From: John Stone (
Date: Mon Apr 06 2015 - 11:36:37 CDT

  You didn't tell us much about what data you have loaded into VMD,
so it is hard to give a concrete suggestion for this question.
If you've loaded something like a density map (e.g. a Gaussian 'cube' file
or something similar), VMD doesn't directly associate regions of density with
the structure that may be loaded in the same molecule, because it doesn't
really know what the density represents. If you have separate density maps
for the different basins, then you could color them independently and the
structure could be colored via the usual atom selections and colorID
assignments. VMD doesn't have any built-in analysis for synaptic order
etc so you would be entirely dependent on having input data that has
already been characterized, e.g. via some external program.

  John Stone

On Tue, Mar 24, 2015 at 08:48:10PM -0400, Maria Ivanova wrote:
> To whom it may concern,
> I am trying to change colors for monosynaptic (blue) and bisynaptic
> (green) basins and core(red) basin using VMD. Could you explain me how it
> could be done.
> Thank you in advance,
> Maria

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