- modeller_usage - salilab.org

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

1 0

leonardo david herrera invited you to check out Dropbox
by Dropbox 18 Apr '14

18 Apr '14

Hi there, leonardo david herrera wants you to try Dropbox! Dropbox lets you bring all your photos, docs, and videos with you anywhere and share them easily. Get started here. https://www.dropbox.com/l/HbVKaB7SvVbSQseQUcDPa82??text=1 Thanks! - The Dropbox Team ____________________________________________________ To stop receiving invites from Dropbox, please go to https://www.dropbox.com/l/2x4tX9ITAIy6bZ8uEZALn02??text=1 Dropbox, Inc., PO Box 77767, San Francisco, CA 94107

1 0

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

2 1

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

2 5

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

2 1

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

2 1

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.

2 5

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 > > >

1 0

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 >

1 0

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

2 3