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