first u have to align your target with template using align2d.py
when alignment will created
         >P1;1ze9A
         structureX:1ZE9.pdb:   1 :A:+16  :A:::-1.00:-1.00
         DAEFRHDSGYEVHHQK*

         >P1;ABCD
         sequence:ABCD:     : :     : ::: 0.00: 0.00
         DAEFRHDSGYEVHHQK*

like this.

then change it like below:-
         >P1;1ze9A
         structureX:1ZE9.pdb:   1 :A:+16  :A:::-1.00:-1.00
         DAEFRHDSGYEVHHQK.*

         >P1;ABCD
         sequence:ABCD:     : :     : ::: 0.00: 0.00
         DAEFRHDSGYEVHHQK.*

and use model-ligand.py script to build model.
gudluck


On Wed, Oct 2, 2013 at 1:34 PM, <modeller_usage-request@salilab.org> wrote:
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Today's Topics:

   1. construct a model with a ligand (fantasticqhl)


----------------------------------------------------------------------

Message: 1
Date: Wed, 02 Oct 2013 10:04:22 +0200
From: fantasticqhl <fantasticqhl@gmail.com>
To: modeller_usage@salilab.org
Subject: [modeller_usage] construct a model with a ligand
Message-ID: <524BD386.4080501@gmail.com>
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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End of modeller_usage Digest, Vol 12, Issue 55
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--
with regards
Rajesh Kumar Gazara
Project Assistant at NIPGR
New Delhi