From: Axel Kohlmeyer (
Date: Fri Mar 02 2007 - 11:48:20 CST

On Fri, 2 Mar 2007, Adrian Roitberg wrote:

AR> Dear all,

dear adrian,

AR> I hacked a bit one of Axel Kohlmeyer wonderful scripts to be able to
AR> visualize gaussian cube files in sequence.
AR> His original script did electron density, but I need the HOMO vs time.
AR> The problem is that I need to create 3 representations, 1 for the
AR> molecule itself, one for positive isosurfaces and one for negative.
AR> I can do that. However, they both come out in gray color, while I need
AR> them, let's say red and blue.
AR> I also do not know how to make them transparent.

just after you created the licorice rep insert a:

mol material Transparent

and all successive representations will use the Transparent
material (or use Glass, Glossy, etc). to make your molecule
look better, you may want to use

mol material Glossy

for the licorice rep.

the color should actually work but it seems that
mol modrep uses the current color state (and material)
so you need to update those every time you update the rep.
also note that only the follwing gives a solid surface.
if you change the last number to an 1.0, you'll get a wireframe.

mol representation IsoSurface -0.02 0.0 0.0 0.0
mol addrep top

you should get a nice solid transparent surface.

AR> I can do this for single snapshots with no trouble.

please try the attached modified version of the script.


AR> Any help is appreciated.

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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