- modeller_usage - salilab.org

modeller parallel
by Yixin Ai 08 Oct '14

08 Oct '14

Dear everyone, i have a question and i need your help. when i use the command 'modpy.sh python model-parallel.py' to perform parallel computation. but i got the empty modelparallel.log file which not contain the molpdf, dope and ga341 score. how can i get the score functions in the log file? thank you very much ai yixin

2 1

Modeller for alignment and modeling
by Michael Meyer 02 Oct '14

02 Oct '14

Hi everyone, I'm relatively new to Modeller, so please bear with me. I have specific applications in-mind for the future, but for now as an exercise I'm trying to accomplish basic tasks. Right now, I'm trying to accomplish some basic multi-chain modeling. Let's say I have two target protein sequences, and I have found a PDB template that is appropriate for modeling them via PSI-BLAST. However, unlike the 2-chain example here: http://salilab.org/modeller/manual/node29.html the two chains that are homologous to my target sequences are not A and B in a two-chain PDB. They are C and E, or worse, F and B. My question: Is there any way to use the PIR format en route to automodel.make() to specify two chains that aren't contiguous in a template? The example given below assumes that the two chains in 2abx are the first two, but what if they were chains C and A?. I could flip their order to get them to be in the order they appear in the PDB file, but there's still the issue that chain B doesn't factor into my modeling step, and so I would like modeller to ignore it? Is there any way to not use chain B without altering the original PDB file to only include the two chains I want to use for modeling? >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* Furthermore, is there any way to use align2d to perform the two sequence-two chain alignment in one step to create the appropriate PIR file for multi-chain modeling. Right now, I'm doing two align2d commands to create two separate PIR files, and then mashing them together afterward. Thanks! Michael

2 1

build_profile problem
by Vinicius Seus 30 Sep '14

30 Sep '14

Hi everyone, I have a problem with build_profile.py. It runs fine but the output file only appear one line about my target sequence. It doesn´t appear about the molecules from my database (seqdump.pir). There is an warning in the midlle of the process that say this: regress_656W> Number of bins for histogram too small - results maybe unreliable, nbins: 4 regress_656W> Number of bins for histogram too small - results maybe unreliable, nbins: 4 regress_656W> Number of bins for histogram too small - results maybe unreliable, nbins: 4 Anyone can help me? Thanks. In attachment, my files.

2 1

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

2 1

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

2 1

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"

2 1

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

2 1