- modeller_usage - salilab.org

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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Retrieving full sequence from PDB file
by sneha bairy 07 Feb '11

07 Feb '11

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

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How to make Modeller run Iteratively
by Ashish Runthala 07 Feb '11

07 Feb '11

Dear Modellers, I am facing a small problem. Just like command line arguments are there in scripts, is it possible to make MODELLER run iteratively, based on my defined set of parameters integrated with MODELLER. If so, how. I want to use Modeller in this way. 1. I want to call salign_iterative/align2d.py with varying proteins and dynamically considered constraints. 2. Run align2d.py ( If salign is called, with my own set of defined parameters). 3. Run model_mult.py (Dynamically changing PDB template names with chainID with every run) 4. Iterate the loop 1-3 until some set of conditions are satisfied. How to make MODELLER functions change the considered parameters declared during the function call. Thanks Ashish

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how to include a pepetide during homology modelling?
by albert 07 Feb '11

07 Feb '11

Hi: I just find that Modeller could build model containing a small molecular within it. And I am wondering how to building model including a peptide from template? THX

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symmetry restrain
by flavio seixas 07 Feb '11

07 Feb '11

Hi, I'm trying to built a protein with 4 identical chains using the symmetry restrain to CA atoms as section "2.2.11 Building multi-chain models with symmetry" from modeller 9v7 manual. This is my input: # Homology modeling with multiple templates from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output # Override the special_restraints and user_after_single_model methods: class MyModel(automodel): def special_restraints(self, aln): # 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') s3 = selection(self.chains['C']).only_atom_types('CA') s4 = selection(self.chains['D']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, s3, s4, 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() # create a new MODELLER environment to build this model in # directories for input atom files #env.io.atom_files_directory = ['.', '../atom_files'] a = MyModel(env, alnfile='xynB1-multiple.ali', knowns=('3C2U', '1YIF', '2EXH'), sequence = 'xynB', assess_methods=(assess.DOPE, assess.GA341)) # code of the target a.starting_model= 1 a.ending_model = 2 a.make() The problem is that the program stops and the following error message appears at the shell: File "model-multiple.py", line 37, in ? a.make() File "/usr/lib/modeller9v7/modlib/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/usr/lib/modeller9v7/modlib/modeller/automodel/automodel.py", line 435, in homcsr self.mkhomcsr(selection(self), aln) File "/usr/lib/modeller9v7/modlib/modeller/automodel/automodel.py", line 523, in mkhomcsr self.special_restraints(aln) File "model-multiple.py", line 19, in special_restraints self.restraints.symmetry.append(symmetry(s1, s2, s3, s4, 1.0)) TypeError: __init__() takes exactly 4 arguments (6 given) This is line 19: self.restraints.symmetry.append(symmetry(s1, s2, s3, s4, 1.0)) Someone could tell me what i am doing wrong? I can not find clues at the google. Thanks for any help. Flavio

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GETF, IUPAC_M and IATMCLS errors
by Seth Tanner 07 Feb '11

07 Feb '11

I could not find what the following three error messages mean in the log file. I would be grateful if you could explain what the causes are and suggest several possible solutions. Thanks. Message 1) getf_______W> RTF restraint not found in the atoms list: residue type, indices: 17 384 atom names : C +N atom indices : 3127 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 17 384 atom names : C CA +N O atom indices : 3127 3123 0 3128 Message 2) iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_484W> Dihedral still outside +-90: -90.3341 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_484W> Dihedral still outside +-90: -90.7680 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. Message 3) << end of ENERGY. DOPE-HR score : -13843.593750 >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: THR:OXT THR iatmcls_286W> MODEL atom not classified: THR:OXT THR iatmcls_286W> MODEL atom not classified: THR:OXT THR iatmcls_286W> MODEL atom not classified: THR:OXT THR

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