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.

Note that the target structures are actually changed by the superpositions carried out by this command. If you want to use these superpositions as a crude initial model for automodel model building (rather than setting automodel.initial_malign3d) please bear in mind that the later templates in your alignment are always fitted on the earlier templates. Thus, a more reliable initial model will be obtained if you list the higher coverage templates earlier in the knowns variable in your automodel script (e.g., always list multimeric templates before monomers).

If you want to use the original non-superposed structures, either avoid calling this command, or delete and recreate the alignment object afterwards to force it to reread the structure files.

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()