From: Strahs, Dr. Daniel Bernard (
Date: Sun Jun 02 2019 - 19:13:53 CDT

Or prepare a 3D probability density and import it as a surface. You could do several (one for each region), and import them as the needed surface. Color and opacity would be controlled within VMD.

I think a text format, like used for opendx, might be what you're looking for.

From: <> on behalf of Abolfazl Musavi <>
Sent: Saturday, June 1, 2019 10:58 PM
Subject: vmd-l: how to draw boxes with semi-transparent sides

Dear all,

I want to draw several cubic boxes to separate different regions in the simulation box. I want their sides to be semi-transparent and with different colors. I do not want to draw a cube by lines because then there will not be any side surfaces.

I would be appreciated if anyone could tell how to do that in VMD.