April 2014 - modeller_usage

Alternate sidechain positions
by meginir urestal 28 Apr '14

28 Apr '14

how does modeller handle alternate sidechain positions in a pdb file?

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Re: [modeller_usage] How do you use MOULDER?
by meginir urestal 28 Apr '14

28 Apr '14

> Hi, > > I was reading the tutorials and one of them cites MOULDER as an iterative > approach to alignment and homology modeling. > The 2003 paper in nucleic acids research says that MOULDER is restricted > to a few users only. > Has MOULDER been implemented in recent MODELLER versions? If not, how can > you use it on the MODWEB server? > > Thanks, > >

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Generate PDB using diheral angles
by Harinder Singh 28 Apr '14

28 Apr '14

Currently i am using the tleap in amber tools to generate a PDB using only dihedral angles. Is it possible to generate a PDB/Model using only dihedral angles and the sequence, just like amber tools. I have read the whole manual, but didn't get anything useful. The only way you can restrain your model is using restrain file .rsr, which i really don't know how to generate from dihedral angles. -- Harinder Singh Senior Research Fellow Dr. G.P.S Raghava Group IMTECH, INDIA.

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(no subject)
by Julian 23 Apr '14

23 Apr '14

Hello everybody, I would like to know how you model helices with a gap or insertion (pi or 310 helices). I noticed that if the gap / insertion is in the middle of the helix, Modeller arranges it quite nicely with the alpha restraint. But how can I solve this problem if the gap / insertion is at the very end of the helix? Thank you for your answers! Julian

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Modeller Parallel work
by Yao, Jianzhuang 21 Apr '14

21 Apr '14

?Dear Sir/Madam, I am running Modeller to build 500 homology models for a methyltransferase. Now I am running serial job. Do you think I can run parallel job? Or do you think I can submit the same script for 500 times and I can get the same results with serial job? Thanks a lot! Jianzhuang

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GPCRs and iterative modeling
by James Starlight 19 Apr '14

19 Apr '14

Dear modeller users! Inspired by modeller's iterative tutorial I wounder to know more about MOULDING concept of modelling and its automatics implementation within the modelling scripts. For instance I'm modelling of Rhodopsin-like membrane receptors from GPCR super-family with very slow sequence overlap with the closest templates (up to 20%) so I'm not sure both in automated-generated alignments as well as in the final models. How I could improve quality of both things using iterative concept? Does anybody have experience with the GPCRs modeling ? Best wishes, James

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by Dropbox 18 Apr '14

18 Apr '14

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Modeling muli-chain protein
by Richard W. Harper 18 Apr '14

18 Apr '14

Attached is a python script to build a model from the sequence PfFT on the template 1JCS. The first residue in 1JCS is numbered 55. For the start residue in chain A of 1JCS nothing less than 55 is accepted. However, if I put in 55, it tries to align residue 55 in the pir alignment file with residue 1 in the sequence. I have tried various combinations without success. I really did read the documentation. Please help. Thanks. -- Richard W. Harper Ph.D. Research Professor Indiana University-Purdue University Indianapolis (IUPUI) Department of Chemistry and Chemical Biology 402 N. Blackford Street, LD326 Indianapolis, IN 46202-3274

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Including ligand from template
by James Starlight 18 Apr '14

18 Apr '14

Dear Modeller users! I've followed 1st modeller tutorial making alignment of my target against 1 template (with the inclusion of hetatm from the template). As the result I've obtained the below alignment >P1;2rh1A structureX:2rh1.pdb: 29 :A:+283 :A:::-1.00:-1.00 ---------DEVWVVGMGIVMS----------LIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGL AVVPFGAAHILMKMWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWI VSGLTSFLPIQ-MH--WYRATHQE-----AINCYAEETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEA KRQLKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIYC-RSPDF RIAFQELLCL------.* >P1;od_r sequence:od_r: : : : ::: 0.00: 0.00 MEGKNLTSISECFLLGFSEQLEEQKPLFGSFLFMYLVTVAGNLLIILVIITDTQLHTPMYFFLANLSLADACFVS TTVPKMLANIQIQSQAISYSGCLLQLYFFMLFVMLEAFLLAVMAYDCYVAICHPLHYILIMSPGLCIFLVSASWI MNALHSLLHTLLMNSLSFCANHEIPHFFCDINPLLSLSCTDPFTNELVIFITGGLTGLICVLCLIISYTNVFSTI LKIPSA-QGKRKAFSTCSSHLSVVSLFFGTSFCVDFSSPSTHSAQKDTVASVMYTV--VTPMLNPFIYSLRNQEI KSSLRKLIWVRKIHSP-* where Od_r is the modeled protein and 2rh1 is the template consisted of ligand ('.' in aliugn file) now I'm running script for making models (where ligand should be included from the template and obtain error about atom mismatches from modeller import * from modeller.automodel import * # Read in HETATM records from template PDBs env.io.hetatm = True env.io.hydrogen= True # directories for input atom files env.io.atom_files_directory = ['.', './results'] env = environ() a = automodel(env, alnfile='result.ali', knowns='2rh1A', sequence='od_r', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 10 a.make() return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) _modeller.ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different: 283 282 For alignment entry: 1 2rh1A how it could be fixed and obtain models with the ligands in the positions identical to the templates ? James

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Loop refining
by James Starlight 18 Apr '14

18 Apr '14

Dear Modeller users! I have a question regarding loop refining. Following modeller advanced tutorial I've tried to do such task on my receptor model consisted of 6 loops (with 2 S-S bridges in one of the loop) which should be refined. 1)Does it possible to make some corrections in the below script to refine all 6 loops at one task keeping intact interloop S-S bonds. E.g I'd like to refine regions 51-58, 87-94, 127-141, 163-195, 228-233 and 260-270 class MyLoop(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): # 10 residue insertion return selection(self.residue_range('127', '139')) 2) What are the most trivial way to rank refinement for all N models? E.g usage of the model_energies.py leading to looping all of the models result in the .profile file. How I could estimate dope scores within the loop selections on all N models ? Thanks for help, James

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