Coulombic Surface Coloring

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

φ = Σ [q_i / (εd_i)]

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.

• Number of colors/values (default 3: red, white, and blue) - up to 11 pairs can be used. Each color can be adjusted by clicking its color well and using the Color Editor. The values can be edited directly (units are kcal/mol·e at 298 K).

  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.

• Distance-dependent dielectric (true/false) - whether ε should vary in proportion to the distance from each charge
• Dielectric constant (default 4.0) - value of C, where ε = Cd if distance-dependent, ε = C if not distance-dependent
• Distance from surface (default 1.4 Å) - how far out from each surface vertex, along its normal, to evaluate the electrostatic potential. The rationale for looking outward is that the values at the centers of any interacting atoms are more relevant than those at their surfaces. A molecular surface is solvent-excluded; it shows where the surface of a spherical probe (typically of radius 1.4 Å) can lie. Thus, 1.4 Å out from the molecular surface is about as close as the probe center can get, the solvent-accessible surface.

• Residue name-based - residue names will be used to determine which histidine sidechain nitrogens should be implicitly protonated: the δ-nitrogen in residues named HID, the ε-nitrogen in HIE, and both nitrogens in HIP. The HIS = setting specifies how residues with the standard histidine name (HIS) should be treated:
  • estimated from H-bonds (default) - choose protonation state based on local H-bonding environment
  • delta - neutral sidechain, implicit hydrogen at δ-nitrogen
  • epsilon - neutral sidechain, implicit hydrogen at ε-nitrogen
  • both - positive sidechain, implicitly protonated at both sidechain nitrogens
• Specified individually... the desired protonation state of each histidine residue will be specified with checkboxes in the dialog

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.