VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 26 2011 - 21:43:49 CDT

Hi,
  Sorry for the delayed reply. It is possible to define an atom selection
based on the value of the voxel associated with the coordinate of each atom,
e.g. to select atoms that fall into the region of space occupied by a voxel
with a value greater than, less than, or within some range of voxel values.
I don't think this is really what you're after, but it's not entirely clear
to me what you're trying to compute from the decription you gave.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Oct 23, 2011 at 03:24:20PM -0400, Michael LeVine wrote:
> Hi all,
>
> I am looking to draw a volume, and then count the number of residues
> in that volume. For example, if I create an occupancy volume for all
> resname A, I would like to then see how many resname B are within that
> volume, but I can't seem to find a way to select residues based on
> being within a volume. Also, I see that when I create a volume, the
> VMD terminal displays the number of voxels. I'd like to write a script
> that creates a volume for each frame of my trajectory and outputs the
> number of voxels. Is their a command which can output the number of
> voxels in a volume, like $sel num outputs the number of atoms in a
> selection? Sorry if this question isn't clear, I am new to using tcl
> scripts in VMD to calculate properties, and have limited programming
> experience. Thank you!
>
> Michael V. LeVine
> Weill Medical College of Cornell University
> Graduate School of Medical Sciences
> Program in Physiology, Biophysics & Systems Biology 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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