[Chimera-users] Electrostatic Potential based on Poisson-Boltzmann using APBS

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 17 07:21:10 PDT 2015


Hi Leila,
Well, “nan” generally means the value is out of range, so one possibility is that your map from APBS does not cover that part of the surface. If you did coloring, it might also show this.

Besides a problem with the map or its placement relative to the surface, a second possiblity is that the script is too old and has stopped working.  However, the feature was added to Chimera in 2011, so no reason to use that script anyway. Just show the Options in the Surface Color (Electrostatic Surface Coloring) tool and turn on "Report value at mouse position”:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>

I just tried this option.  After I clicked Color to apply the coloring, the value-reporting works fine for me, giving the potential value and the XYZ coordinates of the surface point in the status line at the bottom of the Chimera window. 
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 17, 2015, at 1:40 AM, leila karami <karami.leila1 at gmail.com> wrote:

> Also, I used surfvalues.py script. After opening the this script, I encountered with:
> 
> tmpgi8ixd.dx value at surface point = nan
> 
> When I put mouse cursor on the different points of surface, no potential value are seen.
> 
> Why is the reason of this state?
> 
> Best,
> Leila




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