Coulombic Surface Coloring calculates electrostatic potential according to 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.
Coulombic Surface Coloring colors molecular surfaces by the potential values and can handle structures with or without explicit hydrogens. It can also generate a grid of the potential values.
Whereas Coulombic Surface Coloring can only color molecular surfaces based on the charges of the residues they enclose, the coulombic command has an option to use the charges of an arbitrary set of atoms. This allows coloring the surface of one molecule by the potential from another, for example, or coloring nonmolecular surfaces such as density isosurfaces.
The Electrostatic Surface Coloring tool is similar, but uses a previously computed electrostatic potential grid. The grid could be from Coulombic Surface Coloring or from any of several separate (not included with Chimera) programs that solve the Poisson-Boltzmann equation. Chimera does include interfaces to such programs: DelPhiController requires a local (user-installed) copy of DelPhi, and the APBS tool can use either a web service or a locally installed copy of APBS (Adaptive Poisson-Boltzmann Solver).
Poisson-Boltzmann calculations are more complex and, if done correctly, more accurate than simple Coulomb's law approaches. However, a Coulombic potential may suffice for visualization. (See http://tinyurl.com/mzopva for an informal comparison of images made in Chimera using Coulombic Surface Coloring with published figures of Poisson-Boltzmann electrostatic potential.)
See also: Render by Attribute, AddH, Add Charge, PDB2PQR, Values at Atom Positions, Color Key, Color Actions
There are several ways to start Coulombic Surface Coloring, a tool in the Surface/Binding Analysis category. It is also implemented as the command coulombic.
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. Coulombic Surface Coloring does not show the potential from one molecule on the surface of another, although that can be done in an additional step after generating a grid.
Parameters:
The specified color/value pairs or thresholds define a color mapping. The value calculated for each surface vertex will be compared to the thresholds. Surface vertices with values lower than any threshold will be assigned the color of the lowest-value threshold, while vertices with values higher than any threshold will be assigned the color of the highest-value threshold. The colors of the remaining vertices will be obtained by linear interpolation between the nearest lower and higher thresholds. Finally, each surface triangle will be colored by linearly interpolating its vertex colors. Colors are defined by red, green, blue, and opacity/transparency components.
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.
The Compute grid... option generates a grid of the electrostatic potential values (a volume dataset) and starts the Electrostatic Surface Coloring and Volume Viewer tools. This allows:
The Coulombic potential 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. Selenomethionine (MSE) residues are treated as methionines (MET) for purposes of charge assignment. Where hydrogens are missing from the existing structure, their charges are collapsed onto the adjacent heavy atom: such hydrogens are implicit.
A structure may already have explicit hydrogens, or they can be added beforehand in Chimera with AddH. A structure may also have pre-existing charge assignments, from prior use of Add Charge, PDB2PQR, or Coulombic Surface Coloring, or read from a file. If all of the atoms corresponding to the chosen surface already have charges, those values will be used rather than assigned anew the first time Coulombic coloring is applied to that surface. In subsequent applications, the existing charges will be used unless a setting in the Implicit Histidine Protonation section is changed, which forces the charges to be assigned anew. Another way to force reassignment is to remove the charges with the command ~setattr a charge.
While implicit hydrogens are appropriate for most uses, collapsing the hydrogen charges onto the adjacent heavy atoms tends to decrease positive potential magnitudes at the surface. This usually has little effect on the qualitative picture, but if it is of concern, the structure can be protonated beforehand. A disadvantage of explicit hydrogens, however, is that they make surfaces more rugged (bumpier) and complicated to view. To circumvent this problem, one could add first add hydrogens, then generate a grid of the Coulombic potential values, then delete the hydrogens to make the molecular surface less rugged (or show the surface for a separate copy of the structure that does not have hydrogens), and finally, color that surface with Electrostatic Surface Coloring using the Coulombic grid that had been generated in the presence of hydrogens.
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, but it can be done in an additional step after generating a grid.