- modeller_usage - salilab.org

Compatability with Anaconda
by R. Michael Sivley 30 Oct '14

30 Oct '14

I’ve installed Modeller-9.14 on a Mac (Mavericks). If I launch the system python2.7, I can import modeller successfully. However, I use the anaconda python distribution. I have tried creating a symbolic link from /Library/modeller-9.14/modlib/modeller to anaconda/lib/python2.7/site-packages/modeller, but I get the following import error: >>> import modeller Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/mikesivley/anaconda/lib/python2.7/site-packages/modeller/__init__.py", line 93, in <module> import _modeller ImportError: No module named _modeller I wasn’t able to find any mention of Anaconda on Modeller’s installation or FAQ pages. Has anyone successfully installed Modeller and imported from anaconda python? Thanks! Mike Sivley PhD Student Department of Biomedical Informatics Vanderbilt University Medical Center

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Newbie question - Selecting chains and plotting DOPE profiles
by Justin Havird 22 Oct '14

22 Oct '14

Hi, I have just been using MODELLER for a couple weeks now and have a question that is hopefully an easy one. I am trying to model proteins of the cytochrome oxidase (COX) complex from a variety of organisms. I followed the "basic tutorial" online and got great results for the first subunit in the complex (COX1). But, when I tried the same thing for COX2, the align2d.py script aligns my sequence against ChainA in the complex instead of ChainB, so I end up with something that looks like COX1 instead of COX2. This happens even though I change the "aln.append_model" line in align2d.py to align_codes='1v54B', instead of 1v54A. I was able to work around this by following the advanced tutorial and using the multiple templates scripts (even though there is sometimes only a single template to compare the sequence to). However, I am not able to compare the correct DOPE profiles when trying plot_profiles.py; ChainA's profile is being used when comparing to the model instead of ChainB. I would like to be able to get an idea of how good the model is and identify areas of weak reliability, so the DOPE profiles seem like a good tool. Any help would be appreciated, as I really like the MODELLER software so far and hope to be able to make use of it. Thanks, Justin ************************************************************ Justin C. Havird, PhD Department of Biology Colorado State University Room E106 Anatomy/Zoology Building Fort Collins, CO 80523 Lab telephone: 970-491-2058 Fax: 970-491-0649 Email: Justin.Havird(a)colostate.edu Justin's Research Website: http://jchavird.wix.com/jchavird Sloan Lab Website: https://sites.google.com/site/danielbsloan/ ************************************************************

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selection of loop
by Yixin Ai 09 Oct '14

09 Oct '14

Dear everyone, i have a question and i need your help. i want to refine loops (50-60 and 90-100) of my model after building model by modeller9.14. however, i don't know how to set the two regions. the part codes of my script is: return selection(self.residue_range('50:', '60:'), self.residue_range('90:', '100:'), selection_status='INITIALIZE') is right or not? And what's the difference between self.residue_range('90:', '100:') and self.residue_range('90', '100')? thank you very much! ai yixin

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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

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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

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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.

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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

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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,

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