From: John Stone (
Date: Wed Aug 30 2017 - 14:50:24 CDT

  Apparently your email arrived while I was away at Siggraph, and I missed
answering upon my return. If you know what voxel(s) you're interested in,
the cartesian coordinates are easily computed by multiplying the voxel
x/y/z indices by the grid spacing, and adding that to the cartesian coordinate
of the 0/0/0th voxel. You didn't specify what file format this volume is
stored in so it's hard to give further advice there. VMD doesn't have
a text mode analytical interface for this particular type of query for
a loaded volume, although it would be trivial to add since it computes
the cartesian coordinates for half of the things you would do using
volumetric data, so the math for doing that calculation is already there.

Best regards,
  John Stone

On Thu, Aug 03, 2017 at 01:30:30PM -0400, Daniel Strahs wrote:
> Hello all:
> We have a water density map calculated from a simulations; the voxel
> elements represent the frequency of oxygen atoms at a given location.
> We can visually see some high-frequency hydration sites, and would like to
> know what the spatial coordinates (x,y,z) of these elements.
> Is there any method for VMD to report out the information of a specifc
> voxel(s) from a volume loaded into a molecule?
> Thank you! If there isn't, I can always find another approach (like
> Octave).
> --
> Daniel Strahs
> Associate Professor
> Department of Biology
> Pace University, NYC

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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