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

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 17 11:00:05 PDT 2015

Hi Leila,
(1) The “report values” option already gives you the potential value.  It gives 4 values: electrostatic potential, x coord, y coord, z coord.  In general, videos may show an older version of a script and/or Chimera, so things may be different now.  We try to keep the “User’s Guide” HTML documentation that is connected to the Help menu current, but other types of documentation may be for older versions.

(2) Usually a picture isn’t enough information, we would need the data to tell for sure (the dx file and the PDB file). However, I’m pretty sure it is a problem with your map values, which are the first things to check when the coloring is weird.  Does mouseover report reasonable potential values (mostly small negative and small positive)?  If your values are not reasonable, for example “nan”, then it is a problem with the map.  Probably you did not add hydrogens and charges before running APBS.  It is necessary to do both of those things first, and also other structure cleanup may be required.  There are few options for which tools you use for these steps, so I refer you to the manual for more information and links:

The APBS graphical interface in Chimera does check for charges and complains if you try to run it without them.  However, the “apbs” command does not do this error checking.  Most people use the graphical interface first, then switch to the command for scripting after they know the process.  

One option for processing before APBS is PDB2PQR (in menu under Tools… Structure Editing, or command “pdb2pqr”). PDB2PQR will open an additional copy of the structure that has charges.  You would then need to run APBS (in menu under Tools.. Surface /Binding Analysis, or command “apbs”) on the NEW copy of the molecule, not the original copy that still doesn’t have charges.

I hope this helps,
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 8:35 AM, leila karami <karami.leila1 at gmail.com> wrote:

> 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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