Command: swapaa

Usage:
swapaa  residue-spec  ( new-type-list | seq:one-letter-codes ) [ rotLib  rotamer-library ] [ criteria  method | N ]  other-options

Usage:
swapaa interactive  residue-spec  new-type-list [ rotLib  rotamer-library ] [ log  true | false ]

Usage:
swapaa mousemode  residue-spec  new-type-list

The main swapaa command performs virtual mutations by replacing one type of amino acid sidechain with another. A residue can be changed to a different sidechain conformation (rotamer) of the same type of amino acid or mutated into a different type; backbone atoms are not replaced. 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. To simply change a residue's name without changing its coordinates, use setattr instead, for example:

setattr /A:117 residues name UNK

See also: swapna, modeller comparative, alphafold, esmfold, torsion, hbonds, clashes, build, dockprep, altlocs

The swapaa interactive command or the related Rotamers tool can be used to show the entire “bouquet” of rotamers at a position (with an associated rotamer list dialog) so that they can be inspected and chosen interactively.

The command swapaa mousemode simply matches a single conformation of the new residue type onto the backbone atoms of the existing residue. The swapaa mouse mode uses this “quick and dirty” method.

One or more protein residues to change can be specified in a single command. Amino acid residues can be specified with 3-letter codes or with 1-letter codes.

• 3-letter: new-type-list can be either of the following:
  • a single 3-letter code for any of the 20 standard amino acids, (capitalized or not) to use for all specified residues. Examples:

    swapaa /B:243 ser
    swapaa /A:3-5,12 lys

  • a list of such codes separated by commas only, with exactly as many codes as the number of specified residues; the residues will be replaced with the types according to the order in which both were specified. Example:

    swapaa /A:3-5,12 leu,leu,tyr,his

  Except for swapaa mousemode, new-type-list may also be given as:

  • the word same to keep the existing type(s)
  • as detailed below, depending on the rotamer library, any of certain nonstandard 3-letter names to indicate the oxidation or protonation state for which conformational data were collected. However, the resulting rotamers do not include hydrogens and will be given the corresponding standard residue name if incorporated into a structure.
  
  
• Alternatively, the keyword seq: indicates a string of 1-letter codes. As above, either a single code or the same number of codes as residues to swap should be given. Examples:

  swapaa /A:3-5,12 seq:K
  swapaa /A:3-5,12 seq:LLYH

The main swapaa command uses several criteria to choose the best rotamer for a given type and position: lowest clash score, most H-bonds, best agreement with a density map, and/or highest prevalence according to the library. Bond lengths and angles are taken from the Amber parameter files all*94.lib, and hydrogens are not included.

[back to top: swapaa]

Options

The following options apply to the main swapaa command. The swapaa interactive command to show rotamers without swapping only uses the rotLib and log options, and swapaa mousemode does not have any options.

rotLib  rotamer-library
What rotamer library to use; the source of rotamer torsion angles and prevalence values. 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.

  ...with multiple choices of 3-letter code for cysteine and proline:
  • CYH – cysteine reduced free sulfhydryl
  • CYD – cysteine oxidized disulfide-bonded (half-cystine)
  • CYS – combined statistics (CYH + CYD)
  • CPR – cis-proline
  • TPR – trans-proline
  • PRO – combined statistics (CPR + TPR)
  These indicate the species for which conformational data were collected, but the appropriate standard name (CYS or PRO) will be used for what is incorporated into the structure.
  
  
• Dynameomics – Dyameomics 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.

  ...with multiple choices of 3-letter code for cysteine and histidine:
  • 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
  These indicate the species for which conformational data were collected, but the appropriate standard name (CYS or HIS) will be used for what is incorporated into the structure.
  
  
• 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 | N
How to choose the rotamer. 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 agreement with a density map (largest sum of map values at the rotamer sidechain atom positions):
  • if no maps are open but d was just being used by default, this criterion will be skipped; if d was entered explicitly in the command, however, an error will be raised
  • if one map is open, that map will be used
  • if multiple maps are open, which map to use must be specified with the density option
• c – by lowest clash score
• h – by highest number of H-bonds
• p – by highest prevalence according to the rotamer library (prevalence values are simply taken from the library and are not affected by the specific structural environment, except by phi and psi backbone 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 but no map open, 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 prevalence will be used.

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 nearby atoms will be included (at least those in the same model; see ignoreOtherModels). Atoms in the same model that are unwanted for such calculations (for example, solvent) should be deleted beforehand.

Alternatively, an integer N (or comma-separated list of integers) can be given instead of the method. This indicates ignoring all criteria other than prevalence and choosing the rotamer(s) with the Nth highest prevalence. Specifying N as 0 (zero) indicates the rotamer with the lowest prevalence. If a comma-separated list of integers is given, the new sidechains will be assigned different alternative location identifiers.

preserve  angle
Whether to discard rotamers (regardless of the criteria) with any chi angle > angle° 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
What to do with the pre-existing sidechain(s): retain or replace (default). Retention (setting retain true) can only be used when the incoming residue type is the same as the pre-existing type, i.e., the residue is not being “mutated.” Further, the option is ignored/irrelevant if the residue type is alanine or glycine. When the result will be multiple sidechains at a given residue position, the new sidechain(s) will be assigned different alternative location identifiers.

bfactor  value
Specify a bfactor value for the new sidechain atoms; if this option is not used, the atoms will be assigned the highest bfactor value found in the residue before the swap.

log  true | false
Whether to report the rotamer library and various torsion angle values in the Log. Torsion angle values are given 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. In the case of swapaa interactive, only the backbone angles are reported, since no swap has yet occurred when the rotamer list dialog is shown.

ignoreOtherModels  true | false
In clash and H-bond detection, whether to ignore atoms that are not 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.

density  map-model
Specify a map (volume data) to use for the density criterion.

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°).