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
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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
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AIRE-1M9D.ali
Description: Binary data
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AIRE-1XWH.ali
Description: Binary data
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AIRE-2AZW.ali
Description: Binary data