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Command: coulombic

Usage:
coulombic  atom-spec  [ distDep  true | false ] [ dielectric  C ] [ offset  d ] [ surfaces  surf-spec ] [ hisScheme  HID | HIE | HIP ] [ chargeMethod am1-bcc | gasteiger ] [ key  true | false ]  palette-options 

The coulombic command calculates Coulombic electrostatic potential (ESP) on the fly (no input ESP file required) and uses it to color molecular surfaces, with default coloring ranging from red for negative potential through white to blue for positive potential . If the surfaces do not already exist, they will be generated. The calculation can handle structures with or without explicit hydrogens. The atomic charges are looked up for standard residues, and in the rarer case they are needed for nonstandard residues, calculated by Antechamber according to the chargeMethod option (default am1-bcc). However, before the charge assignment, certain modified nucleic acid residues will be mutated automatically to their unmodified counterparts as follows:

Selenomethionine residues (MSE) are simply assigned the charges for the standard residue methionine (MET) without being mutated.

See also: key, color electrostatic, surface, mlp, per-model clipping, measurements, the Protein-Ligand Binding Sites tutorial, the ChimeraX Coulombic ESP highlight, ChimeraX video: coloring by electrostatic potential

Coulombic electrostatic potential is calculated from atomic partial charges and coordinates 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. The resulting potential is in units of kcal/(mol·e) at 298 K.

A distance-dependent dielectric is sometimes used to approximate screening by implicit solvent. By default, distDep true and dielectric 4.0 are used:

ε = 4d
With distDep false, ε is a constant C given with the dielectric option.

The offset d is how far out from each surface vertex, along its normal, to evaluate the data. The default of 1.4 Å is typically used for coloring a molecular surface by 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. By default, a molecular surface shows where the surface of a spherical probe of radius 1.4 Å can lie, the solvent-excluded surface. An offset of 1.4 Å approximates the solvent-accessible surface, about as close as the probe center can get to the molecule. ** However, an offset of 0.0 may be preferred for coloring surface caps (from clipping), and a zero or negative offset may be appropriate for coloring the surface of one structure by the potential from another. **

The default palette-options for coloring are
:

palette red-white-blue  range -10,10

When coulombic is run interactively (in gui mode and not via a script), the key true option can be used to start Color Key and draw a color key with the corresponding colors and values.

By default, a molecular surface is generated as needed for each biopolymer chain that contains any of the specified atoms, colored by the Coulombic ESP from all of the atoms enclosed by that surface, and the surface patches for the specified atoms are displayed. An independent calculation is performed for each surface, using only the charges from the atoms enclosed by that surface. Typically, each biopolymer chain has its own molecular surface that does not include ligand or solvent.

Alternatively, one or more pre-existing molecular surfaces can be specified with the surfaces option, in which case the calculation will use the charges of the specified atoms only. The only way to use different atoms than enclosed by a surface to calculate the ESP for coloring that surface is to use both a non-blank atom-spec and the surfaces option. In that case, care is needed to specify only the intended set of atoms (see atomic charges, below).

Hydrogens

The calculation requires charge assignments, which in turn require hydrogens. However, an existing structure lacking hydrogens is not changed; a copy is created in memory, protonated, and assigned charges from a lookup table.

The hisScheme option indicates how to (implicitly) protonate residues named HIS in structures without hydrogens:

If hisScheme is not specified, the protonation state of each HIS residue will be chosen based on the local H-bonding environment. The option applies only to residues named HIS. Regardless of this option, histidines that already have the special names (HID, HIE, HIP) will be protonated accordingly.

Atomic Charges

Currently there is no choice of different charge sets for standard residues. These charge values are taken from the following files in AmberTools20: all_amino03.in, amino12.in, nucleic10.in, aminont12.in, and aminoct12.in. These include standard amino acid and nucleic acid residues, MSE (selenomethionine), HOH (water), ACE, NH2, NME (peptide-capping residues), ADP, ATP, GDP, GTP, NDP, and NAD (common cofactors).

The presence of any other residues within the biopolymer surface will trigger a charge calculation with Antechamber according to the chargeMethod option (default am1-bcc). Solvent, ligands, ions, and cofactors are normally not enclosed by molecular surfaces, so this situation should be relatively rare.

When the surfaces option is used, however, the calculation is not automatically limited to the atoms enclosed by those surfaces. Thus, care is required to specify only the atoms desired for the calculation, so that ligands, solvent, etc. are not accidentally included and no unnecessary charge calculations are performed. The protein specifier is often useful for this purpose, and can be restricted further by other specifiers such as model ID and chain number:

coulombic protein surfaces #2
coulombic #1/A & protein surfaces #2

UCSF Resource for Biocomputing, Visualization, and Informatics / September 2021