model.to_iupac() — standardize certain dihedral angles

This routine swaps specific pairs of atoms within some residues of MODEL so that certain dihedral angles are within ± 90 °, satisfying the IUPAC convention [IUPAC-IUB, 1970,Kendrew et al., 1970]. These residues, pairs of atoms, and dihedral angles are:

It is possible that for distorted sidechains, neither of the two possibilities satisfies the IUPAC convention. In such a case, a warning message is written to the log file.

Example: examples/commands/

# This will swap certain atom names in some planar sidechains to satisfy
# the IUPAC convention.

from modeller import *

env = environ() = ['../atom_files']
log.level(1, 1, 1, 1, 0)

mdl = model(env, file='2abx')

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