- modeller_usage - salilab.org

dynamic memory allocation failed
by Ilya Shlyakhter 05 Dec '05

05 Dec '05

Dear Modeller users, I'm getting a "dynamic memory allocation failed" message on a very small model. The test examples work fine, but when I modify model-full.py for my own use it gives a problem. Below I give the files I used, and the error message. I would appreciate any suggestions. Ilya model-full-test.py: ------------------------------------------------------------ # A sample script for fully automated comparative modeling from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './' a = automodel(env, # file with template codes and target sequence alnfile = 'myalign.seg', # PDB codes of the templates knowns = ('1fjk', '1yod'), # code of the target sequence = '1qqq') a.auto_align() # get an automatic alignment a.make() # do homology modelling ------------------------------------------------------------ myalign.seg: >P1;1qqq sequence:1qqq:FIRST:@:52:@:phospholamban:Homo sapiens: 0:0 MDKVQYLTRSAIRRASTIEMPQQARQKLQNLYINRCLREICQELKEIRAMLK* >P1;1fjk structureN:1fjk:1:A:52:A:phospholamban:Homo sapiens:0:0 * >P1;1yod structureX:1yod:1:B:51:B:phospholamban:Homo sapiens: 1.80:0 ------------------------------------------------------------ 1fjk.pdb and 1yod.pdb files, downloaded from the PDB, are in the current dir. model-full-test.log: -------------------------------------- Kind, OS, HostName, Kernel, Processor: 4, Linux optima 2.4.22-1.2199.nptl i686 Date and time of compilation : 06/20/2005 12:04:54 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2005/12/05 02:01:13.119 openf5__224_> Open 11 OLD SEQUENTIAL $(LIB)/restyp.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/resdih.lib rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii14.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch1.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch2.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch3.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 runcmd______> alignment.append(align_codes=['1fjk', '1yod'], atom_files=[], file='myalign.seg', (def)remove_gaps=True, (def)alignme\ nt_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True) openf___224_> Open myalign.seg openf5__224_> Open 13 OLD SEQUENTIAL ./1fjk.atm Dynamically allocated memory at amaxalignment [B,kB,MB]: 2124311 2074.522 2.026 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2125365 2075.552 2.027 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2299585 2245.688 2.193 openf5__224_> Open 13 OLD SEQUENTIAL ./1yod.atm Read the alignment from file : myalign.seg Total number of alignment positions: 52 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1fjk 52 1 1fjk phospholamban 2 1yod 0 0 1yod phospholamban runcmd______> alignment.malign((def)rr_file='$(LIB)/as1.sim.mat', (def)off_diagonal=100, (def)local_alignment=False, (def)matrix_of\ fset=0.0, (def)overhang=0, (def)align_block=0, gap_penalties_1d=(-600, -400)) openf5__224_> Open 11 OLD SEQUENTIAL $(LIB)/as1.sim.mat rdrrwgh_268_> Number of residue types: 20 malign__215E> Dynamic memory allocation failed. Routine, variable, status: rrdst 3 --------------------------------------

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Re: modeller_usage Digest, Vol 4, Issue 107
by rathankar rao 02 Dec '05

02 Dec '05

helllo all i have a doubt in this context. while modelling the first model has a least energy what is the necessity for modelling 20 or 50 structures 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 http://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. restrain beta strands and plates (Arnout Voet) 2. RE: How many models to generate? (Frederico Arnoldi) 3. Re: RE: How many models to generate? (Charlotte Habegger-Polomat) 4. Re: max number of optima in resdih.lib (Modeller Caretaker) ---------------------------------------------------------------------- Message: 1 Date: Fri, 2 Dec 2005 13:53:24 +0100 From: Arnout Voet Subject: [modeller_usage] restrain beta strands and plates To: modeller_usage(a)salilab.org Message-ID: <1133528004.439043c4d754d(a)webmail1.kuleuven.be> Content-Type: text/plain; charset=ISO-8859-1 dear modellers i have met a problem in my scripting to restrain the secondary structure element beta sheet beta strand. For alpha helices it works and i see an influence on the modelled structure , however for sheets it does not work and i get the same model with or without the restraining in the script. Could somebody pleez help me with the exact restraining of it kind regards arnout voet phd student biochemistry kuleuven. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm ------------------------------ Message: 2 Date: Fri, 02 Dec 2005 13:22:38 +0000 From: "Frederico Arnoldi" Subject: [modeller_usage] RE: How many models to generate? To: modeller_usage(a)salilab.org Message-ID: Content-Type: text/plain; charset=iso-8859-1; format=flowed Hello Charlotte Habegger-Polomat, I am not an expert modeller user, but what I can "share" about it? I think the number of models generated depends on available time and computational power you have to carry it. I usually generate between 100 and 200, and select that model with the lowest "current energy". Probably somebody could discuss it better, anyway, I tried ;) Frederico Arnoldi UNESP - Rio Claro - Brazil > >Dear Modeller users, > >I was wondering if others would share how many structures you usually >generate for a family of models. > >I am currently working on modelling my protein of interest with 3 known >template structures (>30% sequence similarity). When using Modeller, I >generate a family of 20 models and then evaluate the variability and >quality of models within the family. > >How many do other Modeller users generate? > >How do you decide on this number? > >I've read articles where 3 models, others where 30 models were generated >with Modeller... > >Thanks! > >-Charlotte Habegger-Polomat ------------------------------ Message: 3 Date: Fri, 02 Dec 2005 10:37:18 -0500 From: Charlotte Habegger-Polomat Subject: Re: [modeller_usage] RE: How many models to generate? To: modeller_usage(a)salilab.org Message-ID: <43906A2E.7090503(a)rsvs.ulaval.ca> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hello Frederico Arnoldi! Thanks for your answer...I have been generating 20 models for my protein of interest, and after evaluating the variability within the family of models, I select one or more models to work with. This reminds me that I have only an "approximation" of my structure, and also allows me to retain some variability. I then work with these models as one would work with a family of NMR structures. Does anyone else use more than one model to work with after generating a family with Modeller? Thank you! -Charlotte Habegger-Polomat Frederico Arnoldi wrote: > Hello Charlotte Habegger-Polomat, > > I am not an expert modeller user, but what I can "share" about it? > I think the number of models generated depends on available time and > computational power you have to carry it. I usually generate between > 100 and 200, and select that model with the lowest "current energy". > Probably somebody could discuss it better, anyway, I tried ;) > > Frederico Arnoldi > UNESP - Rio Claro - Brazil > > ------------------------------ Message: 4 Date: Fri, 02 Dec 2005 10:50:59 -0800 From: Modeller Caretaker Subject: Re: [modeller_usage] max number of optima in resdih.lib To: Luis Gracia Cc: modeller_usage(a)salilab.org Message-ID: <43909793.2030905(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Luis Gracia wrote: > Hi! I need to modify the rotamer definitions in resdih.lib, but I get > the following error when adding 4 entries to a residue. > > _modeller.error: rdrdih__223E> Internal error: array too small: MDIHOPT > current maximum, current need: 4 4 > > This is the line that creates the error: > > CA CB CG OD1 4 0.516 0.194 0.161 0.129 -11.9 69.4 > -67.6 154.8 12.5 11.1 23.3 25.7 -180 -90 -90 0 0 90 90 180 > > using only 3 optima values doesn't give any error. Is there a limit in > the maximum number of optima? This info is part of the output but I > don't know if its a limit or the number found: > Maximal number of dihedral angle optima: 3 Yes - unfortunately there is a hard-coded limit of 3 optima. This will be removed in the next release of Modeller, but for the time being, you are restricted to 3. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org http://salilab.org/mailman/listinfo/modeller_usage End of modeller_usage Digest, Vol 4, Issue 107 ********************************************** --------------------------------- Yahoo! Personals Single? There's someone we'd like you to meet. Lots of someones, actually. Yahoo! Personals

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How to choose the best model?
by carromeu＠usp.br 02 Dec '05

02 Dec '05

Dear Modeller users, I'm generating diverses models to my protein (400 - is this to great?). However I don't know how is the best parameter to look when choosing the best model. Objective function from Modeller, ProCheck parameters, Energy parameters... What parameters you use and why? If using Ramachandran plot as a discriminative parameter, how great must be the parameters calculated (for example: >90% in favored regions, <1% in disalowed regions)? Any help is welcome. Thanks for advice, Cassiano Carromeu.

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restrain beta strands and plates
by Arnout Voet 02 Dec '05

02 Dec '05

dear modellers i have met a problem in my scripting to restrain the secondary structure element beta sheet beta strand. For alpha helices it works and i see an influence on the modelled structure , however for sheets it does not work and i get the same model with or without the restraining in the script. Could somebody pleez help me with the exact restraining of it kind regards arnout voet phd student biochemistry kuleuven. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

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Occupancy problem ?
by Nicolas 02 Dec '05

02 Dec '05

Hello everybody, I am trying to use several templates for homology modelleing but some present half-occupancy for some residus of my structures. As soon as I try to modelise my sequence, I get the "structure not read in" message. Is this linked to the occupancy ? I did try the same scripts with a structure which does not present any occupancy uncertainty and it works fine. Thanks Dr. Bischler Nicolas NHRF-IOPC 48a, Vasileos Constantinou 11635 Athens Greece Tel : +302107273895 Fax : +302107273831

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max number of optima in resdih.lib
by Luis Gracia 02 Dec '05

02 Dec '05

Hi! I need to modify the rotamer definitions in resdih.lib, but I get the following error when adding 4 entries to a residue. _modeller.error: rdrdih__223E> Internal error: array too small: MDIHOPT current maximum, current need: 4 4 This is the line that creates the error: CA CB CG OD1 4 0.516 0.194 0.161 0.129 -11.9 69.4 -67.6 154.8 12.5 11.1 23.3 25.7 -180 -90 -90 0 0 90 90 180 using only 3 optima values doesn't give any error. Is there a limit in the maximum number of optima? This info is part of the output but I don't know if its a limit or the number found: Maximal number of dihedral angle optima: 3 Thanks for the help Luis -- Luis Gracia, PhD Department of Physiology & Biophysics Weill Medical College of Cornell University 1300 York Avenue, Box 75 New York, NY 10021 Tel: (212) 746-6375 Fax: (212) 746-8690 lug2002(a)med.cornell.edu

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RE: How many models to generate?
by Frederico Arnoldi 02 Dec '05

02 Dec '05

Hello Charlotte Habegger-Polomat, I am not an expert modeller user, but what I can "share" about it? I think the number of models generated depends on available time and computational power you have to carry it. I usually generate between 100 and 200, and select that model with the lowest "current energy". Probably somebody could discuss it better, anyway, I tried ;) Frederico Arnoldi UNESP - Rio Claro - Brazil > >Dear Modeller users, > >I was wondering if others would share how many structures you usually >generate for a family of models. > >I am currently working on modelling my protein of interest with 3 known >template structures (>30% sequence similarity). When using Modeller, I >generate a family of 20 models and then evaluate the variability and >quality of models within the family. > >How many do other Modeller users generate? > >How do you decide on this number? > >I've read articles where 3 models, others where 30 models were generated >with Modeller... > >Thanks! > >-Charlotte Habegger-Polomat

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How many models to generate?
by Charlotte Habegger-Polomat 30 Nov '05

30 Nov '05

Dear Modeller users, I was wondering if others would share how many structures you usually generate for a family of models. I am currently working on modelling my protein of interest with 3 known template structures (>30% sequence similarity). When using Modeller, I generate a family of 20 models and then evaluate the variability and quality of models within the family. How many do other Modeller users generate? How do you decide on this number? I've read articles where 3 models, others where 30 models were generated with Modeller... Thanks! -Charlotte Habegger-Polomat

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Dope Gnu Plot
by Mattias de Hollander 25 Nov '05

25 Nov '05

Dear Modeller users, How do i make a plot of the DOPE score like the one in the 'basic tutorial'. It says 'This profile is written to a file `TvLDH.profile', which can be used as input to a graphing program such as GNUPLOT', but when a plot it i get a straight line. Also, when i use the evaluate_model.py script on my own sequences, i only get a profile file and no dat files. Mattias -- Student Bio-Informatics Hogeschool Leiden The Netherlands

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Loop redefine on tetramer
by bmbbl＠leeds.ac.uk 25 Nov '05

25 Nov '05

----- Forwarded message from bmbbl(a)leeds.ac.uk ----- Date: Wed, 23 Nov 2005 12:06:42 +0000 From: bmbbl(a)leeds.ac.uk Reply-To: bmbbl(a)leeds.ac.uk Subject: Loop redefine of tetramer To: modeller_usage(a)salilab.org Dear Modellers, I have a tetramer model generated by MODELLER 8v1. I want to redefine one 10-residue long loop on all four subunit. Unfortunately MODLLER only worked on one of the chaines. My question is how I can model the identical-residue loop on all chains at one calculation? Here is the script I used. # Loop refinement of an existing model (RCK4S56-65.pdb) from modeller.automodel import * log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = '.' # Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms (necessary) class myloop(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): # 10 residue insertion self.pick_atoms(selection_segment=('39:', '49:'), selection_status='INITIALIZE') self.pick_atoms(selection_segment=('149:', '159:'), selection_status='INITIALIZE') self.pick_atoms(selection_segment=('259:', '269:'), selection_status='INITIALIZE') self.pick_atoms(selection_segment=('369:', '379:'), selection_status='INITIALIZE') m = myloop(env, inimodel='sample.pdb', # initial model of the target sequence='sample') # code of the target m.loop.starting_model= 1 # index of the first loop model m.loop.ending_model = 100 # index of the last loop model m.loop.md_level = refine.very_fast # loop refinement method m.make() Thank you for any hints. Binbin ----- End forwarded message -----

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