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: > Send modeller_usage mailing list submissions to > modeller_usage@salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request@salilab.org > > You can reach the person managing the list at > modeller_usage-owner@salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > 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 > >