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()

---------------------------

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