Usage:
swapaa  type  atom-spec  options

Swapaa replaces amino acid sidechains using information from a rotamer library; it is the command-line implementation of Rotamers. A residue can be changed to a different sidechain conformation (rotamer) of the same type of amino acid or mutated into a different type. Rotamers can be chosen automatically based on lowest clash score, most H-bonds, best fit to an electron density map, and/or highest probability according to the library, or interactively from a rotamer list. See also: addaa, ramachandran, rotation, swapna, Build Structure, Dock Prep

Although sidechains at multiple positions can be replaced simultaneously, swapaa is not recommended for predicting the conformations of multiple sidechains in an interacting cluster. Programs such as SCWRL are more appropriate for that purpose.

The sidechain of each residue with at least one atom in atom-spec is replaced with a rotamer of type. The type can be specified with a three-letter code for one of the 20 standard amino acids (case is unimportant) or the word same, which allows substitutions at multiple residues of different types to be performed simultaneously.

In the Dynameomics rotamer library only, there are multiple choices of type for cysteine and histidine depending on the oxidation or protonation state of the sidechain:

• CYH - cysteine reduced free sulfhydryl
• CYS - cysteine oxidized disulfide-bonded (half-cystine)
• HID - histidine neutral δ-protonated
• HIE - histidine neutral ε-protonated
• HIS - histidine neutral (HID and HIE combined)
• HIP - histidine positive protonated on both sidechain nitrogens

For nonstandard amino acids, see the SwissSidechain Chimera plugin.

Bond lengths and angles are taken from the Amber parameter files all*94.lib, and hydrogens are not included.

Only the sidechain atoms of a rotamer are evaluated. For clash and H-bond detection, interactions with other rotamers in the same set and the current residue at that position are disregarded, but all other atoms in the vicinity will be included unless ignoreOtherModels is used. In addition, atoms in the same model that are unwanted for such calculations (for example, solvent) should be deleted beforehand.

Examples:

swapaa leu #0:248.a

swapaa his #0:248.a lib dynameomics

swapaa same sel

swapaa tyr :trp.b retain true

Option keywords for swapaa can be truncated to unique strings and their 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.

lib  rotamer-library
What rotamer library to use; the source of rotamer torsion angles and probabilities. Possible values of rotamer-library (capitalization optional):

• Dunbrack (default) - Dunbrack 2010 smooth backbone-dependent rotamer library (5% stepdown; for chain-terminal residues, the Dunbrack 2002 backbone-independent version is used instead):

  A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Shapovalov MV, Dunbrack RL Jr. Structure. 2011 Jun 8;19(6):844-58.

• Dynameomics - Dynameomics rotamer library:

  The Dynameomics rotamer library: amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water. Scouras AD, Daggett V. Protein Sci. 2011 Feb;20(2):341-52.

  The Dynameomics library includes multiple choices of residue type for cysteine and histidine, depending on the oxidation or protonation state; see above.

• Richardson.common - common-atom values (author-recommended) from the Richardson backbone-independent rotamer library:

  The penultimate rotamer library. Lovell SC, Word JM, Richardson JS, Richardson DC. Proteins. 2000 Aug 15;40(3):389-408.

• Richardson.mode - mode values from the Richardson backbone-independent rotamer library

criteria  method | manual
How to choose the rotamer. If manual, all rotamers will be displayed in the graphics window and listed in a dialog so that the user can choose interactively; otherwise (default), a single rotamer will be chosen automatically according to the method. The preserve option can be used to filter the set of rotamers by chi angle similarity to the current sidechain before the method is applied. The method can be any combination, without spaces, of one or more of the following letters (default dchp):

• d - by best fit into density
• c - by lowest clash score
• h - by highest number of H-bonds
• p - by highest probability according to the rotamer library (probabilities are simply taken from the library and are not affected by the structural environment, except by phi and psi angles when the Dunbrack library is used)

Each successive method is only used when the previous method(s) have produced a tie. For example, with the default criteria (dchp), if no density map is specified, clashes will be evaluated; if the clash scoring method is num and more than one rotamer ties for the lowest number of clashes, H-bonds will be evaluated to break the tie; if the lowest-clashing rotamers also have equal numbers of H-bonds, the one with the highest probability will be used. Alternatively, an integer argument N can be used instead of letters to indicate the rotamer with the Nth highest probability, or 0 (zero) to indicate the rotamer with the lowest probability, regardless of any local interactions or density data.

preserve  true | false
Whether to discard rotamers (regardless of the criteria, except ignored if manual) with any chi angle > 40 ° different from that in the current sidechain. If the current sidechain has symmetrical branching (as in Asp, Glu, Phe, Tyr), the chi angle for comparison is calculated in both possible ways.

retain  true | false | sel
What to do with the pre-existing sidechain(s): retain, replace (default), or retain only those with any atom selected (keyword sel). Regardless of this setting, sidechains will always be replaced where the incoming residue type is glycine or alanine. When there will be multiple sidechains at a given residue position, the new sidechain(s) will be assigned different alternative location identifiers.

log  true | false
Whether to report torsion angles in the Reply Log. Values are reported for the backbone (phi, psi, and whether the peptide bond is cis or trans) and the chosen sidechain rotamer (chi angles) for each swapped residue. Pre-swap chi angles are also reported when the preserve option is used.

ignoreOtherModels  true | false
In clash and H-bond detection, whether to include only atoms in the same model as the residue being swapped; useful for preventing superimposed related proteins or additional copies of the starting structure from affecting the results.

densitySpec  mapmodel
The mapmodel is the model number preceded by # of the density map open in Chimera.

overlapCutoff  cutoff
The cutoff is how much VDW overlap should count as a clash (default 0.6 Å). A larger positive cutoff restricts the results to more severe clashes (details).

hbondAllowance  allowance
When VDW overlap is calculated, an allowance (default 0.4 Å) is subtracted for atom pairs comprised of a possible hydrogen bond donor (or its hydrogen) and a possible acceptor (details).

scoreMethod  sum | num
How to calculate the clash score: as a simple count of the number of clashes (num) or a sum of all overlaps ≥ cutoff (sum).

relax  true | false
Whether to relax the precise criteria for hydrogen bonding.

distSlop  tolerance
The tolerance is how much to relax the distance criteria if relax is true (default 0.4 Å).

angleSlop  tolerance
The tolerance is how much to relax the angle criteria if relax is true (default 20.0 degrees).