within a particular
radius, but that's something we could possibly implement in a future
version of VMD.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 06, 2007 at 04:24:24PM -0500, Subramanian Vaitheeswaran wrote:
> Hi John,
>
> I have also been exploring vmd's volmap plugin. It looks like it can identify a channel as a region of low/zero density. Would it also be possible to write out a list of adjacent atoms?
>
> Thanks for your help.
>
> Vaithee
>
> ---- Original message ----
> >Date: Tue, 6 Mar 2007 15:01:33 -0600
> >From: John Stone <johns_at_ks.uiuc.edu>
> >Subject: Re: vmd-l: Locating channel using hole
> >To: Subramanian Vaitheeswaran <vaithee_at_umd.edu>
> >
> >
> >Hi,
> > You could do it radially from channel axis, or you could simply trim
> >the edges of the simulation box, whatever works and allows HOLE to run
> >and give correct results..
> >
> > John
> >
> >On Tue, Mar 06, 2007 at 03:34:09PM -0500, Subramanian Vaitheeswaran wrote:
> >> Thanks, that helps. You mean by specifying a cutoff distance from the channel?
> >>
> >> Vaithee
> >>
> >> ---- Original message ----
> >> >Date: Tue, 6 Mar 2007 12:43:42 -0600
> >> >From: John Stone <johns_at_ks.uiuc.edu>
> >> >Subject: Re: vmd-l: Locating channel using hole
> >> >To: Subramanian Vaitheeswaran <vaithee_at_umd.edu>
> >> >Cc: vmd-l_at_ks.uiuc.edu
> >> >
> >> >
> >> >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
> >
> >--
> >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 

-- 
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