ROTAMER (CCP4: Supported Program)

NAME

rotamer - list amino acids whose side chain torsion angles deviate from the "Penultimate Rotamer Library"

SYNOPSIS

rotamer xyzin foo_in.pdb
[Keyworded input]

DESCRIPTION

This program reads a protein coordinate file in PDB format and lists all amino acids whose side chain torsion angles deviate more than a user-defined threshold from the rotamers of the "Penultimate Rotamer Library" (ref. 1, Table I, "common-atom values").
An amino acid is listed if at least one side chain torsion angle deviates more than a user-defined threshold DELT  from the equivalent one of the nearest rotamer. Empirically, the following two-step procedure to find the nearest rotamer seems to work quite reasonably, producing only a few false negatives or false positives: The first step is to choose a subset of potential nearest rotamers in a hierarchical order going from the first side chain torsion angle Chi(1) to the last side chain torsion angle Chi(n). For a side chain with four Chi-angles, first, all rotamers deviating less than the user-defined threshold in Chi(1) are chosen, then of those all rotamers that deviate less in Chi(2) are chosen, then of those all rotamers that deviate less in Chi(3) are chosen, and finally of those all rotamers that deviate less in Chi(4) are chosen. If a subset for Chi(i) is empty, the subset for the previous Chi(i-1) is chosen and the hierarchical search is terminated. If the subset for Chi(1) is empty, simply all rotamers are chosen as a "subset". The second step is to find the nearest rotamer out of the previously chosen subset of rotamers. Here, the nearest rotamer is the one with the minimum sum over the absolute Delta-Chi(i) values.

Some remarks and hints

Known limitations:

1. All necessary coordinates for calculating side chain torsion angles must be provided, otherwise the program issues a warning and skips the residue.
2. The output side chain torsion angles for residues with multiple side chain conformations depend on the order of the atoms: the last atoms in the coordinate file of all alternate conformations determine the values. For example, the following order of atom records in a valine residue with two alternate side chain conformations will result in the output of the side chain torsion angle of conformation B:

   ATOM    650  CG1AVAL C 444       4.997  -1.309   3.806  0.60 19.67 
   ATOM    651  CG1BVAL C 444       2.959  -1.564   5.384  0.40 29.48 
   ATOM    652  CG2AVAL C 444       3.111  -1.499   5.347  0.60 12.83 
   ATOM    653  CG2BVAL C 444       5.395  -2.257   5.300  0.40 12.68 

   whereas the following order of atom records will produce nonsense:

   ATOM    651  CG1BVAL C 444       2.959  -1.564   5.384  0.40 29.48 
   ATOM    650  CG1AVAL C 444       4.997  -1.309   3.806  0.60 19.67 
   ATOM    652  CG2AVAL C 444       3.111  -1.499   5.347  0.60 12.83 
   ATOM    653  CG2BVAL C 444       5.395  -2.257   5.300  0.40 12.68 

INPUT AND OUTPUT FILES

XYZIN

Input coordinates in PDB format.

KEYWORDED INPUT

DELT <threshold>

List all amino acids with at least one side chain torsion angle deviating more than |threshold| from its nearest rotamer. If this keyword is not supplied or if its value is outside the allowed range of [0,180]°, the default value of 30° is taken.

END

(Optional) Specifies the end of keyworded input and starts ROTAMER running.

EXAMPLES

List all amino acids with at least one side chain torsion angle deviating more than 40° from its nearest rotamer:

  rotamer XYZIN foo_in.pdb << eof 

  delt 40

  end

  eof

Unix examples script found in $CEXAM/unix/runnable/