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# Illustrates the SALIGN multiple structure/sequence alignment
from modeller import *
log.verbose()
env = environ()
env.io.atom_files_directory = './:../atom_files/'
aln = alignment(env)
for (code, chain) in (('3F1O', 'A'), ('3H7W', 'A'), ('3H82', 'A')):
mdl = model(env, file=code, model_segment=('FIRST:'+chain, 'LAST:'+chain))
aln.append_model(mdl, atom_files=code, align_codes=code+chain)
for (weights, write_fit, whole) in (((1., 0., 0., 0., 1., 0.), False, True),
((1., 0.5, 1., 1., 1., 0.), False, True),
((1., 1., 1., 1., 1., 0.), True, False)):
aln.salign(rms_cutoff=3.5, normalize_pp_scores=False,
rr_file='$(LIB)/as1.sim.mat', overhang=30,
gap_penalties_1d=(-450, -50),
gap_penalties_3d=(0, 3), gap_gap_score=0, gap_residue_score=0,
dendrogram_file='fm00495.tree',
alignment_type='tree', # If 'progresive', the tree is not
# computed and all structues will be
# aligned sequentially to the first
feature_weights=weights, # For a multiple sequence alignment only
# the first feature needs to be non-zero
improve_alignment=True, fit=True, write_fit=write_fit,
write_whole_pdb=whole, output='ALIGNMENT QUALITY')
aln.write(file='fm00495.pap', alignment_format='PAP')
aln.write(file='fm00495.ali', alignment_format='PIR')
aln.salign(rms_cutoff=1.0, normalize_pp_scores=False,
rr_file='$(LIB)/as1.sim.mat', overhang=30,
gap_penalties_1d=(-450, -50), gap_penalties_3d=(0, 3),
gap_gap_score=0, gap_residue_score=0, dendrogram_file='1is3A.tree',
alignment_type='progressive', feature_weights=[0]*6,
improve_alignment=False, fit=False, write_fit=True,
write_whole_pdb=False, output='QUALITY')
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