Dear Austin,
align_codes include PDB_ID + Chain_ID.
So include 2vqj with its Chain_ID.
Good Luck,
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
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Subject: modeller_usage Digest, Vol 11, Issue 69
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Today's Topics:
1. Re: Align Code Error (Ignacio Ibarra)
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Message: 1
Date: Wed, 20 Jun 2012 12:11:16 -0400
From: Ignacio Ibarra <>
To: Austin Baker <>
Cc:
Subject: Re: [modeller_usage] Align Code Error
Message-ID:
<>
Content-Type: text/plain; charset="iso-8859-1"
#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 <> 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*
>
>
>
>
>
> _______________________________________________
> modeller_usage mailing list
>
> https://salilab.org/mailman/listinfo/modeller_usage
>
>
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