- modeller_usage - salilab.org

Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 33
by Ashish Runthala 16 Feb '11

16 Feb '11

You remove the chain identifier from both align2d.py and model_multiple.py (Or, whatever you are using) This is how i did it in one of the run. Thus, Align2d.py becomes mdl = model(env, file='Run2BestModel', model_segment=('1','292')) #No ChainID is here with model residue positions aln.append_model(mdl, align_codes='Run2BestModel', atom_files='Run2BestModel') So, Model_multiple.py will be a = automodel(env, alnfile = 'alignment.ali', knowns = ('Run2BestModel'), sequence = 'target', assess_methods=(assess.DOPE, assess.GA341,assess.normalized_dope)) a.starting_model= 1 a.ending_model = 1000 a.make() Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Birla Institute of Technology & Science, Pilani Rajasthan, INDIA

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mutiple CPU error
by albert 16 Feb '11

16 Feb '11

Hi I try to build model with my own constrain(beta sheet) with multiple CPU, but it said: ----------------log-------------------- raise RemoteError(obj.exc, self) modeller.parallel.communicator.RemoteError: AttributeError: 'module' object has no attribute 'MyModel' from <Slave on localhost> I ues the following script for multiple CPU: -------------script------------------------ from modeller import * from modeller.automodel import * from modeller.parallel import * j = job() j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) env = environ() log.verbose() ---------------------------------------------- THX

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initial model error
by albert 16 Feb '11

16 Feb '11

Hi: I would like to build a model staring from my own model. but it didn't work, it is said: -------log-------------- _modeller.ModellerError: rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " ", chain " "; atom file name: init.pdb -------------------------- In fact in the alignment file I already add something like this: -------------------align---------------------------- >P1;seq sequence:seq: : : : ::: 0.00: 0.00 aaaaaaaaaaaaaaaaaaaaaaaaaaaaaa >P1;init structureX:init.pdb:1 :A: :A:::-1.00:-1.00 aaaaaaaaaaaaaaaaaaaaaaaaaaaaaa >P1;temp structureX:temp.pdb:1 :A: :A:::-1.00:-1.00 aaaaaaaaaaaaaaaaaabbbbbbbbbbbb ----------script------------------------------------- class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Two beta-strands: rsr.add(secondary_structure.strand(self.residue_range('146:', '150:'))) rsr.add(secondary_structure.strand(self.residue_range('156:', '161:'))) a = MyModel(env, alnfile='mult.ali', knowns=('tempA'), sequence='my', inifile = 'init.pdb') a.starting_model = 1 a.ending_model = 2 ---------------------------------------------------------------------------- the seq and init share the same sequences. The starting model init.pdb contains a china named A. could you give me some advices? THX

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Modeling circular permutation
by bharat lal 16 Feb '11

16 Feb '11

Hi, I am trying to model circular permutation in my protein which is a beta barrel and I modeled it the following way-- AAAA-----BBB--------CCC------- A and B comprise the two halves of beta barrel and ---- refers to a cut in the loop region of beta barrel where the other domain has to be attached ... I generated some 20 models but none of them was satisfactory as the beta-barrel gets distorted in each of those models.. Can any body tell how can I achieve good models for modeling circular permutation ??? ---------- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 E-mail : monu46010(a)yahoo.com

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Differences using Xeon vs Opteron systems
by Robert Healey 15 Feb '11

15 Feb '11

Hello. I'm the systems administrator for a research lab using Modeller 9v3. I've installed the x86_64 RPM file on a pair of Xeon X5355 based systems and some Opteron 6136 based systems. The researchers are reporting getting radically different results between these two systems. I've done some testing and Opteron 252 based systems give the same results as the Opteron 6136 systems and Xeon X5570 systems give the same results as the Xeon X5355. I'm working on getting a set of results I can post, but has anyone seen anything like this before? I was being shown summaries where the final results were different in value by 1.5 Thank you. -- Bob Healey Systems Administrator Biocomputation and Bioinformatics Constellation and Molecularium healer(a)rpi.edu (518) 276-4407

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how to run modeller at different seeds?
by albert 15 Feb '11

15 Feb '11

hi: when we use modeller to build model, it start from a random xyz.SO, I am wondering how can we run it in different random seeds? THX

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Re: [modeller_usage] Modeling domain within a domain
by bharat lal 11 Feb '11

11 Feb '11

Hi, I want to model circular permutation in beta-barrel protein and when I tried it the following way I didnot get the result as expected coz the beta barrel gets distorted.. >templateAAAAAAAAAABBBBB-------BBBBBBBB >template--------------------------------CCCC----------------- >targetAAAAAAAAAABBBBBCCCCBBBBBBBB Also I want to connect the original termini with a linker which I have created using modeler Can anybody help ?? ----Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 E-mail : monu46010(a)yahoo.com

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align_codes problem
by Tuğba Küçükkal 11 Feb '11

11 Feb '11

Hi, I am new to both Modeller and homology modeling, and trying to do a simple modeling with the following script but I keep getting the error: Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = proe # Homology modeling by the automodel class 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 = ['.', '.'] a = automodel(env, alnfile = 'alignment6.ali', # alignment filename knowns = 'proe', # codes of the templates sequence = 'alp7') # 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 the actual homology modeling Here is my alignment6.ali file: >P1; PROE structureX:PROE:1:E:476:E:::-1.00:-1.00 -----------------------NEEGRLIEKLLGDYDKRIKPAKTLDHVIDVTLKLTLT NLISLNEKEEALTTNVWIEIQWNDYRLSWNTSEYEGIDLVRIPSELLWLPDVVLENNVDG QFEVAYYANVLVYNDGSMYWLPPAIYRSTCPIAVTYFPFDWQNCSLVFRSQTYNAHEVNL QLSAEEGIDPEDFTENGEWTIRHRPAKKNYNWQLTKDDIDFQEIIFFLIIQRKPLFYIIN IIAPCVLISSLVVLVYFLPAQAGGQKCTLSISVLLAQTIFLFLIAQKVPETSLNVPLIGK YLIFVMFVSLVIVTNCVIVLNVSLRTPN-------------------------------- ------------------------------------------------------------ -----------------THSCVEACNFIAKSTKEQNDSGSENENWVLIGKVIDKACFWIA LLLFSLGTLAIFLTG--HLNQVPE---* >P1; ALP7 sequence:ALP7:::::::0.00:0.00 MRCSPGGVWLALAASLLHVSLQGEFQRKLYKELVKNYNPLERPVANDSQPLTVYFSLSLL QIMDVDEKNQVLTTNIWLQMSWTDHYLQWNVSEYPGVKTVRFPDGQIWKPDILLYNSADE RFDATFHTNVLVNSSGHCQYLPPGIFKSSCYIDVRWFPFDVQHCKLKFGSWSYGGWSLDL QMQEAD---ISGYIPNGEWDLVGIPGKRSERFYECCKEP-YPDVTFTVTMRRRTLYYGLN LLIPCVLISALALLVFLLPADSG-EKISLGITVLLSLTVFMLLVAEIMPATSDSVPLIAQ YFASTMIIVGLSVVVTVIVLQYHHHDPDGGKMPKWTRVILLNWCAWFLRMKRPGEDKVRP ACQHKQRRCSLASVEMSAVAPPPASNGNLLYIGFRGLDGVHCVPTPDSGVVCGRMACSPT HDEHLLHGGQPPEGDPDLAKILEEVRYIANRFRCQDESEAVCSEWKFAACVVDRLCLMAF SVFTIICTIGILMSAPNFVEAVSKDFA* Thanks, tkucuk

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Re: [modeller_usage] Retrieving full sequence from PDB file
by Romain.Studer＠unil.ch 10 Feb '11

10 Feb '11

Hello, You can try the PDB module of the Biopython, it does it very well. http://biopython.org/DIST/docs/cookbook/biopdb_faq.pdf How do I extract polypeptides from a Structure object? Use PolypeptideBuilder. You can use the resulting Polypeptide object to get the sequence as a Seq object or to get a list of C atoms as well. Polypeptides can be built using a C-N or a C -C distance criterion. Example: # Using C-N ppb=PPBuilder() for pp in ppb.build_peptides(structure): print pp.get_sequence() # Using CA-CA ppb=CaPPBuilder() for pp in ppb.build_peptides(structure): print pp.get_sequence() Note that in the above case only model 0 of the structure is considered by PolypeptideBuilder. However, it is possible to use PolypeptideBuilder to build Polypeptide objects from Model and Chain objects as well. How do I get the sequence of a structure? The first thing to do is to extract all polypeptides from the structure (see previous entry). The sequence of each polypeptide can then easily be obtained from the Polypeptide objects. The sequence is represented as a Biopython Seq object, and its alphabet is defined by a ProteinAlphabet object. Example: > > > seq=polypeptide.get_sequence() > > > print seq Seq(SNVVE..., <class Bio.Alphabet.ProteinAlphabet>) Best regards, Romain ----- Original Message ----- Expéditeur: sneha bairy <bairysneha(a)gmail.com> à: modeller_usage(a)salilab.org Sujet: [modeller_usage] Retrieving full sequence from PDB file Date: Mon, 7 Feb 2011 11:23:10 -0600 > Hello, > For the project I am working on, I need all the sequence > residues from the pdb file irrespective of whether the > residues have atom information or not. I saw that there is > a way to write out the residues with atom information from > the pdb file. But is there a way to write out all the > sequence residues mentioned at the top of the pdb file? > > Thanks, > Sneha > > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > ----- Romain Studer Dept of Structural and Molecular Biology Darwin Building University College London Gower Street, WC1E 6BT London Tel +44(0)20 7679 3890 Fax +44(0)20 7679 7193

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assess multiple chain modelling
by Dimitri Gilis 10 Feb '11

10 Feb '11

Hello, I have successfully modelled a population of tetramers. But I would like to assess them. I found that the DOPE and the GA341 scores are not suitable to assess multiple chain proteins. So, which scoring scheme can I use ? Thanks in advance. Dimitri ---------------------------------------------------------------------------------------- Dimitri Gilis Genomic and Structural Bioinformatics 3BIO - Service de Biosystèmes, Biomodélisation et Bioprocédés (Biosystems, Biomodelling and Bioprocess Department) Université Libre de Bruxelles Av. F. Roosevelt, 50 CP 165/61 1050 Brussels Belgium Tel: +32 2 650 36 15 Fax: +32 2 650 35 75 e-mail: dgilis(a)ulb.ac.be

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