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

----- Original Message ----- From: "modeller usage-request" modeller_usage-request@salilab.org To: "modeller usage" modeller_usage@salilab.org Sent: Wednesday, June 20, 2012 9:41:18 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi 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 ibarra.ignacio@gmail.com To: Austin Baker asb93@pitt.edu Cc: modeller_usage@salilab.org Subject: Re: [modeller_usage] Align Code Error Message-ID: CAHQkVidqJvn_t3NFFN-snJcVM_PNgFNsy1DR7mDOrppB01KdTQ@mail.gmail.com 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 asb93@pitt.edu 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 > asb93@pitt.edu > Graduate Student > Department of Chemistry > University of Pittsburgh > > *Everything is Experimental* > > > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >