VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 28 2004 - 15:11:03 CDT

Dear Randall,
  Unless you've chosen a grid resolution with an odd number of sample
points, and the grid is precisely centered, the result you mention would
not be surprising, since the grid points and thus the borders of the
volume would not be concentric with the sphere you generated density
values from. I assume you're using VMD 1.8.2? Are you using the latest
version of the plugins, or an older version? (we fixed a bug in the PLT
plugin a while back, as I recall)

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jun 28, 2004 at 10:14:20AM -0500, Randall Hall wrote:
> Hello, I have a question about how VMD is displaying an isosurface I
> have created in .plt format. As a test, I created a gaussian density
> centered at the origin of the box. When the isosurface is displayed, I
> see a sphere for large isovalues, as I expect. When I reduce the
> isovalue, the sphere grows in size until the sides bump into the walls
> of the box and "holes" develop in the sphere. What is surprising to me
> is that the holes do not appear symmetrically. It appears that the
> isosurface is truncated before it hits the wall in positive x, y, and z
> directions. That is, the sphere never reaches 3 of the size box sides.
> Can anyone explain why this truncation is happening? thanks
>
> Randall W. Hall
> Professor of Chemistry
> Louisiana State University
> Baton Rouge, LA 70803-1804
> Email: rhall_at_lsu.edu Web: http://chemistry.lsu.edu/hall
> Phone: 225-578-3472 Fax: 225-578-3458
> 

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