modeller_usage

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3151 discussions

Adding missing residues to PDB with two chains
by Anjela Manandhar 29 Sep '14

29 Sep '14

Hi, I am new to Modeller. Here, I am trying to add missing residues in my PDB. My PDB has two chains A and B. I checked the tutorial and mailing lists where they talk about PDB with single chain. So, how can I get an .ali file for my protein and how should I label the residues to be inserted. Thank You. Anjela Manandhar

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problem with the separate homo-trimer antiparallel beta sheet
by Namita Dube 19 Sep '14

19 Sep '14

Dear Modeller, I am really new in the field of building a model and I have a small peptide chain comprising of 16 residues and I am trying to build a homo-trimer anti-parallel beta sheet for all the 16 residue , the three chains are separate. I am trying to put secondary structure restraints (strand and sheet) to the model, but it didn't work. It just produce the three separate chains but do not restrain them in the form of beta sheet. My script is as below: from modeller import * from modeller.automodel import * log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # Build 50 models, and assess with both DOPE and GA341 class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Selecting the chains as A B and C respectively s1 = selection(self.chains['A']). only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') s3 = selection(self.chains['C']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) # self.restraints.symmetry.append(symmetry(s2, s3, 1.0)) # Residues 0 through 15, 16 through 31 and 32 through 47 should be in the form of a beta strand: # Three beta-strand: rsr.add(secondary_structure.strand(self.residue_range(0,15))) # from residue 0 to 15 rsr.add(secondary_structure.strand(self.residue_range(16,31))) # from residue 16 to 31 rsr.add(secondary_structure.strand(self.residue_range(32,47))) # form residue 32 to 47 # An anti-parallel sheet composed of the two strands: rsr.add(secondary_structure.sheet(at['N:1:A'],at['O:31:B'], sheet_h_bonds=-16)) # antiparallel sheet starting between N of residue 1 of chain A and O of residue 31 of Chain B rsr.add(secondary_structure.sheet(at['N:17:B'], at['O:47:C'], sheet_h_bonds=-16)) # antiparallel sheet starting between N of residue 17 of chain B and O of residue 47 of Chain C # My model input files: a = MyModel(env, alnfile='test.pir', # alignment filename knowns=('1CD1'), # codes of the templates sequence='query', # code of the target assess_methods=(assess.DOPE, assess.GA341)) a.starting_model= 1 # index of the first model a.ending_model = 50 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling # Get a list of all successfully built models from a.outputs ok_models = filter(lambda x: x['failure'] is None, a.outputs) # Rank the models by DOPE score key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) # Get top model m = ok_models[0] print "Top model: %s (DOPE score %.3f)" % (m['name'], m[key]) My pir file is: >P1;query sequence:query:0:A:16:B:32:C:: NYTFRCLQMSSFANRS/NYTFRCLQMSSFANRS/NYTFRCLQMSSFANRS * >P1;1CD1 structureN:1CD1.pdb:7:A:22:A:::: NYTFRCLQMSSFANRS/----------------/---------------- * Kindly look into the matter and let me know what is the problem with my script and the system files. i will be really grateful for your help. Waiting for your early reply, Kind Regards, Namita Dube

2 1

problem with the separate homo-trimer antiparallel beta sheet
by Namita Dube 19 Sep '14

19 Sep '14

Dear Sir/Ma'am, Kindly refer my email dated yesterday, where I have asked about the problem I am facing with the antiparallel beta sheet. I am forwarding the same email again, Please let me know if you have any suggestions on how I should proceed to solve this problem. I have a small peptide chain comprising of 16 residues and I am trying to build a homo-trimer anti-parallel beta sheet for all the 16 residue , the three chains are separate. I am trying to put secondary structure restraints (strand and sheet) to the model, but it didn't work. It just produce the three separate chains but do not restrain them in the form of beta sheet. My script is as below: from modeller import * from modeller.automodel import * log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # Build 50 models, and assess with both DOPE and GA341 class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Selecting the chains as A B and C respectively s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') s3 = selection(self.chains['C']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) # self.restraints.symmetry.append(symmetry(s2, s3, 1.0)) # Residues 0 through 15, 16 through 31 and 32 through 47 should be in the form of a beta strand: # Three beta-strand: rsr.add(secondary_structure.strand(self.residue_range(0,15))) # from residue 0 to 15 rsr.add(secondary_structure.strand(self.residue_range(16,31))) # from residue 16 to 31 rsr.add(secondary_structure.strand(self.residue_range(32,47))) # form residue 32 to 47 # An anti-parallel sheet composed of the two strands: rsr.add(secondary_structure.sheet(at['N:1:A'],at['O:31:B'], sheet_h_bonds=-16)) # antiparallel sheet starting between N of residue 1 of chain A and O of residue 31 of Chain B rsr.add(secondary_structure.sheet(at['N:17:B'], at['O:47:C'], sheet_h_bonds=-16)) # antiparallel sheet starting between N of residue 17 of chain B and O of residue 47 of Chain C # My model input files: a = MyModel(env, alnfile='test.pir', # alignment filename knowns=('1CD1'), # codes of the templates sequence='query', # code of the target assess_methods=(assess.DOPE, assess.GA341)) a.starting_model= 1 # index of the first model a.ending_model = 50 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling # Get a list of all successfully built models from a.outputs ok_models = filter(lambda x: x['failure'] is None, a.outputs) # Rank the models by DOPE score key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) # Get top model m = ok_models[0] print "Top model: %s (DOPE score %.3f)" % (m['name'], m[key]) My pir file is: >P1;query sequence:query:0:A:16:B:32:C:: NYTFRCLQMSSFANRS/NYTFRCLQMSSFANRS/NYTFRCLQMSSFANRS * >P1;1CD1 structureN:1CD1.pdb:7:A:22:A:::: NYTFRCLQMSSFANRS/----------------/---------------- * Kindly look into the matter and let me know what is the problem with my script and the system files. i will be really grateful for your help. Waiting for your early reply, Kind Regards, Namita Dube

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using an external multiple sequence alignment
by ashika torikora 04 Sep '14

04 Sep '14

Hi, I was wondering if one could use an external multiple sequence alignment (instead of align2d or equivalent functions) with modeller and how I could go about doing that. Thanks for any help you could provide. Ashika,

3 2

renumbering residues
by Jan Kosinski 04 Sep '14

04 Sep '14

Hi, I need to renumber residues after building a model using a list that maps residue indexes (0,1,2...) to residue numbers (1390,1391,1392...). The residue numbers list is not continuous, for example: [..., 1400, 1401, 1450, 1451,...] thus I cannot use rename_segments() method, which takes only the number of first residue. I tried with: class MyModel(automodel): num_map = None def fix_numbering(self): for old_resi, new_resi in zip(self.residues, self.num_map): old_resi.num = str(new_resi) def user_after_single_model(self): self.fix_numbering() where num_map is assigned to [..., 1400, 1401, 1450, 1451,...]: m = MyModel(...) m.num_map = [..., 1400, 1401, 1450, 1451,...] and it would be fine, but I get the residue numbers in wrong columns of the PDB: ATOM 1 N SER A 1390 37.882 25.941 -19.658 1.00 8.49 N ATOM 2 CA SER A 1390 36.454 26.059 -20.028 1.00 8.49 C ATOM 3 CB SER A 1390 35.958 24.759 -20.682 1.00 8.49 C ATOM 4 OG SER A 1390 36.013 23.692 -19.747 1.00 8.49 O ATOM 5 C SER A 1390 35.622 26.326 -18.821 1.00 8.49 C ATOM 6 O SER A 1390 36.138 26.652 -17.753 1.00 8.49 O instead of: ATOM 1 N SER C1390 37.882 25.941 -19.658 1.00 8.49 N ATOM 2 CA SER C1390 36.454 26.059 -20.028 1.00 8.49 C ATOM 3 CB SER C1390 35.958 24.759 -20.682 1.00 8.49 C ATOM 4 OG SER C1390 36.013 23.692 -19.747 1.00 8.49 O ATOM 5 C SER C1390 35.622 26.326 -18.821 1.00 8.49 C ATOM 6 O SER C1390 36.138 26.652 -17.753 1.00 8.49 O If, for test, I use rename_segments() with renumber_residues=[1390], the position if the residue numbers is fine. The problem happens only if the my residue numbers have four digits. I use modeller version 14. Thanks in advance for your help, Jan Kosinski

2 2

malign3d error with different structures but the same sequence
by Felipe Villanelo 03 Sep '14

03 Sep '14

Hello Modellers users: I want to analyze a set of PDB models, all with same sequence (84 Aa peptide) but different conformations (obteined by different methods). So I used the compare.py script from tutorial to do a first classification from structure but I get the error: _modeller.ModellerError: fit2xyz_296E> Number of equivalent positions < 3: 0 I search this error, and most of the time is related to too different proteins that do not align well in sequence. But in my case all the protein are the same sequence!. Even I add a write step between malign() and malign3d() in the script so I see a perfect sequence alignment. Some idea? could be the reason that some structures are too different? Thanks! Felipe Villanelo Lizana Bioquímico Laboratorio de Biología Estructural y Molecular Universidad de Chile "La curiosidad no mató al gato, sino que la falta de ella"

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Models based on the multiple templates
by James Starlight 03 Sep '14

03 Sep '14

Dear Modeler users! Could you provide me with the ideas bases on which the modeler build the final models having several templates as well as its multiple-structural alignment as the inputs? In my case I'd like to build model of the GPCR having 5 templates of other receptors (with known X-ray structures) having low sequence identity against my target. What will be better i) to include all structures as the templates or ii) choose only one template with the highest sequence identify to my target? In the first case we will obtain trivial result: model will looks like the template but in the second case ( model built based on the multiple templates) - what type of averaging between templates will be used by modeler to produce final model? Please provide me with some ideas and reading about this topic. Thanks for suggestions, James

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secondary structure restrain error
by Albert 18 Aug '14

18 Aug '14

Hello: I am trying to use the following script for restrain my secondary structure: 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:’))) a = MyModel(env, alnfile='CBM-mult.ali', knowns=('2z73A','3uonA'), sequence='CBM', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model= 1 a.ending_model = 1 a.make() But it always failed with messages: File "model_mult.py", line 36 SyntaxError: Non-ASCII character '\xe2' in file model_mult.py on line 36, but no encoding declared; see http://www.python.org/peps/pep-0263.html for details 02-modeller/work> python test.py File "test.py", line 7 SyntaxError: Non-ASCII character '\xe2' in file test.py on line 7, but no encoding declared; see http://www.python.org/peps/pep-0263.html for details Does anybody have any idea where is the problem? THX ALbert

2 1

distance restraint
by flavio seixas 13 Aug '14

13 Aug '14

Hi Ben, I try to make a distance restraint between two atoms (protein and cofator) in a homodimer protein. However, I face another error: [flavios@localhost]$ mod9.13 model-mult-simmetry-bond.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 Traceback (most recent call last): File "model-mult-simmetry-bond.py", line 40, in ? a.make() File "/usr/lib/modeller9.13/modlib/modeller/automodel/automodel.py", line 108, in make self.multiple_models(atmsel) File "/usr/lib/modeller9.13/modlib/modeller/automodel/automodel.py", line 212, in multiple_models self.outputs.append(self.single_model(atmsel, num)) File "/usr/lib/modeller9.13/modlib/modeller/automodel/automodel.py", line 308, in single_model self.model_analysis(atmsel, filename, out, num) File "/usr/lib/modeller9.13/modlib/modeller/automodel/automodel.py", line 350, in model_analysis self.user_after_single_model() File "model-mult-simmetry-bond.py", line 34, in user_after_single_model rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['NZ:38'], at['C4:382']), mean=1.5, stdev=0.1)) NameError: global name 'rsr' is not defined I am certain that it must be an script error, but I do not know how to fix (I am not familiar with python script). My script is: # Homology modeling with single template from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class 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 env.io.water = True class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Constrain the A, B, C and D 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)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) #Restrain between LYS and PLP (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['NZ:38'], at['C4:382']), mean=1.5, stdev=0.1)) rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['NZ:424'], at['C4:768']), mean=1.5, stdev=0.1)) a=MyModel(env, alnfile='AlRacem-mult.ali', knowns=('4A3Q', '1BD0'), sequence='AlRacem', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 10 a.make() # Get a list of all successfully built models from a.outputs ok_models = filter(lambda x: x['failure'] is None, a.outputs) # Rank the models by DOPE score key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) # Get top model m = ok_models[0] print "Top model 1: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[1] print "Top model 2: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[2] print "Top model 3: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[3] print "Top model 4: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[4] print "Top model 5: %s (DOPE score %.3f)" % (m['name'], m[key]) ------------------------------------- Flavio Augusto Vicente Seixas Laboratory of Structural Biochemistry Department of Biochemistry Universidade Estadual de Maringá, PR, Brazil http://www.uem.br

2 1

User restriction
by flavio seixas 11 Aug '14

11 Aug '14

Hi, I was trying to make a restriction to generate a covalent bond between NZ atom from Lisine with C4 atom of PLP cofator. I search Manual and modeler-List to find some clues about how to do, but USER restriction appears to be not supported by 9.13 version: [flavios@localhost AlaninaRacemase-Saureus-T9]$ mod9.13 model-mult-simmetry-restr.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 Traceback (most recent call last): File "model-mult-simmetry-restr.py", line 35, in ? a.make() File "/usr/lib/modeller9.13/modlib/modeller/automodel/automodel.py", line 103, in make self.rd_restraints() File "/usr/lib/modeller9.13/modlib/modeller/automodel/automodel.py", line 191, in rd_restraints self.restraints.append(file=self.csrfile) File "/usr/lib/modeller9.13/modlib/modeller/restraints.py", line 77, in append return _modeller.mod_restraints_read(self.__mdl.modpt, fh.file_pointer) _modeller.ModellerError: rdcsrs__703E> USER restraints format is no longer supported. My script contains model-mult-simmetry-restr.py contains: # Homology modeling from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class 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 env.io.water = True class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Constrain the A, 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)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) a=MyModel(env, alnfile='AlRacem-mult.ali', knowns=('4A3Q', '1BD0'), sequence='AlRacem', csrfile='my.rsr', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 1 a.make() # Get a list of all successfully built models from a.outputs ok_models = filter(lambda x: x['failure'] is None, a.outputs) # Rank the models by DOPE score key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) # Get top model m = ok_models[0] print "Top model 1: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[1] print "Top model 2: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[2] print "Top model 3: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[3] print "Top model 4: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[4] print "Top model 5: %s (DOPE score %.3f)" % (m['name'], m[key]) my.rsr file contains: MODELLER5 VERSION: USER FORMAT R 3 1 1 1 2 2 0 1.5000 0.2000 NZ:38:A C4:382:A R 3 1 1 1 2 2 0 1.5000 0.2000 NZ:424:B C4:768:B I appreciate any help. Best regards, Flavio ------------------------------------- Flavio Augusto Vicente Seixas Laboratory of Structural Biochemistry Department of Biochemistry Universidade Estadual de Maringá, PR, Brazil http://www.uem.br

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modeller_usage