- modeller_usage - salilab.org

Modelling with Side chain Restraints
by Lalith Kumar 09 Oct '13

09 Oct '13

Hi I want to build a complete structure for a protein that has partial crystal structure available but with out any deviations for the side chains of residues that are copied from template (crystal structure). Please let me know if there is any script available for restraining side chains of these residues. with kind regards, lalith

2 1

Re: [modeller_usage] modeller_usage Digest, Vol 12, Issue 55
by Rajesh gazara 03 Oct '13

03 Oct '13

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(a)salilab.org> wrote: > Send modeller_usage mailing list submissions to > modeller_usage(a)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(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)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(a)gmail.com> > To: modeller_usage(a)salilab.org > Subject: [modeller_usage] construct a model with a ligand > Message-ID: <524BD386.4080501(a)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 > >

1 0

construct a model with a ligand
by fantasticqhl 02 Oct '13

02 Oct '13

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

2 1

modelling a protein with hetero-atoms
by pr＠tibh＠ 25 Sep '13

25 Sep '13

How to model a protein having hetero-atoms in it from a template protein

2 1

modelling with multiple templates
by HIDDEN 24 Sep '13

24 Sep '13

Hello, I have been modelling GPCRs using multiple templates and have noticed that in the code below in my salign.py file: aln = alignment(env) for (code, chain) in (('1', 'A'), ('2', 'A'), ('3', 'A')): mdl = model(env, file=code, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(mdl, atom_files=code, align_codes=code+chain) if I switched the order of the templates to be 3, 1, 2 instead of the order shown above (1,2,3), I get different models with different DOPE scores. Is this possible or am I doing something wrong? If this is the case, how can I determine which order of my templates is optimal for homology modelling? Thanks in advance,

2 4

trans proline
by Tomek Wlodarski 24 Sep '13

24 Sep '13

Hi, I found that there is routine to force Pro to cis conformation -> cispeptide() Is there a routine to force Pro from cis to trans conformation? Thanks. Best, tomek

2 3

Loop refining
by HERBERT MAX VENTHUR PE¥A 23 Sep '13

23 Sep '13

Hi modeller users I've already modeled a structure of an OBP (insect proteins). I picked the structure (pdb) with the lowest DOPE score, which is actually has the best stereochemical quality according to Procheck. After that, I used the script for "loop refining" in a positive range of values according to Anolea (showed as red bars). I was waiting a better stereochemical quality after the loop refinement, however, more bad contacts among residues and low allowed positions were obtained. My question is, What aspects must I take into consideration for loop refinement?, Is possible that the modeled structure do not need any loop refining? Best regards Herbert -- *Herbert Venthur Peña Profesor de Estado en Ciencias con Mención en Química* *Estudiante de Doctorado en Ciencias de Recursos Naturales * *Laboratorio de Ecología Química Universidad de La Frontera Temuco, Chile * *08-3104992*

2 1

Workshop on Theoretical Model Archiving, Validation and PDBx/mmCIF Data Exchange Format” on October 21 & 22, 2013 at Rutgers University, NJ.
by Torsten Schwede 19 Sep '13

19 Sep '13

Dear colleagues, As you all know, coordinates derived by theoretical modeling cannot be deposited in the PDB (1,2). As a result, many manuscripts reporting results of theoretical modeling or simulations are published today without making the model coordinates available. This makes it impossible for the reader and reviewer of a manuscript to validate and use the model, which clearly hampers a more widespread use and acceptance of modeling in life science research (3). We would like to invite you for a “Workshop on Theoretical Model Archiving, Validation and PDBx/mmCIF Data Exchange Format” on October 21 & 22, 2013 at Rutgers University, NJ. The first day (Monday) will be dedicated to the development of standards for model data deposition (model archiving) and validation of models for peer-reviewed publications. On the second day, we offer a workshop on the PDBx/mmCIF format, which the wwPDB has established as the new standard format for data exchange and archiving in structural biology. Please feel to register for one or both days according to your interests: http://www.proteinmodelportal.org/workshop-2013/ We would very much appreciate your input on which information should be captured in a macromolecular model archive for comparative models, de novo predictions, protein-protein docking and virtual screening, and what should be minimal standards for information archiving and validation reports for models published in peer-reviewed publications. Looking forward to meeting you at the workshop! All the best, Torsten Schwede & Andrej Sali PS: Meeting participation is free, but registration is required. Coffee, lunch and dinner on Monday are provided by the organizers. Please make your own arrangements for travel and accommodation. 1) Berman HM, Burley SK, et al. Outcome of a workshop on archiving structural models of biological macromolecules. (2006) Structure. 14:1211-7. 2) http://www.wwpdb.org/news/news.html#20060815 3) Schwede T, Sali A, et al. Outcome of a workshop on applications of protein models in biomedical research. (2009) Structure. 17:151-9. Prof. Dr. Torsten Schwede Biozentrum Universität Basel & SIB Swiss Institute of Bioinformatics Klingelbergstrasse 50-70 4056 Basel http://www.biozentrum.unibas.ch/schwede/

1 0

additional restraints in Modeller
by fantasticqhl 06 Sep '13

06 Sep '13

Hi Modeller users, I want to add some additional restraints during homology modelling, but it seems to be not working. And I did not found any error complaining the restraints. Here is my script: from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = '/home/qinghua/Projects/Tycko/HM' class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # CONSTRAINTS ON HISTIDINE 6 rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['CG:13:B'],at['CG:14:B']), mean=4.00, stdev=0.05)) # rsr.add(forms.gaussian(group=physical.xy_distance, # feature=features.distance(at['NE2:14:B'],at['O:13:B']), # mean=3.03, stdev=0.05)) env = environ() a = automodel(env, alnfile='2LMO-aln.ali', knowns='abcdB', sequence='2LMO', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 5 a.make() This is just a test, I want to make sure that the restraints work here. However, I checked the output pdb files, and I found that the distance between Atom CG and CG is larger than 4 angstrom. Could someone give me some suggestion for it? Thanks very much! All the best, Qinghua

2 1

Interpretation of family.mat automated template selection
by Jurgens de Bruin 04 Sep '13

04 Sep '13

Hi, I am relatively new to modeller and would appreciate some help on the following: I have look for some more information on the family.mat file but I am unsuccessful. If the following is the family.mat file how can it be interpreted: * 1uzeA @1.8 0 56 72 1j36A @2.4 56 0 78 1r42A @2.2 72 78 0* The reason for this is I am in the process of writing a small pipeline to generate crude models and would like to make the template selection automated. Any ideas or pointers would be wonderful and greatly appreciated. Thanks -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin

2 1