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. Tom
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