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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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Mutate_model.py :How to specify model number , if the PDB is NMR structure ?
by Priya Chaudhary 12 Aug '13

12 Aug '13

Dear Sir Mutate_model.py How to specify model number , if the PDB is NMR structure ? It only has the provision to mention chain ID. what if the structure is NMR, and we need to specify model number. mutate_model.py # # Usage: python mutate_model.py modelname respos resname chain > logfile # # Example: python mutate_model.py 1t29 1699 LEU A > 1t29.log # Thank you Priya

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Make non-adjacent mutations, preserve backbone and avoid clashes
by David Johnson 30 Jul '13

30 Jul '13

I would like to make a handful of mutations that are not necessarily in sequential order in the primary structure. I would like to preserve the backbone of the model and to keep fixed all side-chains except those of the mutations and possibly nearby residues, which are to be moved ONLY if necessary to void steric clashes. Thus far I have tried Selecting all but the mutated atoms and setting env.edat.nonbonded_sel_atoms = 2 a.library_schedule = autosched.slow a.md_level = None OR a.md_level = refine.very_fast a.repeate_optimization = 3 It is not clear to me exactly what each refinement protocol does. I would appreciate any assistance in understanding this. David

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Build missing residues for multisubunit protein
by Kelly Tran 29 Jul '13

29 Jul '13

Hi, Do you have suggestions on how to build missing residues for a multisubunit protein while restricting non-missing residues from moving? --- from modeller import *from modeller.automodel import * # Load the automodel classlog.verbose()env = environ()# directories for input atom filesenv.io.atom_files_directory = ['.', '../atom_files'] class MyModel(automodel): def select_atoms(self): return selection(self.residue_range('1', '1'), self.residue_range('1', '2'), self.residue_range('181','181')) a = MyModel(env, alnfile = 'alignment.ali', knowns = 'nqo2', sequence = 'nqo2_fill')a.starting_model= 1a.ending_model = 1a.make() --- Thank you, Kelly

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Ligand Introduction from non-homologous protein
by Rohitesh Gupta 16 Jul '13

16 Jul '13

Dear Team, I am writing this mail again. Not sure, if my earlier mail was received by the group. I am trying to model a protein using a template that is 85% similar to it, but also wants to transfer ligand from another protein that is 10% similar. In doing so, I am introducing restraints while creating the final model with ligand. But the final output as .pdb, the ligand seems to miss all the restraints that is being introduced. Please find herein the code: from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints for ids in (('O:234:', 'N4:286:'), ('O:242:', 'N4:286:'), ('N:234:', 'O2:286:')): atoms = [self.atoms[i] for i in ids] rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(*atoms), mean=3.0, stdev=0.2)) log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files # env.io.atom_files_directory = './:../atom_files/' # Read in HETATM records from template PDBs env.io.hetatm = True a = MyModel(env, alnfile = 'alignment.ali', # alignment filename knowns = ('2ebd_model','1ro7'), # codes of the templates sequence = '2ebd') # assess_methods=(assess.DOPE, assess.GA341)) # code of the target a.starting_model= 1 # index of the first model a.ending_model = 5 # index of the last model # (determines how many models to calculate) a.make() This code runs fine but the ligand doesn't have any of the above mentioned restraints. How could one instruct modeller to consider these restraints? I understand that modeller would by default consider the non-bonded interaction between ligand and the catalytic site amino acids. In such case, is there a way to override those interactions? If so, which files should be edited? It will be really helpful to receive suggestions on these lines. Thanking you in anticipation, Rohitesh

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Modeling Ligand from non-homologous protein
by Rohitesh Gupta 16 Jul '13

16 Jul '13

Hello everyone, I have a query which is similar to the process followed in transferring ligand from non-homologous protein under the advanced modelling section on the website. To obtain the restraints on pyruvate, we first superpose the structures of several LDH and MDH enzymes solved with ligands. Such a comparison allows us to identify absolutely conserved electrostatic interactions involving catalytic residues Arg161 and His186 on one hand, and the oxo groups of the lactate and malate ligands on the other hand. The modeling script can now be expanded by creating a new class 'MyModel', which is derived from automodel but which differs in one important respect: the special_restraints routine is redefined to add, to the default restraints, some user defined distance restraints between the conserved atoms of the active site residues and their substrate. In this case, a harmonic upper bound restraint of 3.5±0.1Å is imposed on the distances between the three specified pairs of atoms. A trick is used to prevent MODELLER from automatically calculating distance restraints on the pyruvate-TvLDH complex; the ligand in the 1emd_bs template is moved beyond the upper bound on the ligand-protein distance restraints (i.e., 10). I am unable to understand the process of moving the ligand in 1emd_bs beyond the upper bound? As in, how does one not let modeller choose the default restraints from the template such that the user-defined restraints are considered for modeling ligand into the target protein. Any suggestions on these lines would be very much appreciated. Thanking you in anticipation, Rohitesh

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