- modeller_usage - salilab.org

Re: [modeller_usage] Including ligand from template
by James Starlight 15 Apr '14

15 Apr '14

Thanks for suggestion! I've already done this placing '.' instead of '_' at the end of the sequence but the result was the same error which might indicate that ligand could not be found in template PDB where it present at the end of the sequence as the HETATM. Also I wounder to know 1) How I could easily convert alignment in FASTA done by the external servers to the modeler PIR format ? 2) how I could precisely define salt bridges between selected residues in the residues (or simply take it from the template with the homology cysteins in the same positions)? Thanks for help, James 2014-04-15 15:13 GMT+04:00 Lalith Kumar <lalithkumar07(a)gmail.com>: > The heteroatom tag . is missing in the Query of your interest. Please > place it at the end of your alignment (i.e., after HSP like this HSP.) in > query. > > > On Tue, Apr 15, 2014 at 2:35 PM, James Starlight <jmsstarlight(a)gmail.com>wrote: > >> 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 >> >> _______________________________________________ >> modeller_usage mailing list >> modeller_usage(a)salilab.org >> https://salilab.org/mailman/listinfo/modeller_usage >> >> > > > -- > Lalith Kumar K > Research Associate, > CADD Division, > Dr. Reddy's Institute of Life Sciences (Formerly known as Institute of > Life Sciences) > University of Hyderabad Campus > Gachibowli, Hyderabad 500046, India > Tel: +91 9502074040 >

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loop missing in a crystal structure
by flavio seixas 08 Apr '14

08 Apr '14

Hi Ben. I'm interested in using a crystal structure deposited in the PDB (structure A). However, there are two important loops missing. There is another homologous structure B from another source organism, where those loops are well defined inside electron density. I like to use the experimental data from this template B to model the missing loops in the structure A. I've tried to model the entire sequence of protein A using the B structure as a template, then cut and paste the generated loops from the model and put into the structure A. However, it did not work because many steric collisions occurred between the side chains of those loops and protein A. Carrying out loop modeling (loop.py) correct the clashes, but gives results extremely different from observed in template B. How do I model the missing loops directly in the structure A? Is it possible? I appreciate any suggestion. Regards Flavio ------------------------------------- Flavio Augusto Vicente Seixas Laboratory of Structural Biochemistry Department of Biochemistry Universidade Estadual de Maringá, PR, Brazil http://www.uem.br

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Changing dir and printing hydrogens
by Manoj Singh 02 Apr '14

02 Apr '14

Hi I am using mutate_model.py for making mutations. I have two questions. 1. How can I read the original pdb from different directory and put output structure in current directory. 2. How can I read and print hydrogen of original pdb in mutated pdb structure (except of mutated residue)

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Question
by Francisco garcia 02 Apr '14

02 Apr '14

Hi! I tried to generate a theoretical alpha-helix with the example from Modeller's Manual, but just don't work, because rasmol not identified as helix (my sequence is longer than example). I use more iterations ( 1x10^9) and get a better result but is not enough. Somebody know a better way to generate a perfect alpha helix?? I really need a theoretical helix for my work, please help me. This is the example: # Example for model.build_sequence(), secondary_structure.alpha() from modeller import * from modeller.optimizers import conjugate_gradients # Set up environment e = environ() e.libs.topology.read('${LIB}/top_heav.lib') e.libs.parameters.read('${LIB}/par.lib') # Build an extended chain model from primary sequence, and write it out m = model(e) m.build_sequence('GSCASVCGV') m.write(file='extended-chain.pdb') # Make stereochemical restraints on all atoms allatoms = selection(m) m.restraints.make(allatoms, restraint_type='STEREO', spline_on_site=False) # Constrain all residues to be alpha-helical # (Could also use m.residue_range() rather than m.residues here.) m.restraints.add(secondary_structure.alpha(m.residues)) # Get an optimized structure with CG, and write it out cg = conjugate_gradients() cg.optimize(allatoms, max_iterations=100) m.write(file='alpha-helix.pdb') P.D. I apologize for my English, i hope you understand me. Thanks!

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PYTHONPATH on Windows 7
by chris.wood＠stfc.ac.uk 01 Apr '14

01 Apr '14

Hello, I’ve got Python 2.7.3 on Windows 7: Python 2.7.3 |EPD 7.3-2 (64-bit)| (default, Apr 12 2012, 15:20:16) [MSC v.1500 64 bit (AMD64)] on win32 Type "copyright", "credits" or "license()" for more information. I’ve installed Modeller 9.12; but typing from modeller import * results in the “ImportError: No module named modeller” error, even though I've got modeller in my python path: >>> sys.path ['', 'C:\\Python27\\Lib\\idlelib', 'C:\\Program Files (x86)\\Modeller9.12\\modlib\\modeller', 'C:\\Program Files (x86)\\Modeller9.12\\modlib\\python2.7', 'C:\\Python27\\python27.zip', 'C:\\Python27\\DLLs', 'C:\\Python27\\lib', 'C:\\Python27\\lib\\plat-win', 'C:\\Python27\\lib\\lib-tk', 'C:\\Python27', 'C:\\Python27\\lib\\site-packages', 'C:\\Python27\\lib\\site-packages\\PIL', 'C:\\Python27\\lib\\site-packages\\win32', 'C:\\Python27\\lib\\site-packages\\win32\\lib', 'C:\\Python27\\lib\\site-packages\\Pythonwin'] >>> import modeller Traceback (most recent call last): File "<pyshell#5>", line 1, in <module> import modeller ImportError: No module named modeller I'm sure I've missed something obvious, but can't see it! Cheers, Chris ------------------- Dr Chris Wood STFC Rutherford Appleton Laboratory Didcot OX11 0QX chris.wood(a)stfc.ac.uk www.ccpem.ac.uk Tel: +44(0)1235 567864 Tel: +44(0)7909 586624 Fax: +44(0)1235 567801 Skype: chris_c_wood<callto://chris_c_wood/> -- Scanned by iCritical.

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How to override the build_seq() command in loopmodel class
by Abhijit Muley 21 Mar '14

21 Mar '14

I am having knots in my structure, same problem as this person had- http://salilab.org/archives/modeller_usage/2005/msg00394.html I went through the manual but could not find any specific part where such instructions have been mentioned (althought they could have been in some section I have missed). Can anyone please direct me to the appropriate resources to solve this problem?

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(no subject)
by Ankita Nagpal 17 Mar '14

17 Mar '14

hi I have just started using modeller with the help of tutorial example.In the aligning step when iam aligning 1bdm with TvLDH IAM getting error only 317 residue out of 318 contain atom of type CA .Can you plz help me out what is going wro <http://wrong.it/>ng

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Use some local alignments
by fakharian 15 Mar '14

15 Mar '14

Hi I want to build a model for my target protein base on a known template structure. And I have some target-template local alignments. I want to use(and force) these local alignments on known regions; and align other regions of target by MODELLER alignment functions such as align2d or salign. Can anyone suggest a method to perform this? Thank you.

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Select and remove atoms from automodel
by Ignacio Ibarra 04 Mar '14

04 Mar '14

Hello, Currently I am generating nucleic acid models using the MODELLER suite. I would like to remove the initial phosphate group declared in the first residue of each nucleic acid chain. Those atoms should not be present in real structures. I would like to do it without writing new text in the .lib files that are into the modlib folder I read about a pick_atoms() method in an older version of MODELLER, but it is not commented in the 9v11 manual ( http://binf.gmu.edu/software/MODELLER/node131.html) Is there something similar currently available for removing atoms from the model in the automodel or another class? Regards, Ignacio

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Alignment missing
by Paul Zair Leyva Miranda 25 Feb '14

25 Feb '14

Dear Modeller team, I need your quick suggestions and corrections on my scripts that I have been using to run on multiple computers. I am not getting any errors when I run the script3.py. But, when I compare the files .pap and .ali with other alignment servers like muscle, there are aminoacids missing in the alignment with Modeller. I don`t know where is the problem, if it is related to the alignmet with Modeller or if there is a problem in the script.py. Best regards. Paul Zair Leyva Miranda Laboratory of Molecular Modeling ESM-IPN

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