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

leila karami karami.leila1 at gmail.com
Fri Jul 17 08:35:10 PDT 2015


Dear Elaine,

Thanks for your answer.

1) I turned on "Report value at mouse position" in Surface Color
(Electrostatic Surface Coloring) tool.

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 used this scripts from the following tutorial:

http://www.cgl.ucsf.edu/chimera/videodoc/SurfaceValues/index.html

Please note to the time 3:20 in this video in which there is following line
in the status line at the bottom of the Chimera window.

*.dx value at surface point = 0.78023.

What is the reason of this state? How to have value at surface point
instead of XYZ coordinates of the surface point.

2) Please answer my first question in mailing list:

I did following steps to obtain  Electrostatic Potential based on
 Poisson-Boltzmann using APBS:

open... pr.pdb
action... surface... show
to obtain *.dx file, I typed APBS in command line, after minutes, *.dx file
was created and
surface color window was opened, I pressed color tab.

Please see the figure in following link:
https://www.dropbox.com/s/99gjecypqu910hu/apbs.png?dl=0

Why are the colors black and white in the surface, instead of blue and red?
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