September 2013 - modeller_usage

Select and remove atoms from automodel
by Ignacio Ibarra 04 Mar '14

04 Mar '14

Hello, Currently I am generating nucleic acid models using the MODELLER suite. I would like to remove the initial phosphate group declared in the first residue of each nucleic acid chain. Those atoms should not be present in real structures. I would like to do it without writing new text in the .lib files that are into the modlib folder I read about a pick_atoms() method in an older version of MODELLER, but it is not commented in the 9v11 manual ( http://binf.gmu.edu/software/MODELLER/node131.html) Is there something similar currently available for removing atoms from the model in the automodel or another class? Regards, Ignacio

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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

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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,

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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

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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*

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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/

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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

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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

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mutate model syntax error
by Daffodil Canson 04 Sep '13

04 Sep '13

I'm new to Modeller and I tried using the mutate model script that I copied from http://salilab.org/modeller/wiki/Mutate%20model. I got the following message instead. C:\Program Files (x86)\Modeller9.10\bin\test>mod9.10 mutate_model.py 1r3a 116 PR O A > 1r3a_1.log 'import site' failed; use -v for traceback File "mutate_model.py", line 54 1r3a, 116, PRO, A, = sys.argv[1:] ^ SyntaxError: invalid syntax Can anyone help me with this? I don't know what's wrong with the input. I thought I only need a pdb file to execute this script. Many thanks, Daffodil

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query related to modelling with ligand using multiple templlate
by Rajesh gazara 04 Sep '13

04 Sep '13

i want to make a model with ligand using multiple templates having same ligand . is it possible? please reply as soon as possible -- with regards Rajesh Kumar Gazara Project Assistant at NIPGR New Delhi

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