VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 12 2012 - 10:42:53 CDT

Hi,

On Thu, Jun 28, 2012 at 03:22:29PM +0200, FX wrote:
> Hi all,
>
> Two things have been bugging me about displaying isosurfaces extracted from volumetric data (cube file) in VMD, as well as volume slices:
>
> 1. Is there any way to plot the isosurfaces with their two sides painted in different colors? In the case of open volumes (such as accessible space in a periodic unit cell), this is a great visual cue for distinguishing the interior and exterior of the surface. Is it something that could be patched easily? I should mention that I tried to achieve that by plotting two different isosurfaces, with different color and close isovalues, but this is not extremely stable, and the surfaces obtained sometimes intersect, yielding patches of the wrong color.

It isn't possible to do this in VMD yet, but it's on my TODO list. The main
issue is that not all of the renderers are capable of using different colors
or material properties for two-sided lighting/shading. So, while I can make
this work for OpenGL and for Tachyon renderings, most likely it would not be
supported by other tools such as POV-Ray, and many of the commercial renderers.
Most scene file formats don't have a way to express two-sided lighting/shading
parameters.

> 2. It seems that trying to display periodic images of the main isosurface (even though it has a well-defined box) doesn't work. Is that expected? Again, is there a workaround?

I'll have to ponder whether or not there's a workaround. Let me get back to
you about this issue.

> 3. How can the color scheme for a VolumeSlice of my volumetric data be changed? I'd like it to go between colors other than blue, white and red.

Choose a different VMD color scale, or use a user-defined color scale.

If you search the VMD-L list archive, you will find that I've posted various
example scripts for user-defined color scales, such as the Matlab style
color schemes...

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078