Some sample images produced using Michael Lerner's APBS plugin for PyMOL:

Email questions to cmura AT ucsd DOT edu.


Electrostatic potentials were calculated by APBS 'on-the-fly' in PyMOL (via the "APBS Tools" wizard) and then displayed (via the "Electrostatics" wizard) for this small protein (<50-aa residues). The bounding box used by the PBE solver is shown, and the electrostatic potential is mapped onto a transparent VdW molecular surface of the same peptide:

pymol_apbs_ex1_view1.png

Same potentials as above displayed as isopotential surfaces contoured at levels of +2 kT/e (blue) and -2 kT/e (red):

pymol_apbs_ex1_view2.png

This second set of illustrations is similar to the above, but for a larger protein (~550-residues total in the dimer). The color ramp for the potentials is indicated at the bottom of this GRASP-like representation. Although probably unnecessary, the OpenDX-formatted electrostatic map for this much larger system was pre-calculated in a standalone APBS run and then loaded into PyMOL via the load_dx() function.

pymol_apbs_ex2_view1.png

NOTE!!!
This second image of positive (blue) and negative (red) transparent isopotential surfaces involved direct visualization/display of the LARGE OpenDX maps (>90M!) rather than projection of values onto the molecular surface. Therefore, the scene is NOT ray-traced due to memory limitations (decreasing/increasing PyMOL's hash_max doesn't seem to help)...

pymol_apbs_ex2_view2.png