- modeller_usage - salilab.org

Re: [modeller_usage] HowTo Fix Position of Atoms?
by SaTa 05 Dec '06

05 Dec '06

Dear Mr. Webb, thank you very much for your quick and accurate answer. >You seem to be confused between atom selections and restraints. Actually, I was thinking of fixing the position of atoms in space. To me, this means adding constraints. Since I learned, that Modeller features no constraints, my next idea was to add a upper-bond harmonic potential, i.e. restraints to the r(1),r(2),r(3)-components in space. Studying this mailinglist, I found out that in Modeller, deselection would be the appropiate way. > I don't know where you got that link from; My apologize, I thought this was an official mirror, sorry for that. > I can't give you an example that does "exactly what has been requested" because you didn't give the exact problem. Anyway, your example tackled "exactly what has been requested" ;-) I was just confused by the first redefinition of the member actually *initializing* the selection_status parameter. However, I got it, now: The status is initializes *before* selecting the residues selected in selection_segment ;-) *That* was my confusion... Sincerly yours

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HowTo Fix Position of Atoms?
by SaTa 04 Dec '06

04 Dec '06

Dear all, having spend a couple of hours in reading the FAQ (e.g. http://salilab.org/modeller/FAQ.html#5 ), the manual (e.g.http://www.msg.ucsf.edu/local/programs/modeller/node29.html) this Mailinglist (e.g. http://salilab.org/archives/modeller_usage/2005/msg00143.html http://salilab.org/archives/modeller_usage/2003/msg00265.html ...) it is still a complete mystery to my how to fix the position of atoms when annealing. It was suggested to simply DESELECT the atoms I do not want to move at all (http://salilab.org/archives/modeller_usage/2005/msg00155.html) but the link to the manual given did not made clear HOW TO deselect atoms. However, I made my way to http://www.msg.ucsf.edu/local/programs/modeller/node29.html (Refining only part of the model). Still, this did not help. I simply do not understand how to realize this: Do Not Move The Position Of The Atoms Of Residue 75 to 80 in All Chains! >From the mailing-list I deduced, that quite a number of other people have been messing with the same question , and that referring to the manual or the F.A.Q doesn't really help. Instead, an example that does exactly what has been requested would be a pleasure! Thank you very much in advance

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(no subject)
by SaTa 04 Dec '06

04 Dec '06

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Please remove me from the mailing list, Thank you!
by Omid Khalouei 30 Nov '06

30 Nov '06

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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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