VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 10 2004 - 16:38:23 CDT

Hi,
  Just to followup on this, I've found and fixed the problem that
Randall discovered, there was an off-by-one bug in the scaling of
isosurface vertices to the size of the full box, thus the resulting
surface is (1.0 / grid resolution) % smaller than it should be in
VMD 1.8.2. VMD 1.8.3 will include this fix. The bug is difficult to
detect unless you use a low resolution grid, for high resolution grids
the effect is much less obvious.

Thanks to Randall for catching and reporting this!

  John

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