Coulombic Surface Coloring Coulombic Surface Coloring icon

Coulombic Surface Coloring colors molecular surfaces by electrostatic potential calculated with Coulomb's law:

φ = Σ [qi / (εdi)]
φ is the potential (which varies in space), q are the atomic partial charges, d are the distances from the atoms, and ε is the dielectric, representing screening by the medium or solvent. A distance-dependent dielectric (ε = Cd where C is some constant) is sometimes used to approximate screening by implicit solvent.

The Electrostatic Surface Coloring tool is similar, but uses an electrostatic potential map previously calculated with any of several separate programs not included with Chimera. These continuum electrostatics programs perform calculations that are more complex and (if done correctly) more accurate than simple Coulomb's law approaches. However, a Coulombic potential may suffice for visualization.

See also: Render by Attribute, AddH, Add Charge, ResProp, Color Key

There are several ways to start Coulombic Surface Coloring, a tool in the Surface/Binding Analysis category.

The molecular surface(s) should first be displayed (using Actions... Surface... show or the command surface) and then chosen from the list of Surfaces to color by ESP. Only the residues enclosed by a surface will be used to calculate the potential on that surface. For example, nearby ions, solvent, or ligand molecules will not affect the results for a surface that encloses only protein, and it is not possible to show the potential from one molecule on the surface of another.

The Implicit Histidine Protonation section controls the charge states of histidines in structures without hydrogens. Although hydrogens will not be added explicitly, the implicit protonation states will affect the results because the charges differ throughout the residue for different protonation states, and the charges of the implicit hydrogens will be merged with those of the attached heavy atoms. Clicking Apply (or OK, which also dismisses the dialog) calculates the electrostatic potential and applies the coloring.

The calculation requires charge assignments, which in turn require hydrogens. An existing structure lacking hydrogens is not changed, but a copy is created in memory, protonated, and assigned charges (details), which are then transferred to the existing structure. Where hydrogens are missing from the existing structure, their charges are collapsed onto the adjacent heavy atom.

Pre-existing hydrogens and/or charges. A structure may already have explicit hydrogens, or they can be added beforehand with AddH. Note surfaces are more rugged (have more small bumps) for structures with hydrogens. A structure may also have pre-existing charge assignments, such as from Add Charge or a previous use of Coulombic Surface Coloring. If all of the atoms corresponding to the chosen surface already have charges, those values will be used rather than assigned anew, with the exception: changing a setting in the Implicit Histidine Protonation section indicates that existing charges on those atoms should be erased and charges assigned anew when Apply or OK is clicked.

Create corresponding color key opens the Color Key dialog and populates it with the current colors and values; a color key can then be created interactively with the mouse.

Close simply dismisses the dialog, while Help opens this manual page in a browser window.


Subsequent coloring operations may erase surface custom colors. Unless explicitly limited to non-surface items, subsequent use of Actions... Color or the command color on the molecule model corresponding to a molecular surface will reset the surface's color source to atoms and wipe out the Coulombic potential colors. The custom surface coloring will be erased even when only parts of the molecule model that do not contribute to the molecular surface are recolored.

Subsequent recomputation of the molecular surface erases custom colors. Anything that triggers surface recalculation, such as deleting atoms from the molecule model or changing certain molecular surface parameters, will erase the Coulombic potential colors.

Surface caps not colored. This tool does not color caps on clipped surfaces.

UCSF Computer Graphics Laboratory / September 2009