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

Tom Goddard goddard at sonic.net
Mon Mar 26 15:05:53 PDT 2012

Hi Soca,

So the problem was the APBS potential file (.dx) was computed with a PDB 
that was not aligned to the PDB you were using for displaying the 
potential.  Glad you figured it out.


> Hi Tom,
> Thanks for your quick response. I believe I have figured out the 
> problem. I followed your suggestion and manipulated the volume Viewer. 
> As I did so, at first nothing happened...however, just changing views, 
> I zoomed out and found a volume mass non alined with the molecule to 
> which I hoped to show potential. (Please see attached image)
> I found out what my problem was however. As I generated my .pqr file 
> (PDB2PQR) for the .dx APBS, I failed to realize that the model (PDB) I 
> had used for file generation had different coordinates that the model 
> I was visualizing, since I had lined these molecules away from their 
> original coordinates. Once I figured that out, I was able to align 
> everything corrected and generate the electrostatic potential surface 
> map.
> I figured the issue was something trivial.
> Thanks for your help nonetheless.
> Soca
> On Mon, Mar 26, 2012 at 2:46 PM, Tom Goddard wrote:
>     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.
>        Tom
>         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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