From: J. Nathan Scott (
Date: Tue Jun 28 2011 - 11:34:19 CDT

Hello VMD users,

I have a Tcl script I wrote a while back to do some per-atom
per-timestep coloring (based on previously calculated data) of water
molecules around a residue of interest depending on the electric field
they generate at a point in the protein. I have recently written a new
program that analyzes my coordinate files and determines which water
molecules are within a conic volume emanating from a residue in the
protein for each frame in my trajectory. Essentially now I have a
ASCII file with the resids of the water molecules contained within the
conic volume, with each line of the file belonging to a single frame.

What I would really like to do now is have the molecules within the
conic volume represented using VDW, while all other waters would use
CPK or anything else. The resids change each frame of course. Does
this sound possible and/or practical? I suppose what I am really after
is per-atom per-timestep representation. From what I can tell this
doesn't seem to be built in to VMD, but I thought I'd ask here for
advice before junking the idea. Being able to represent these waters
within the conic volume differently would be of great aid in our
analysis I think.

J. Nathan Scott, Ph.D.
Postdoctoral Fellow
Department of Chemistry and Biochemistry
Montana State University