CHECK_ALIGNMENT -- check alignment for modeling

ATOM_FILES = <string:0>	''	complete or partial atom filenames
ALIGN_CODES = <string:0>	'all'	codes of proteins in the alignment

Description:

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:

# Example for: READ_ALIGNMENT, WRITE_ALIGNMENT, 
#              READ_ALIGNMENT2, WRITE_ALIGNMENT2,
#              CHECK_ALIGNMENT

# 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.

SET OUTPUT_CONTROL = 1 1 1 1 0

READ_ALIGNMENT FILE = 'toxin.ali', ALIGN_CODES = 'all'
WRITE_ALIGNMENT FILE = 'toxin.pap', ALIGNMENT_FORMAT = 'PAP'
WRITE_ALIGNMENT FILE = 'toxin.fasta', ALIGNMENT_FORMAT = 'FASTA'
CHECK_ALIGNMENT