VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 19 2015 - 14:39:00 CDT

Hi,
  I don't know anything specifically about the particular analysis
you're trying to use, so I can only answer in general:
  If you have no negative values in the density map, then
you can't possibly view a negative isosurface, so I think the
question you must ask is why you have no negative values coming
from your analysis?

Cheers,
  John

On Wed, Aug 19, 2015 at 11:40:08AM +0300, Ozan Dernek wrote:
> This info pops up when I load the volumetric map:
> Info) Analyzing Volume...
> Info) Grid size: 108x108x108 (19 MB)
> Info) Total voxels: 1259712
> Info) Min: 0.012902 Max: 3.427300 Range: 3.414398
> As I understand I cannot use any value less than Min. value. Thats why I
> cannot see any isosurface for the negative isovalue. If that is the
> situation, how can I visualize my Bader charge analysis ?
> By the way thanks for your kind attitude,
> Regards,
> Ozan Dernek
> 18 AÄ*u 2015 tarihinde 18:09 saatinde, John Stone <[1]johns_at_ks.uiuc.edu>
> Å*unları yazdı:
>
> 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
> [2]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
> [3]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [4]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. http://www.ks.uiuc.edu/~johns/
> 4. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
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/