[Chimera-users] Electrostatic Potential using APBS .dx file

Tom Goddard goddard at sonic.net
Mon Mar 26 11:46:03 PDT 2012

Hi Soca,

   Sounds like you are doing everything right.  That makes me suspect 
that something is wrong with your APBS file -- like all the potential 
values are zero.  To see what the distribution of the potential values 
are, open the APBS file and then use menu Tools / Volume Data / Volume 
Viewer, and click on the histogram (empty rectangle in the middle of the 
volume dialog).  That will show a histogram of the potential values.  
You can move the vertical bar on the histogram to see what the potential 
value is at that position.  Check if -5 to 5 is a reasonable range.


> Hello,
> I have been attempting to generate a electrostatic surface map in 
> chimera using an external potential file generated from APBS (.dx).
> I understand that Chimera has an internal surface calculation protocol 
> via Coulombic Surface Coloring, however, I would like to use the 
> Electrostatic Surface Coloring.
> However, when I open my molecule (PDB), show surfaces, and choose its 
> MSMS main surface to color by electrostatic potential using the .dx 
> file, the surface map is not the red, white, blue that I have set in 
> my parameterts under Surface color. Everything turns to grey. My other 
> parameters include:
> red -5, white 0, blue 5. Colors 3. Palette Red-Blue. Surface offset 1.4.
> I feel as though I am missing something trivia that would allow me to 
> generate the surface image I want, however I am lost after may 
> searches for advice through the forums and tutorials.
> Please let me know what I am missing.
> Thanks
> Soca
> -- 
> Ardian Soca Wibowo, Ph.D.
> Postdoctoral Associate
> Dann Research Group
> Department of Chemistry
> Indiana University

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