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APBS/Electrostatic potentials


- To display two electrostatic maps (1 and 3) at the same time (same session), type:
load pdbset1.pqr load pdbset_1.dx load pdbset3.pqr load pdbset_3.dx ramp_new ramp1, pdbset_1, [ -3, 0, 3] ramp_new ramp3, pdbset_3, [ -3, 0, 3] show surface set surface_ramp_above_mode set surface_color, ramp1, pdbset1 set surface_color, ramp3, pdbset3
The surface_ramp_above_mode setting colors surfaces based on the potential that would be felt by an atom in contact with the surface, as opposed to the potential at the molecular surface itself (which is less meaningful, since no atom could ever feel such a potential)
Example:

Surface representation of hCKPChol colored on the basis of the electrostatic potential of the molecule (ranging from − 15, red, to + 15 kT/e, blue) calculated byAPBS as implemented in Pymol.

Reference 
Malito et al. 
Elucidation of human choline kinase crystal structures in complex with the products ADP or phosphocholine 
J Mol Biol (2006) vol. 364 (2) pp. 136-51