VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 18 2015 - 10:09:40 CDT

Hi,
  When you load your volumetric map, what does VMD say about the
data range? When you first load your map, I would expect you to see
something like this:
  Info) Analyzing Volume...
  Info) Grid size: 169x136x138 (48 MB)
  Info) Total voxels: 3171792
  Info) Min: 0.000000 Max: 3.071364 Range: 3.071364
  Info) Computing volume gradient map for smooth shading

The "Min: xxxx" value is the part of interest if you're not seeing any
isosurface when you use a negative isovalue. What is the minimum value
in your dataset?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 18, 2015 at 05:31:29PM +0300, Ozan Dernek wrote:
> Hello,
>
> I am trying to visualize my Bader charge calculation. I stumbled upon a few web sites that say it can be done by creating two isosurfaces, and assigning same values with opposite signs to isovalue to them.
> However, I cannot get any visual from the isosurface that i assigned a negative isovalue. For example, for the first one I set the isovalue 0.06, and the second one -0.06 . As i said, the second one gives no visual.
> My question is, what does the isovalue defines here, and what can i derive from this fact that I have nothing on the negative isovalue.
>
> Regards,
> Ozan Dernek 

-- 
NIH Center 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/