Chimera Commands Index

coulombic  options  value1  color1  value2  color2  [... valueN  colorN]  surface-spec

Coulombic is the command-line implementation of Coulombic Surface Coloring, which colors 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 is sometimes used to approximate screening by implicit solvent. By default, coulombic uses a distance-dependent dieletric (ε = 4d). The calculation can handle structures with or without explicit hydrogens, and a grid of the values can be generated (see why this might be useful).

Whereas Coulombic Surface Coloring can only color molecular surfaces based on the charges of the residues they enclose, the coulombic command allows specifying which atoms to use independently of which surface to color. This allows coloring the surface of one molecule by the potential from another, for example, or coloring nonmolecular surfaces such as density isosurfaces.

The value/color pairs define how surface electrostatic potential is mapped to colors. At least two value/color pairs must be supplied. Electrostatic potential values (value1, value2, etc.) are in units of kcal/(mol·e) at 298 K. Each color name (color1, color2, etc.) can be any color name that specifies a single color. The command does not have default color settings, but the defaults in the Coulombic Surface Coloring tool correspond to -10 red 0 white 10 blue.

The surface of interest should already be displayed. The surface-spec can be:

Entire surface models will be affected, even if only partly specified. A blank surface-spec will be taken to mean all applicable surface models: all molecular surfaces, or if atoms are given, all surface models. The atoms option is mandatory for coloring nonmolecular surfaces.

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. 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.

Alternatively, a structure may already have explicit hydrogens, or they can be added beforehand in Chimera. A structure may also have pre-existing charge assignments, such as from addcharge or a previous use of coulombic. If all of the atoms corresponding to the chosen surface already have charges, those values are 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 the hisScheme 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.

See Coulombic Surface Coloring for more details, including discussions of implicit vs. explicit hydrogens and limitations of the method. See also: apbs, scolor, rangecolor, addh, addcharge, pdb2pqr


Option keywords for coulombic can be truncated to unique strings and keyword case does not matter. A vertical bar “|” designates mutually exclusive options, and default values are indicated with bold. Synonyms for true: True, 1. Synonyms for false: False, 0.

atoms  atom-spec
Use only the charges of the atoms in atom-spec, plus their implicit hydrogens, if any, to compute the potential. Otherwise, the charges of all residues enclosed in the molecular surface to be colored (all atoms in the corresponding surface category, plus their implicit hydrogens, if any) will be used. The atoms option allows coloring the surface of one molecule by the potential from another, for example, or coloring nonmolecular surface models (types other than MSMSModel). **When using this option, one should consider carefully whether to change the offset with surfDist; a zero or negative value may be appropriate.**
distDep true | false
Whether the dielectric should be distance-dependent; whether ε should vary in proportion to the distance from each charge.
dielectric C
Set the dielectric constant to C (default 4.0), where ε = Cd if distDep is true, ε = C if distDep is false.
surfDist offset
How far out from each surface vertex, along its normal, to evaluate the electrostatic potential (default 1.4 Å). 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. However, for coloring the surface of one molecule by the potential from another molecule using the atoms option, a zero or negative offset may be appropriate.
hisScheme HID | HIE | HIP | none
How to determine the charge states of histidines in structures without hydrogens: These settings apply only to residues named HIS. Histidines that already have the special names (HID, HIE, HIP) will be protonated accordingly. Changing the hisScheme from what was used previously (via command or graphical interface) indicates that the charges on the molecule should be erased and assigned anew.
Bring up the Color Key tool, filled in with the appropriate colors and values, and set to Use mouse for key placement for creating/positioning the color key in the graphics window. The mouse setting can be toggled to allow moving models with the mouse. See also the colorkey command.
Using any of the following three options generates a grid of the Coulombic potential values and starts the Electrostatic Surface Coloring and Volume Viewer tools (see why this might be useful):
gspacing r
Grid point spacing in each dimension (default r = 1.0 Å).
gpadding d
Distance to extend the grid in each dimension beyond the atoms enclosed in the surface (default d = 5.0 Å).
gname data-name
Dataset name (default Coulombic ESP).