From: Ajasja Ljubetič (
Date: Tue Jun 28 2011 - 12:48:11 CDT


You could write a TCL script that would set the user field of the waters to
one if they are inside the cone and zero if they are outside, for each frame
of course. Then you could create a VDW representation with the selection
text "user>0", making sure that the update selection every frame is

Best regards,

On Tue, Jun 28, 2011 at 18:34, J. Nathan Scott <> wrote:

> 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