<div style>#the lines that generates your error</div><div style>aln.append(file='HDAC9a_Cat.ali', align_codes='2vqj')</div><div style><br></div><div style><font color="#222222" face="arial, sans-serif">Check that you have declared the code "2vqj" after some of the "P1>;" statements in the file HDAC9a_Cat.</font><font color="#222222" face="arial, sans-serif">ali (i.e. ">P1;2vqj"). If MODELLER does not find it, then it is missing or not typed properly.</font></div>
<div style><font color="#222222" face="arial, sans-serif"><br></font></div><div style><font color="#222222" face="arial, sans-serif">Cheers,</font></div><div style><font color="#222222" face="arial, sans-serif">Ignacio</font></div>
<div><br></div><br><div class="gmail_quote">On Wed, Jun 20, 2012 at 11:24 AM, Austin Baker <span dir="ltr"><<a href="mailto:asb93@pitt.edu" target="_blank">asb93@pitt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">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.<div><br></div><div>ERROR GENERATED:</div><div><span style="white-space:pre-wrap"> 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</span></div><div><br></div><div>SCRIPT I'M USING</div><div><div># Demonstrating ALIGN2D, aligning with variable gap penalty</div>
<div><br></div><div>from modeller import *</div><div>log.verbose()</div><div>env = environ()</div><div><br></div><div>env.libs.topology.read('$(LIB)/top_heav.lib')</div><div>env.io.atom_files_directory = ['./atom_files']</div>
<div><br></div><div># Read aligned structure(s):</div><div>aln = alignment(env)</div><div>aln.append(file='HDAC9a_Cat.ali', align_codes='2vqj')</div><div>aln_block = len(aln)</div><div><br></div><div># Read aligned sequence(s):</div>
<div>aln.append(file='HDAC9a_Cat.ali', align_codes='2vqj')</div><div><br></div><div># Structure sensitive variable gap penalty sequence-sequence alignment:</div><div>aln.align2d(overhang=0, gap_penalties_1d=(-100, 0),</div>
<div> gap_penalties_2d=(3.5, 3.5, 3.5, 0.2, 4.0, 6.5, 2.0, 0., 0.),</div><div> align_block=aln_block)</div><div><br></div><div>aln.write(file='align2d.ali', alignment_format='PIR')</div>
<div>aln.write(file='align2d.pap', alignment_format='PAP',</div><div> alignment_features='INDICES HELIX BETA STRAIGHTNESS ' + \</div><div> 'ACCESSIBILITY CONSERVATION')</div>
<div>aln.check()</div><div><br></div><div># Color the first template structure according to gaps in alignment:</div><div>aln = alignment(env)</div><div>aln.append(file='align2d.ali', align_codes=('HDAC9a_Cat', '2vqj'),</div>
<div> alignment_format='PIR', remove_gaps=True)</div><div>mdl = model(env)</div><div>mdl.read(file=aln['HDAC9a_Cat'].atom_file,</div><div> model_segment=aln['HDAC9a_Cat'].range)</div>
<div>mdl.color(aln=aln)</div><div>mdl.write(file='HDAC9a_Cat.aln.pdb')</div><div><br></div><div># Color the first template structure according to secondary structure:</div><div>mdl.write_data(file='HDAC9a_Cat', output='SSM')</div>
<div>mdl.write(file='HDAC9A_Cat.ssm.pdb')</div><div><br></div><div># Superpose the target structure onto the first template:</div><div>mdl2 = model(env)</div><div>mdl2.read(file=aln['2vqj'].atom_file,</div>
<div> model_segment=aln['2vqj'].range)</div><div>sel = selection(mdl).only_atom_types('CA')</div><div>sel.superpose(mdl2, aln)</div><div>mdl2.write(file='2vqj.fit.pdb')</div></div><div><br>
</div><div><br></div><div><br></div><div><div>
<div style="word-wrap:break-word"><div>Austin Baker</div><div><a href="mailto:asb93@pitt.edu" target="_blank">asb93@pitt.edu</a></div><div>Graduate Student</div><div>Department of Chemistry</div><div>University of Pittsburgh</div>
<div><br></div></div><span style="font-family:'Apple Chancery'"><i>Everything is Experimental</i></span><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;text-align:-webkit-auto;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:medium;white-space:normal;font-family:Helvetica;word-spacing:0px"><div style="word-wrap:break-word">
<div><br></div></div></span><br><br>
</div>
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