November 2006 - modeller_usage

structure not read in
by Nicolas Fusseder 30 Nov '06

30 Nov '06

Hello, I have an application which models protein sequences based on template structures which are found by blasting the query sequence against all sequences from pdbaa. The entire modeling process works fine, only when one of the templates structures found via blast was solved with Cryo-EM the modelling process fails with the following error (sorry for the nasty formatting): C:\bea\user_projects\domains\mydomain\applications\tools\temp\FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks>mod8v2 C:\bea\user_projects\domains\mydomain\applications\tools\temp\FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks\model_FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks.py C:\bea\user_projects\domains\mydomain\applications\tools\temp\FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks 'import site' failed; use -v for traceback Traceback (most recent call last): File "C:\bea\user_projects\domains\mydomain\applications\tools\temp\FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks\model_FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks. py", line 8, in ? a.make() File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\automodel.py", line 100, in make self.homcsr(exit_stage) File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\automodel.py", line 331, in homcsr aln.check() File "C:\Program Files\Modeller8v2\modlib\modeller\alignment.py", line 153, in check io=io.modpt, libs=libs.modpt, **vars) File "C:\Program Files\Modeller8v2\modlib\modeller\util\top.py", line 37, in check_alignment return _modeller.check_alignment(aln, io, libs, *args) _modeller.error: check_a_337E> Structure not read in (please consult the log file for more details): 1 1D3E1 ExitValue: 0 Status(3): Loading file... Status(1): Load failed! alignment file looks like this: C; Produced by MODELLER >P1;1D3E1 structureE:1D3E:1 :1:285 :1:MOL_ID 1; MOLECULE INTERCELLULAR ADHESION MOLECULE-1; CHAIN I; FRAGMENT:MOL_ID 1; FRAGMENT 1 - 185; ORGANISM_SCIENTIFIC HOMO SAPIENS; ORGANISM_CO:28.00:-1.00 APVAAYVDEVLNEVLVVPNINQSHPTTSNAAPVLDAAETGHTNKIQPEDTIETRYVQSSQTLDEMSVESFLGRSG CIHESVLDIVDNYNDQSFTKWNINLQEMAQIRRKFEMFTYARFDSEITMVPSVAAKDGHIGHIVMQYMYVPPGAP IPTTRDDYAWQSGTNASVFWQHGQPFPRFSLPFLSIASAYYMFYDGYDGDTYKSRYGTVVTNDMGTLCSRIVTSE QLHKVKVVTRIYHKAKHTKAWCPRPPRAVQYSHTHTTNYKLSSEVHNDVAIRPRTNLTTV* >P1;FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks sequence:FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks:1 : :113 : :::-1.00:-1.00 ----VGHD------------SGGFSTTVSTGQSVPDPQVGITTM---KDLKANR-----GKMDVSGVQAPVG--- ----AITTIED---------------------------------------PVLAKK------------------- VPET---------------------FPELK-----------------PGE---SRH----------------TSD HM-------SIYKFMGRSHFLC---------TFTFNSNNK---EKEYTFPI---TL----* I also noticed that unlike sucessful modelling attemps, when I attempt to model with 1D3E (Cryo-EM structure) as a template structure the .RSR as well as a .D00000001 file are never created. All help would be greatly appreciated, Sincerely, -- Nicolas Fusseder

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Using DOPE with membrane proteins
by John Simms 30 Nov '06

30 Nov '06

Hi all, I was wondering if DOPE could be used with membrane proteins? Would the stat potential still hold if i assume membrane proteins are just soluble proteins in side out ? dunno? Cheers John

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Error in 8v2
by Dhananjay 29 Nov '06

29 Nov '06

Hello all, I am getting followin error while running mod8v2 model-default.py [dhananjay@cdfd-wstn7 automodel] mod8v2 model-default.py Traceback (most recent call last): File "model-default.py", line 18, in ? a.make() # do the actual homology modelling File "/users/dhananjay/bin/modeller8v2/modlib/modeller/automodel/automodel.py", line 100, in make self.homcsr(exit_stage) File "/users/dhananjay/bin/modeller8v2/modlib/modeller/automodel/automodel.py", line 318, in homcsr aln = self.read_alignment() File "/users/dhananjay/bin/modeller8v2/modlib/modeller/automodel/automodel.py", line 312, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "/users/dhananjay/bin/modeller8v2/modlib/modeller/alignment.py", line 36, in append return self.__int_append('alignment.append', io, libs, vars) File "/users/dhananjay/bin/modeller8v2/modlib/modeller/alignment.py", line 68, in __int_append libs=libs.modpt, **vars) File "/users/dhananjay/bin/modeller8v2/modlib/modeller/util/top.py", line 33, in read_alignment return _modeller.read_alignment(aln, io, libs, *args) _modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 1M1G I am new to this software. Please tell me whats wrong here Thanking you in advance -- Dhananjay C Joshi Project Assistant LT & LSB, C D F D ECIL Road, Nacharam Hyderabad-500 076, INDIA Tel : +91-40-27151344 Fax : +91-40-27155610

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Psipred output in MODELLER
by doppelt olivia 29 Nov '06

29 Nov '06

Hello, Is it possible de use PSIPRED program on a sequence and then use the output file, directly in MODELLER for it to generate MODELS using psipred's predictions as constraints ? If not, how can i use secondary prediction as constraint in MODELLER ? Thanks in advance, Olivia Doppelt ___________________________________________________________________________ Découvrez une nouvelle façon d'obtenir des réponses à toutes vos questions ! Profitez des connaissances, des opinions et des expériences des internautes sur Yahoo! Questions/Réponses http://fr.answers.yahoo.com

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RROR: command not recognized from modeller.automodel import *
by gadde suneetha 29 Nov '06

29 Nov '06

Hai, I executed the following program from the tutorial by using mod7 build.top at the command prompt.mod7 is the alias name. from modeller.automodel import * log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './:../atom_files' a = automodel(env, alnfile = 'alignment.ali', knowns = '5fd1', sequence = '1fdx', inifile = 'my-initial.pdb') a.starting_model= 1 a.ending_model = 1 a.make() when i executed the above command i got the following error: rdactio_534E> Command not recognized: FROM MODELLER.AUTOMODEL IMPORT * recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Please let me know how to overcome this error. Regards, suneetha __________________________________________________________ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/

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Re: [modeller_usage] Atom index is out of range
by Modeller Caretaker 20 Nov '06

20 Nov '06

andreyvoronkov wrote: > Dear MADELLER administration and MODELLER users, my MODELLER job, > using modeller for "initial model" procedure failed. I wanted to > replace a part of protein by the data of X-ray analysis and used > initial model procedure. I've got the error: > > "nselat__596E> Atom index is out of range (iatm,natm): 5009 > 5008" > > What might be the problem? I've browsed archives and found same > question, but there the problem was in mismatch of number of atoms. I > don't have such mismatch. The initial model is assumed to be produced by a previous Modeller run, which is not the case for your example. It has the wrong number of atoms, in the incorrect order. You can fix this problem by first reading your model into Modeller, 'correcting' it, and then writing it out again, with a script similar to that below (similar to examples/commands/energy.py): env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') aln = alignment(env) code = "FZD1" mdl = model(env, file=code) aln.append_model(mdl, atom_files=code, align_codes=code) aln.append_model(mdl, atom_files=code+'.ini', align_codes=code+'-ini') mdl.generate_topology(aln, sequence=code+'-ini') mdl.transfer_xyz(aln) mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') mdl.write(file='new%s.pdb' % code) 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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_modeller.errorS
by Tamas Hegedus 20 Nov '06

20 Nov '06

Hi, I'm using mod8v2 on RH AS4. ************************************************** I have an alignment file with 7 proteins (including the 'sequence'). I got the following error: _modeller.error: crsplin_223E> Internal error: array too small: MAXSPL current maximum, current need: 400 488 My guess: you have some hard coded buffer size, and I have too many and large (?) proteins in the alignment file... ************************************************** If I have 1XMI in the alignment file, I have the following error: _modeller.error: rdpir___648E> Alignment sequence not found in PDB file: 1 ./pdb/1XMI.pdb I checked for extra spaces, numbering, sequence, but I do not find the problem... You can find my script, alignment and pdb files at: http://www.biohegedus.org/modNbd2.py http://www.biohegedus.org/testB.pir http://www.biohegedus.org/1XMI.pdb *********** Thanks for your help in advance, Tamas -- Tamas Hegedus, PhD | phone: (1) 919-966 0329 UNC - Biochem & Biophys | fax: (1) 919-966 5178 6107 Thurston-Bowles Bldg | mailto:hegedus@med.unc.edu Chapel Hill, NC, 27599-7248 | http://biohegedus.org

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make_chains problem
by Nicolas Fusseder 17 Nov '06

17 Nov '06

Hello, When I run my make_chains.py script to generate a .chn file from a pdb file I have been encountering an issue. It works perfectly for pdb files where the chains are denoted as letters (A, B, C, D, ...) but pdb files where numerics are used to denote chains (1, 2, 3, 4, ...) no .chn file output. Below is the make_chains.py script I have been using: -------------------------------------------------- env = environ() mdl = model(env, file='c:/pdb/pdb1d3e.ent') mdl.make_chains(file='1D3E', minimal_chain_length=30, minimal_resolution=4.0, minimal_stdres=30, chop_nonstd_terminii=True, structure_types='structureN structureX', alignment_format='PIR') ---------------------------------------------------- for pdb id 1d3e (uses numerics): NO .CHN FILE OUTPUT for pdb id 1e3l (uses letters): WORKS, 2 .chn files are output Thank you for your help, -- Nicolas Fusseder

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(no subject)
by doppelt olivia 17 Nov '06

17 Nov '06

Hello, I've been using MODELLER 2 ways : first with only one template second with 2 templates Is the Objective Function of the modeles generated comparable ? and if so, how ? The first is around 600, and the second around 3000 for a 151 residus query sequence. Thanks in advance for your help, Olivia Doppelt ___________________________________________________________________________ Découvrez une nouvelle façon d'obtenir des réponses à toutes vos questions ! Profitez des connaissances, des opinions et des expériences des internautes sur Yahoo! Questions/Réponses http://fr.answers.yahoo.com

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Re: [modeller_usage] can't bond disulfide
by Modeller Caretaker 16 Nov '06

16 Nov '06

jitrayut jitonnom wrote: > I want to bond two disulfides (residue 20 and residue 66, res 105 > and res 164) by using script below. But i did not bond any > disulfides so why ? ... > a = automodel(env, alnfile='CD147-mult.ali', > knowns=('1F97A','1NBQA','1EPFB'), sequence='CD147') This line should start as a = mymodel(env, ... rather than a = automodel(env, ... so that you use the newly-defined 'mymodel' class, with the disulfide restraints. 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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