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Re: [modeller_usage] Align Code Error



#the lines that generates your error
aln.append(file='HDAC9a_Cat.ali', align_codes='2vqj')

Check that you have declared the code "2vqj" after some of the "P1>;" statements in the file HDAC9a_Cat.ali (i.e. ">P1;2vqj"). If MODELLER does not find it, then it is missing or not typed properly.

Cheers,
Ignacio


On Wed, Jun 20, 2012 at 11:24 AM, Austin Baker <" target="_blank">> wrote:
I am trying to run a 2d align and I keep getting this error. I can't seem to figure out what the problem is.

ERROR GENERATED:
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

SCRIPT I'M USING
# 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')



Austin Baker
Graduate Student
Department of Chemistry
University of Pittsburgh

Everything is Experimental





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