VMD-L Mailing List

From: Ozan Dernek (ozandernek_at_gmail.com)
Date: Wed Aug 19 2015 - 03:40:08 CDT

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 Ağu 2015 tarihinde 18:09 saatinde, John Stone <johns_at_ks.uiuc.edu> şunları 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
> 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/