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Dear modeller team,
I am using a variant of the align2d_mult.py script on your homepage.
I want to use a multi-sequence alignment, align several template structures and the query sequence to it without changing the initial multi-sequence alignment.
On the webpage it is mentioned that one can use align_block to fix a specific part of the alignment. Just to make sure - by using the script:
#!/usr/bin/python
from modeller import *
log.verbose()#output=1, notes=1, warnings=1, errors=1, memory=0)
env = environ()
env.libs.topology.read(file='$(LIB)/top_heav.lib')
# Read aligned sequences:
aln = alignment(env)
aln.append(file='../alignments/test.pir', align_codes='all')
aln_block = len(aln)
# Read aligned structures:
aln.append(file='../templates/pdb_fit/alignment_test_structures.ali', align_codes='all')
# Structure sensitive variable gap penalty sequence-sequence alignment:
aln.salign(output='', max_gap_length=20,
gap_function=False, # to use structure-dependent gap penalty
alignment_type='PAIRWISE', align_block=aln_block,
feature_weights=(1., 0., 0., 0., 0., 0.), overhang=0,
gap_penalties_1d=(-450, 0),
gap_penalties_2d=(0.35, 1.2, 0.9, 1.2, 0.6, 8.6, 1.2, 0., 0.),
similarity_flag=True)
aln.write(file='../alignments/modeller_multi.ali', alignment_format='PIR')
aln.check()
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where "alignment_test_structures.ali" contains an alignment of potential template structures; is each of the sequence in "alignment_test_structures.ali" independently aligned to the alignment given in "test.pir" without changing
the "test.pir" alignment?
Thanks in advance!
Kind regards,
Simone
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