Traceback (most recent call last): File "align2d_HDAC9a_Cat.py", line 12, in <module> aln.append(file='HDAC9a_Cat.ali', align_codes='2vqj') File "/Library/modeller-9.10/modlib/modeller/alignment.py", line 78, in append allow_alternates) _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 2vqj

# Demonstrating ALIGN2D, aligning with variable gap penalty

from modeller import *

log.verbose()

env = environ()

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

env.io.atom_files_directory = ['./atom_files']

# Read aligned structure(s):

aln = alignment(env)

aln.append(file='HDAC9a_Cat.ali', align_codes='2vqj')

aln_block = len(aln)

# Read aligned sequence(s):

aln.append(file='HDAC9a_Cat.ali', align_codes='2vqj')

# Structure sensitive variable gap penalty sequence-sequence alignment:

aln.align2d(overhang=0, gap_penalties_1d=(-100, 0),

gap_penalties_2d=(3.5, 3.5, 3.5, 0.2, 4.0, 6.5, 2.0, 0., 0.),

align_block=aln_block)

aln.write(file='align2d.ali', alignment_format='PIR')

aln.write(file='align2d.pap', alignment_format='PAP',

alignment_features='INDICES HELIX BETA STRAIGHTNESS ' + \

'ACCESSIBILITY CONSERVATION')

aln.check()

# Color the first template structure according to gaps in alignment:

aln = alignment(env)

aln.append(file='align2d.ali', align_codes=('HDAC9a_Cat', '2vqj'),

alignment_format='PIR', remove_gaps=True)

mdl = model(env)

mdl.read(file=aln['HDAC9a_Cat'].atom_file,

model_segment=aln['HDAC9a_Cat'].range)

mdl.color(aln=aln)

mdl.write(file='HDAC9a_Cat.aln.pdb')

# Color the first template structure according to secondary structure:

mdl.write_data(file='HDAC9a_Cat', output='SSM')

mdl.write(file='HDAC9A_Cat.ssm.pdb')

# Superpose the target structure onto the first template:

mdl2 = model(env)

mdl2.read(file=aln['2vqj'].atom_file,

model_segment=aln['2vqj'].range)

sel = selection(mdl).only_atom_types('CA')

sel.superpose(mdl2, aln)

mdl2.write(file='2vqj.fit.pdb')