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Today's Topics:
1. construct a model with a ligand (fantasticqhl)
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Message: 1
Date: Wed, 02 Oct 2013 10:04:22 +0200
From: fantasticqhl <">>
To: ">
Subject: [modeller_usage] construct a model with a ligand
Message-ID: <">>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
Dear all,
I am trying to construct a model with a ligand, a zinc ion, but I failed.
Firstly, I did the alignment with align.py:
from modeller import *
env = environ()
aln = alignment(env)
mdl = model(env, file='1ze9', model_segment=('FIRST:A','LAST:A'))
aln.append_model(mdl, align_codes='1ze9A', atom_files='1EZ9.pdb')
aln.append(file='ABCD.ali', align_codes='ABCD')
aln.align2d()
aln.write(file='ABCD-1ze9.ali', alignment_format='PIR')
aln.write(file='ABCD-1ze9.pap', alignment_format='PAP')
align2d.py (END)
It finished successfully, and I got the aligned ali and pap files:
ABCD-1ze9.ali:
>P1;1ze9A
structureX:1ZE9.pdb: 1 :A:+16 :A:::-1.00:-1.00
DAEFRHDSGYEVHHQK-*
>P1;ABCD
sequence:ABCD: : : : ::: 0.00: 0.00
DAEFRHDSGYEVHHQK.*
ABCD-1ze9.pap
_aln.pos 10
1ze9A DAEFRHDSGYEVHHQK-
ABCD DAEFRHDSGYEVHHQK.
_consrvd * * *** * ** ** ******
The template is a 16-residue peptide coordinate with a zinc ion, which
is residue 17 in the same chain A. The sequence of the unknown structure
is the same as the template's.
This is a test of how to construct a model with a ligand.
And then I tried to construct the model using model-single.py, which is
the same as the one in the manual:
from modeller import *
from modeller.automodel import *
log.verbose()
env = environ()
env.io.atom_files_directory = ['./:../atom_files']
# Read in HETATM records from template PDBs
env.io.hetatm = True
a = automodel(env, alnfile='ABCD-1ze9.ali',
knowns='1ze9A', sequence='ABCD',
assess_methods=(assess.DOPE, assess.GA341))
a.starting_model = 1
a.ending_model = 5
a.make()
However, I failed to get the model, I get some error like this:
File "model-single.py", line 16, in ?
a.make()
File
"/usr/lib/modeller9.11/modlib/modeller/automodel/automodel.py", line 96,
in make
self.homcsr(exit_stage)
File
"/usr/lib/modeller9.11/modlib/modeller/automodel/automodel.py", line
423, in homcsr
self.check_alignment(aln)
File
"/usr/lib/modeller9.11/modlib/modeller/automodel/automodel.py", line
405, in check_alignment
aln.check()
File "/usr/lib/modeller9.11/modlib/modeller/alignment.py",
line 197, in check
self.check_structure_structure(io=io)
File "/usr/lib/modeller9.11/modlib/modeller/alignment.py",
line 206, in check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.ModellerError: read_te_290E> Number of residues in
the alignment and pdb files are different: 16 17 For alignment
entry: 1 1ze9A
Right now, I guess that the error is coming from the alignment, but I
did not find how the alignment was done in the tutorial. So could
someone tell me how to solve this problem? Any suggestions would be
highly appreciated.
All the best,
Qinghua
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