[Chimera-users] visualizing potential with volume data

Christos Deligkaris deligkaris at gmail.com
Mon Feb 24 11:57:41 PST 2020

dear all,

I have obtained a cube file from NWChem with the electrostatic
potential around a molecule. I visualized the molecular surface using
Actions->Surface->Show and then colored it using the volume data
(followed instructions
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html in
tools->surface color (electrostatic surface coloring)) .

Since I do not have my data stored in a potential file, can I still do
the surface offset? The chimera tool webpage discusses why that is
preferred than showing the potential on the solvent excluded surface
and it seems to me that option to not be available with volume data.

Also, my surface does not look like the electrostatic potential
surface shown here:
. The molecular surface we get with Action->Surface->Show seems to be
constructed with greater atomic radii than the one shown in that
image. I am not sure how important that is though. Is there a way to
ask Chimera to visualize the electrostatic potential volume data with
the same options Chimera would use if it was reading a Delphi, PBS

Best wishes,

Christos Deligkaris, PhD
Assistant Professor of Physics

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