[Chimera-users] Electrostatic Potential using APBS .dx file
goddard at sonic.net
Mon Mar 26 15:05:53 PDT 2012
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
> I figured the issue was something trivial.
> Thanks for your help nonetheless.
> 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.
> 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
> Please let me know what I am missing.
> Ardian Soca Wibowo, Ph.D.
> Postdoctoral Associate
> Dann Research Group
> Department of Chemistry
> Indiana University
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