- modeller_usage - salilab.org

run two file or two restrained together
by Pablo Fernandez Millan 13 Feb '12

13 Feb '12

Hello, I try to modeller my protein, and I had two different files which succerful good independely, but I need to uses the restrained from the firts file in combination of the symetry restrained of the second file. Down, I just copied the type file I have used. How can I run both at the same time? thank you !! # Addition of restraints to the default ones from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Add some restraints from a file: # rsr.append(file='my_rsrs1.rsr') # Residues 20 through 30 should be an alpha helix: rsr.add(secondary_structure.alpha(self.residue_range('20:', '30:'))) # Two beta-strands: rsr.add(secondary_structure.strand(self.residue_range('1:', '6:'))) rsr.add(secondary_structure.strand(self.residue_range('9:', '14:'))) # An anti-parallel sheet composed of the two strands: rsr.add(secondary_structure.sheet(at['N:1'], at['O:14'], sheet_h_bonds=-5)) # Use the following instead for a *parallel* sheet: # rsr.add(secondary_structure.sheet(at['N:1'], at['O:9'], # sheet_h_bonds=5)) # Restrain the specified CA-CA distance to 10 angstroms (st. dev.=0.1) # Use a harmonic potential and X-Y distance group. rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['CA:35'], at['CA:40']), mean=10.0, stdev=0.1)) a = MyModel(env, alnfile = 'alignment.ali', # alignment filename knowns = '5fd1', # codes of the templates sequence = '1fdx') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do homology modeling ---------------------------------------------------------- # Homology modeling by the automodel class # # Demonstrates how to build multi-chain models, and symmetry restraints # from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() # Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # Be sure to use 'MyModel' rather than 'automodel' here! a = MyModel(env, alnfile = 'twochain.ali' , # alignment filename knowns = '2abx', # codes of the templates sequence = '1hc9') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do homology modeling *Example: examples/automodel/twochain.ali<http://salilab.org/modeller/examples/automodel/twochain.ali> * C; example for building multi-chain protein models >P1;2abx structureX:2abx: 1 :A:74 :B:bungarotoxin:bungarus multicinctus:2.5:-1.00 IVCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQPG/ IVCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQPG* >P1;1hc9 sequence:1hc9: 1 :A:148:B:undefined:undefined:-1.00:-1.00 IVCHTTATSPISAVTCPPGENLCYRKMWCDVFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNPHPKQRPG/ IVCHTTATSPISAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNPHPKQRPG*

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Re: [modeller_usage] modeling of movement of domain
by Ahmadreza Mehdipour 11 Feb '12

11 Feb '12

Hi Ben My script is as follows: from modeller import * env = environ() env.io.atom_files_directory = ['.'] mdl = model(env, file='test1') # Keep two domains rigid: r1 = rigid_body(mdl.residue_range('48:A', '124:A')) r2 = rigid_body(mdl.residue_range('132:A', '205:A')) r3 = rigid_body(mdl.residue_range('212:A', '304:A')) mdl.restraints.rigid_bodies.append(r1) mdl.restraints.rigid_bodies.append(r2) mdl.restraints.rigid_bodies.append(r3) # put the restraints on domains at=mdl.atoms mdl.restraints.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['CG2:128:A'], at['OD1:148:A']), mean=40, stdev=0.1)) mdl.restraints.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['O1:123:A'], at['O1:185:A']), mean=43, stdev=0.1)) mdl.restraints.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['O1:123:A'], at['O1:160:A']), mean=45, stdev=0.1)) mdl.restraints.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['O1:123:A'], at['O1:201:A']), mean=32, stdev=0.1)) mdl.restraints.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['O1:106:A'], at['O1:185:A']), mean=25, stdev=0.1)) mdl.restraints.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['O1:106:A'], at['O1:160:A']), mean=35, stdev=0.1)) mdl.write(file='test.pdb') Thanks Reza

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(no subject)
by ARVIND PAL 10 Feb '12

10 Feb '12

I have a problem. when i am using cryo-em. plz tell me what is the format of current working directory.

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modeling of movement of domain
by Ahmadreza Mehdipour 10 Feb '12

10 Feb '12

Hello I am working with a protein having three domains and two hinge between them. I have x-ray structure of protein. now, I want to keep the domains rigid and then apply some experimental data(EPR distances) in order to have new conformation. I use rigid body command to keep domains rigid and then use restraints to define the distances. But modeller does not apply the distance. What is the problem and how I can apply such restraints. Thanks Reza

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Re: [modeller_usage] Regarding Scoring Parameters
by Mensur Dlakic 09 Feb '12

09 Feb '12

I am not sure I understand your question, and I will assume that by "normal set of these parameters" you mean "unifying set across different programs". If that's your question, the answer is that there is no common set of lambda and kappa parameters (extreme value distribution factors) between different programs, or even within the same program. The values of these parameters are dependent on the scoring scheme used, so when you change the substitution matrix in PSI-BLAST, they will change. If you calibrate HHPRED models in "local" and "global" modes, you'll get different kappa and lambda values, and the same is true if you change other program parameters that affect the scoring and alignments. If you take a sequence (or profile) with certain composition and length and calculate lambda and kappa, they will be different from the next sequence depending on its length and sequence composition. In an extreme case, you can even take the same HHPRED profile and calibrate it against two different databases, for example the one provided with the program, and another database with similar number of profiles, and you'll most likely get different extreme value distribution parameters. Before anyone freaks out because of this uncertainty, it bears mentioning that most of these changes would affect only borderline matches. This is to say that you can't determine these parameters in one program and then use them with others. You can't even determine these parameters for local scoring and then use them for global scoring with the same program. In short, extreme value distribution parameters are both sequence-, program- and scoring parameter-specific. Hope this helps, Mensur At 12:16 AM 2/9/2012, you wrote: >Dear Modellers, >For E-value and alignment scoring systems, we use the parameters >lambda and K. >Specifying these scores is must for a scoring system. So what is/are >the normal set of these parameters used in PSI-BLAST/CS-BLAST/HHPRED >or other profile inclusion based template searching methods? >Tell me the commonly used values for these two parameters lambda and >K for the calculation of alignment scores. > >Thanks >Ashish > >Ashish Runthala, >Lecturer, Structural Biology Cell, >Biological Sciences Group, >BITS, Pilani >Rajasthan, INDIA >_______________________________________________ >modeller_usage mailing list >modeller_usage(a)salilab.org >https://salilab.org/mailman/listinfo/modeller_usage ========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic(a)montana.edu | ==========================================================================

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Regarding Scoring Parameters
by Ashish Runthala 08 Feb '12

08 Feb '12

Dear Modellers, For E-value and alignment scoring systems, we use the parameters lambda and K. Specifying these scores is must for a scoring system. So what is/are the normal set of these parameters used in PSI-BLAST/CS-BLAST/HHPRED or other profile inclusion based template searching methods? Tell me the commonly used values for these two parameters lambda and K for the calculation of alignment scores. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Regarding Model Clustering
by Ashish Runthala 02 Feb '12

02 Feb '12

Dear Modellers, What is the best way to cluster the high scoring model decoys into a well refined conformation with almost correct domain topology, as existing in the considered models. I tried using transfer_xyz to pool 2 best complete models(being best for each of the 2 individual domains, considered on TM-score,GDT). I also tried building the new model through these 2 models using them as templates in different salign modules, but i failed to improve the model for both the individual domains and the overall model together. For 1 domain my prediction with a set of templates and my representative alignment had GDT-TS of 96.875 for Domain1. For D2 best model, it was 99.645. The moment i used Salign, topology got messed up. So when i just pooled (copied) the individual correct domain coordinates from best models for D1 and D2 into the complete model, RMSD became 2.433 with GDT-TS of just 63.309. WHY IT HAPPENED? So only refinement is used by many CASP9 teams to further refine this topology. But this big difference of GDT-TS can't be corrected by refinement. WHY 2 CORRECT DOMAIN MODELS PUT OR COPIED TOGETHER CAN'T GIVE AN OVERALL CORRECT MODEL. HOW TO USE SPICKER. TELL ME THE CORRECT PATH TO CLUSTER THE MODELS FOR BUILDING AN OVERALL CORRECT MODEL TOPOLOGY. Thanks for support, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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generating homology models of reduced disulfide bonds
by Stephanie Schaefer 02 Feb '12

02 Feb '12

Hello, I recently obtained the xray structure of my wildtype protein which I am using as my template. This protein has a redox active disulfide (an other structural disulfides). I would like to generate homology models in which the redox active disulfide bond is broken (the model would represent the cysteines in a reduced environment). I am new to modeler, but what I have done is edited the template PDB (wildtype) to remove the active site disulfide (SSbond) and then generated a homology model using the modified wt PDB as the template. Is this the correct approach to generating a reduced active site model? If this is not an acceptable approach what would you suggest? Thank you for your time, Stephanie Schaefer University of Delaware Biochemistry PhD Student 302-831-2658

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problems with filling missing residue without moving exing ones
by Francesco Pietra 02 Feb '12

02 Feb '12

I could nicely fill missing residues 519-522 and 683-684 by using the normal protocol at /wiki/Missing residue. However, as I would like the existing residues not being modified, I used a script: from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] class MyModel(automodel): def select_atoms(self): return selection(self.residue_range('518', '521'), self.residue_range('681', '683')) a = MyModel(env, alnfile = 'alignment.ali', knowns = myPDB, sequence = 'myPDB_fill') a.starting_model= 1 a.ending_model = 1 a.make() based on the last part of the wiki. Consistently, the error is: ................................. File "fill_resid_no-move.py", line 20, in ? a.make() File "/usr/lib/modeller9.10/modlib/modeller/automodel/automodel.py", line 106, in make atmsel = self._check_select_atoms() File "/usr/lib/modeller9.10/modlib/modeller/automodel/automodel.py", line 490, in _check_select_atoms atmsel = self.select_atoms() File "fill_resid_no-move.py", line 12, in select_atoms return selection(self.residue_range('518', '521'), File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 304, in residue_range start = self.residues[start]._num File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 234, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/modeller9.10/modlib/modeller/util/modutil.py", line 23, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 298, in _indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: 518' I tried different selections as '518', '521' always getting error in finding the first residue in this '...' list. alignment.ali is constructed, as in the wiki, of first the structure, then the sequence. At any event, the alignment.ali is the same that works well with the script that allows all atoms to move. I serched the web; hope this is no duplication. Thanks for advice francesco pietra

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libraries issue
by Francesco Pietra 31 Jan '12

31 Jan '12

Hello: with debian amd64, python 2.6, I am at filling missing residues with script from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] a = loopmodel(env, alnfile = 'alignment.ali', knowns = 'FlaK', sequence = 'FlaK_fill') a.starting_model= 1 a.ending_model = 1 a.loop.starting_model = 1 a.loop.ending_model = 2 a.loop.md_level = refine.fast a.make() and command # mod9.10 fill_res.py I had some(overcome) problems of alignment. Now, suddenly: francesco@gig64:~/tmp$ mod9.10 fill_resid.py Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback francesco@gig64:~/tmp$ which is curious as I am at Modeller modules, so that Python's version should be immaterial. At any event, I can't install a previous version of Python. Thanks for advice francesco pietra

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