April 2014 - modeller_usage

Blast search for structures related to target
by James Starlight 16 Apr '14

16 Apr '14

Dear Modeler users! I have a question about 1st part of basic modeller tutorial. As I understood the* profile.build() method could be useful for scanning *seq_database_file='pdb_95.pir' file where the sequences of the possible templates with known structures are provided against target which are defined further by means of aln.append(file='TvLDH.ali'). Does it possible to use blast search method within the modeller script to create such seq_database_file pir file firstly which will consist of all found pdb's structures with the defined threshold sequence against target sequence (e.g not less as 50% of sequence homology)? Thanks for help, James

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Multiple sequence alignment + modeling in one script
by James Starlight 16 Apr '14

16 Apr '14

Dear modeler users, I'm looking for the posible modeling script which could do: i - multiple sequence alignment of several sequences agains target sequence (for which experimental structure is exist) to detect common functional-relevant motifs in each sequence of ensemble ii- select the aligned sequence from the ensemble iii- make a homology model for this structure based on the provided experimental (reference) structure including S-S bridges and ligand's coppied from the reference. Please provide me with simolple python example of such fussion of sequence analysis and homology modeling, Best, James S.

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Re: [modeller_usage] modeller_usage Digest, Vol 13, Issue 23
by Rajesh gazara 15 Apr '14

15 Apr '14

Dear James, you have to define it with alignment file. like you have template sequence for example... >P1;xyz structureX:xyz.pdb: 11 :A:+364 :A LGDTNLFKPIKIGNNELLH.* >P1;ABC sequence:ABC: : : : ::: 0.00: 0.00 MSDSRLFKPLKVGSIELL.* here . defines the Heteroatom then use ali.py script and don't forget ligand must be present in template pdb file with regards, Rajesh Kumar Gazara On Wed, Apr 16, 2014 at 9:40 AM, <modeller_usage-request(a)salilab.org> wrote: > Send modeller_usage mailing list submissions to > modeller_usage(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. Re: Multiple sequence alignment + modeling in one script > (Modeller Caretaker) > 2. Re: Including ligand from template (Modeller Caretaker) > 3. Re: Including ligand from template (James Starlight) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 15 Apr 2014 11:55:30 -0700 > From: Modeller Caretaker <modeller-care(a)salilab.org> > To: James Starlight <jmsstarlight(a)gmail.com>, modeller_usage > <modeller_usage(a)salilab.org> > Subject: Re: [modeller_usage] Multiple sequence alignment + modeling > in one script > Message-ID: <534D80A2.5090504(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 4/15/14, 12:11 AM, James Starlight wrote: > > I've forced with small problem during installation of the ModPipe: while > > running setup file it ask me > > > > You need to have a copy of MODELLER in the ext/mod/ directory. > > Please install it (see the documentation) then rerun this script. > > > > (here my modeller have been installed in the default dirs using > > sudo env KEY_MODELLER=***** dpkg -i modeller_9.13-1_amd64.deb > > > > how I could provide correct install path to dpkg? > > See the documentation, like it suggests? ;) You need the .tar.gz > installer, as detailed at > http://salilab.org/modpipe/doc/install-ext.html#install-ext > > > 2) Are there any usefull tutotials for the ModPipe besides presented in > > readme ? > > See above... > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 2 > Date: Tue, 15 Apr 2014 12:03:07 -0700 > From: Modeller Caretaker <modeller-care(a)salilab.org> > To: James Starlight <jmsstarlight(a)gmail.com>, modeller_usage > <modeller_usage(a)salilab.org> > Subject: Re: [modeller_usage] Including ligand from template > Message-ID: <534D826B.6060002(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 4/15/14, 2:05 AM, James Starlight wrote: > > 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 > > As pointed out already, you haven't told Modeller to put the ligand in > the model. Is it possible that you modified the 2rh1.pdb file? Your > template sequence doesn't match the one in 2rh1 from PDB (there's an > extra sequence in the official PDB from residue 1002:A to 1161:A that > isn't in yours). Maybe you removed the ligand by mistake too. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > ------------------------------ > > Message: 3 > Date: Wed, 16 Apr 2014 10:40:08 +0400 > From: James Starlight <jmsstarlight(a)gmail.com> > To: Modeller Caretaker <modeller-care(a)salilab.org>, modeller_usage > <modeller_usage(a)salilab.org> > Subject: Re: [modeller_usage] Including ligand from template > Message-ID: > < > CAALQopx1nYLFQAGxct_5SGeMJDMLpwBx2t2_b44Oy38esCxeuQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Thanks for suggestions again! > > Could you tell me as well > 1) what should I provide to the below ali.py script to copy HETATM from > the template to the model > > env = environ() > aln = alignment(env) > # Read in HETATM records from template PDBs > env.io.hetatm = True > env.io.hydrogen= True > > mdl = model(env, file='3eml', model_segment=('FIRST:A','LAST:A')) > aln.append_model(mdl, align_codes='3emlA', atom_files='3eml.pdb') > aln.append(file='od_r.ali', align_codes='od_r') > aln.align2d() > aln.write(file='result3.ali', alignment_format='PIR') > aln.write(file='result3.pap', alignment_format='PAP') > > 2) how salt bridges can be defined in the model taken from the template > with the homology cysteins in the same positions? > > > James > > > 2014-04-15 23:03 GMT+04:00 Modeller Caretaker <modeller-care(a)salilab.org>: > > > On 4/15/14, 2:05 AM, James Starlight wrote: > > > >> 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 > >> > > > > As pointed out already, you haven't told Modeller to put the ligand in > the > > model. Is it possible that you modified the 2rh1.pdb file? Your template > > sequence doesn't match the one in 2rh1 from PDB (there's an extra > sequence > > in the official PDB from residue 1002:A to 1161:A that isn't in yours). > > Maybe you removed the ligand by mistake too. > > > > Ben Webb, Modeller Caretaker > > -- > > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > >

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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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