alignment.check() -- check alignment for modeling

check(io=None)

This command evaluates an alignment to be used for comparative modeling. It uses two criteria:

First, it checks the alignment of the template structures (all but the last entry in the alignment): For each pairwise superposition of the templates, it reports those equivalent pairs of ${C}_\alpha$ atoms that are more than 6 away from each other. Such pairs are almost certainly misaligned. The pairwise superpositions are done using the ${C}_\alpha$ atoms and the given alignment.

Second, the command checks the alignment of the target sequence (the last entry in the alignment) with each of the templates: For all consecutive pairs of ${C}_\alpha$ atoms in the target, it calculates the distance between the two equivalent ${C}_\alpha$ atoms in each of the templates. If the distance is longer than 8, it is reported. In such a case, the alignment between the template and the target is almost certainly incorrect.

Example: examples/commands/read_alignment.py

# Example for: alignment.append(), alignment.write(),
#              alignment.check()

# Read an alignment, write it out in the 'PAP' format, and 
# check the alignment of the N-1 structures as well as the 
# alignment of the N-th sequence with each of the N-1 structures.

from modeller import *

log.level(output=1, notes=1, warnings=1, errors=1, memory=0)
env = environ()
env.io.atom_files_directory = '../atom_files'

aln = alignment(env)
aln.append(file='toxin.ali', align_codes='all')
aln.write(file='toxin.pap', alignment_format='PAP')
aln.write(file='toxin.fasta', alignment_format='FASTA')
aln.check()