[modeller_usage] Multiple Alignment Problem

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Hello,

I had already sent a mail but did got any response. Please help me out in this problem. Which alignment method should I go for?

I have done alignment through salign as mentioned in advance tutorial  but i think it dosent gives good alignment.File AIRE_mult.ali and align2d_mult are attached. 
Thats why I separately aligned template sequences with protien sequence using align2d.py one by one and then wrote the result in one file by myself i-e. Mannual_Alignment.ali. 

 Is this the rite way ? or M doing wrong?

Which way should I use ?


Regards,
Thanks

 
from modeller import *

log.verbose()
env = environ()

env.libs.topology.read(file='$(LIB)/top_heav.lib')

# Read aligned structure(s):
aln = alignment(env)
aln.append(file='AIRE_res.ali', align_codes='all')
aln_block = len(aln)

# Read aligned sequence(s):
aln.append(file='AIRE.ali', align_codes='AIRE')

# Structure sensitive variable gap penalty sequence-sequence alignment:
aln.salign(output='', max_gap_length=20,
           gap_function=True,   # 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='AIRE-mult.ali', alignment_format='PIR')
aln.write(file='AIRE-mult.pap', alignment_format='PAP')

Attachment: AIRE-mult.ali
Description: Binary data

Attachment: Mannual_Alignment.ali
Description: Binary data

env = environ()
aln = alignment(env)

mdl = model(env, file='1M9D', model_segment=('FIRST:C','LAST:C'))
aln.append_model(mdl, align_codes=('1M9DC'), atom_files='1M9D.pdb')

aln.append(file='AIRE.ali', align_codes='AIRE')
aln.align2d()
aln.write(file='AIRE-mult.ali', alignment_format='PIR')
aln.write(file='AIRE-mult.pap', alignment_format='PAP')

Attachment: AIRE-1H5P.ali
Description: Binary data

Attachment: AIRE-1M9D.ali
Description: Binary data

Attachment: AIRE-1XWH.ali
Description: Binary data

Attachment: AIRE-2AZW.ali
Description: Binary data