September 2002 - modeller_usage

# SET SELECTION_SEARCH = 'SPHERE_SEGMENT', SPHERE_RADIUS = 6
by Bozidar Yerkovich 11 Dec '02

11 Dec '02

On behalf of kinsellg(a)tcd.ie... Hi all, I've recently started using modeller and I've been able to generate models and loops, so far. I tried optimising my alignment and I've now hit this snag. I get this error when trying to generate loops. Also I havn't been able to get the command to optimise the loop envirionment to work yet. The top and log files are attached. # SET SELECTION_SEARCH = 'SPHERE_SEGMENT', SPHERE_RADIUS = 6 Any ideas?? I am very grateful for all your help, Gemma The error: TOP_________> 189 674 SET OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200, MIN_ OM_SHIFT = 0.001 TOP_________> 190 675 OPTIMIZE SCHEDULE_STEP = 1 preppdf_457W> Both soft sphere and statistical potential terms selected. pair4___223E> Array too small. Increase MPAIRS current maximum, current need: 33600 33600 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 14325865 13990. Starting time : 2002/09/05 09:56:49. Closing time : 2002/09/05 09:57:00. Total CPU time [seconds] : 11.04

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TvLDH Example
by Alex Brown 27 Sep '02

27 Sep '02

Hi. I have just finished modeling TvLDH, following the example given in the paper "Comparative Protein Structure Modeling with MODELLER: A Practical Apporach". Methods in Enzymology. (submitted), by Andràs Fiser and Andrej Sali (http://salilab.org/modeller/methenz/) I have had a few problems running some of the scripts, but I have mainly been able to over come most of these. I have, however, picked up a couple of problems : 1) The results I obtained from the 'align2d.top' script were slightly different from that reported in the paper, and those on the web-page quoted above (my alignment is attached ). This, of course, means that the resulting models are slightly different. 2) The structure file 4mdh.pdb contains a residue coded ACE, numbered resdue 0. This is an acetylated (acylated ??) N-terminus. However, 'align2d.top' appears to recognize this as a GLY, which is entered into the alignment files. This, of course, causes a problem in the final modeling, as the ACE residue is not recognized and the run fails. Editing the PIR alignment file to correct this (remove the G and change the 0 to 1). 3) Throughout the procedure, I had to use the PDB file 4mdh.pdb - for the template comparisons and alignments. However, I had to rename this file 4mdhA.pdb for the modeling - presumably because that is the sequence name given in the alignment file. Is there any way to prevent having to do this ? Could someone explain the above problems. I am using MODELER6v2, on a Mac PowerBook G4, running OS X/Darwin (10.1.5). Cheers, Alex Brown.

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align2d warnings
by Alex Brown 26 Sep '02

26 Sep '02

Hi. A small problem with the align2d script from the TvLDH tutorial examples. The align2d.top script is as follows: READ_MODEL FILE = '4mdh.pdb' SEQUENCE_TO_ALI ALIGN_CODES = '4mdhA' READ_ALIGNMENT FILE = 'TvLDH.ali', ALIGN_CODES = ALIGN_CODES 'TvLDH', ADD_SEQUENCE = on ALIGN2D WRITE_ALIGNMENT FILE='TvLDH-4mdhA.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE='TvLDH-4mdhA.pap', ALIGNMENT_FORMAT = 'PAP' Running this produced the following warnings in the align2d.log file : iatmcls_286W> MODEL atom not classified: ALA:OT1 ALA iatmcls_286W> MODEL atom not classified: ALA:OT2 ALA pdbnam__217W> Filename for PDB code not found: 4mdhA Directories: ./ Extensions : :.atm:.pdb:.ent:.crd rdabrk__288W> Protein not accepted: 1 mkapsa__293W> No TOPOLOGY_LIB is in memory. Use READ_TOPOLOGY to read one. This seems to indicate that the template file or template sequence cannot be found. However, the alignment goes ahead and is fine (ie. both target and template sequences were present). Could someone please explain. As usual, I'm running MODELLER 6v2 on Mac OS/X Darwin. Cheers, Alex.

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SEQUENCE_SEARCH Question
by Alex Brown 25 Sep '02

25 Sep '02

Hi, again. Is there a script that can be used to extract the 'other closely related' structures from the 'CHAINS_3.0_40_XN.grp' file, other than just using a text-editor search ? Thanks, Alex.

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Problem with SEQUENCE_SEARCH
by Juan Palacios 25 Sep '02

25 Sep '02

My .top file is: -------------------------------------------------------------------------------------------------------------- INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET SEARCH_RANDOMIZATIONS = 3 SET FILE = 'TvLDH.ali' SEQUENCE_SEARCH ALIGN_CODES = 'TvLDH', DATA_FILE = ON ----------------------------------------------------------------------------------------------------------------- the log file is: ---------------------------------------------------------------------------------------------------------------- MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux bioinf4 2.4.4-4GB i686 Date and time of compilation : 05/24/2002 09:27:23 Job starting time (YY/MM/DD HH:MM:SS): 2002/09/23 15:16:01.528 TOP_________> 105 705 SET SEARCH_RANDOMIZATIONS = 3 TOP_________> 106 706 SET FILE = 'TvLDH.ali' TOP_________> 107 707 SEQUENCE_SEARCH ALIGN_CODES = 'TvLDH', DATA_FILE = ON openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//CHAINS_3.0_40_XN.cod Dynamically allocated memory at amaxchn [B,kB,MB]: 2306323 2252.269 2.199 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//CHAINS_3.0_40_XN.cod openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//CHAINS_all.seq Dynamically allocated memory at amresdb [B,kB,MB]: 5689471 5556.124 5.426 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//CHAINS_all.seq Dynamically allocated memory at amaxseq [B,kB,MB]: 5877209 5739.462 5.605 Dynamically allocated memory at amaxbnd [B,kB,MB]: 110299725 107714.600 105.190 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//as1.sim.mat rdrrwgh_268_> Number of residue types: 20 openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ali --------------------------------------------------------------------------------------------------------------------------------------------------------------- After 2 hours of executing delivery the following mistake The error is: /usr/local/modeller6v2/bin/mod6v2 : line38 : 2030 terminated $NICE ${EXECUTABLE} $STEERF >$LOGF WHAT IS A PROBLEM???

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problem with "Sequence_search".. After executing "sequence_search" for two hours does not deliver result
by Juan Palacios 25 Sep '02

25 Sep '02

After executing "sequence_search" for two hours does not deliver result: The file .top used is the following one: -------------------------------------------------------------------------------------------------------------- INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET SEARCH_RANDOMIZATIONS = 3 SET FILE = 'TvLDH.ali' SEQUENCE_SEARCH ALIGN_CODES = 'TvLDH', DATA_FILE = ON ----------------------------------------------------------------------------------------------------------------- The used file of sequence is the following one: >P1;TvLDH sequence:TvLDH:::::::0.00: 0.00 MSEAAHVLITGAAGQIGYILSHWIASGELYG-DRQVYLHLLDIPPAMNRLTALTMELEDCAFPHLAGFVATTDPK AAFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPSVKVLVIGNPDNTNCEIAMLHAKNLKPE NFSSLSMLDQNRAYYEVASKLGVDVKDVHDIIVWGNHGESMVADLTQATFTKEGKTQKVVDVLDHDYVFDTFFKK IGHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPVPEGNPYGIKPGVVFSFPCNVDKEGKIHV VEGFKVNDWLREKLDFTEKDLFHEKEIALNHLAQGG* -------------------------------------------- The file .log obtained is : ---------------------------------------------------------------------------------------------------------------- MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux bioinf4 2.4.4-4GB i686 Date and time of compilation : 05/24/2002 09:27:23 Job starting time (YY/MM/DD HH:MM:SS): 2002/09/23 15:16:01.528 TOP_________> 105 705 SET SEARCH_RANDOMIZATIONS = 3 TOP_________> 106 706 SET FILE = 'TvLDH.ali' TOP_________> 107 707 SEQUENCE_SEARCH ALIGN_CODES = 'TvLDH', DATA_FILE = ON openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//CHAINS_3.0_40_XN.cod Dynamically allocated memory at amaxchn [B,kB,MB]: 2306323 2252.269 2.199 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//CHAINS_3.0_40_XN.cod openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//CHAINS_all.seq Dynamically allocated memory at amresdb [B,kB,MB]: 5689471 5556.124 5.426 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//CHAINS_all.seq Dynamically allocated memory at amaxseq [B,kB,MB]: 5877209 5739.462 5.605 Dynamically allocated memory at amaxbnd [B,kB,MB]: 110299725 107714.600 105.190 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//as1.sim.mat rdrrwgh_268_> Number of residue types: 20 openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ali --------------------------------------------------------------------------------------------------------------------------------------------------------------- passed the 2 hours it orders the following message: /usr/local/modeller6v2/bin/mod6v2 : line38 : 2030 terminated $NICE ${EXECUTABLE} $STEERF >$LOGF WHAT IS A PROBLEM??? That can do?

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Fwd: SEQUENCE_SEARCH problems
by Alex Brown 25 Sep '02

25 Sep '02

> From: Alex Brown <abrown(a)nimr.mrc.ac.uk> > Date: Wed Sep 25, 2002 09:37:02 am Europe/London > To: Bozidar Yerkovich <bozidar(a)salilab.org> > Subject: Re: SEQUENCE_SEARCH problems > > Hi. > > I tried your suggestion of running my machine overnight. The > SEQUENCE_SEARCH took > 6 hr, 15min, 1.32sec, almost reducing my PowerBook to a heap of glowing > titanium :). > > The results were slightly different to those published, but I take it > this could be due to database updates, etc. I did, however, get a > series of error reports in the .log file : > > addgrp__223E> Array too small. Increase MAXSEQ > current maximum, current need: 40 46 > addgrp__223E> Array too small. Increase MAXSEQ > current maximum, current need: 40 41 > addgrp__223E> Array too small. Increase MAXSEQ > current maximum, current need: 40 42 > addgrp__223E> Array too small. Increase MAXSEQ > current maximum, current need: 40 42 > addgrp__223E> Array too small. Increase MAXSEQ > current maximum, current need: 40 41 > addgrp__223E> Array too small. Increase MAXSEQ > current maximum, current need: 40 41 > addgrp__223E> Array too small. Increase MAXSEQ > current maximum, current need: 40 45 > > I can't find any refernce to a variable MAXSEQ in the manual. > > Cheers, > > Alex. > > On Monday, September 23, 2002, at 02:43 pm, Bozidar Yerkovich wrote: > >> >> >> Alex, >> >> 1. MODELLER ftp services are down indeed. I apologize for that. We had >> some >> security problems, but they have been solved. Those files should be >> accessible again by the end of a day. >> >> 2. SEQUENCE_SEARCH can indeed take a long time. It depends on your >> machine's >> CPU and RAM. Just let it run, maybe in the evening. If it's still >> running >> next morning that something is wrong. It should finish in 2 hours or >> so, but >> then again this might be way off for your particular computer. >> >> 3. I am sure if you try google, you find them somehow. >> >> God luck, >> Bozidar >> >

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Subject: models for MR
by Bozidar Yerkovich 24 Sep '02

24 Sep '02

>From Katherine Kantardjieff: We have tried this with some success on several TB proteins as part of = the efforts of the TB Structural Genomics Consortium. These have not yet = been formally published. Basically, we have produced both homology and = comparative models using SwissModeller or Modeller, as well as other = servers such as 3D PSSM and the prediction servers at LLNL. Each model = is slightly different, but can be evaluated using whatCheck, ProCheck, = ProsaII etc. We have also used different MR algorithms, and epmr and = amore seem to work the best, although one may find a solution while the = other won't. My advice is to try each model and each MR algorithm = available. We then take the MR results and run the initial maps through phase bias = removal shake& warp (Segelke and Rupp)before viewing. In the best case, = we had an interpretable map and model that could be rebuilt in a day = with XtalView. In the worst case, we obtained a map with interpretable = features, but still poor connectivity and a great deal of work ahead. In = this case, the hybrid fold and sequence match was low to anything in the = available databases. But, we may still be able to pull it out. Professor Katherine Kantardjieff Director, W.M. Keck Foundation Center for Molecular Structure Department of Chemistry and Biochemistry California State University Fullerton 800 N. State College Blvd. Fullerton, CA 92834-6866 Office: (714) 278-3752 eFax: (734) 939-4225 eMail: <mailto:kkantardjieff@fullerton.edu> kkantardjieff(a)fullerton.edu =20

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/pipe1/databases/pdb/uncompressed_files/pdb1hci.ent
by Bozidar Yerkovich 24 Sep '02

24 Sep '02

Hi all, I noticed that some people reported the following error: /pipe1/databases/pdb/uncompressed_files/pdb1hci.ent Command line: INCLUDE assgn___525E> Error in TOP variable assignment. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 To fix this go to modlib directory where you installed MODELLER and remove pdbent.lib file. Good luck, Bozidar -- Bozidar Yerkovich, PhD Postdoctoral Research Associate Sali Lab, Rockefeller University New York, NY, 10021, USA 212-327-7206 bozidar(a)salilab.org http://salilab.org/modeller

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HETATM_IO
by Ralf Schmid 24 Sep '02

24 Sep '02

Dear all, I'm trying to model a protein including a cofactor, but get an error message pointing towards problems in the alignment and/or pdb file. Modelling without cofactor (i.e. removing "/." from the alignment file) works fine. I can't figure out what causes the problem. Any help will be appreciated, please see the files below. Thanks in advance, ralf xxx.log: <snip> TOP_________> 120 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL xxx.ali openf5__224_> Open 13 OLD SEQUENTIAL ./yyy.pdb Dynamically allocated memory at amaxbnd [B,kB,MB]: 9440821 9219.552 9.003 openf5__224_> Open 11 OLD SEQUENTIAL xxx.ali openf5__224_> Open 13 OLD SEQUENTIAL ./yyy.pdb rdpir___648E> Alignment sequence not found in PDB file: 1 ./yyy.pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 xxx.top: INCLUDE SET OUTPUT_CONTROL= 1 1 1 1 1 SET ALNFILE = 'xxx.ali' SET KNOWNS = 'yyy' SET SEQUENCE = 'xxx' SET STARTING_MODEL = 20 SET ENDING_MODEL = 20 SET HETATM_IO = on CALL ROUTINE = 'model' xxx.ali: >P1;xxx sequence:xxx:.:.:.:.:.:.:.:. VKNER/.* >P1;yyy structureX:yyy:.:.:.:.:.:.:.:. VKQER/.* yyy.pdb: <snip> ATOM 3488 OXT ARG A 447 31.403 66.404 103.394 1.00 65.84 O TER 3489 ARG A 447 HETATM 3490 AP FAD 448 60.780 56.948 67.003 1.00 33.65 P <snip> ----------------------------------------------------------------- Dr. Ralf Schmid ICMB The University of Edinburgh Michael Swann Building 3.14 -----------------------------------------------------------------

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