- modeller_usage - salilab.org

ProsaII and Procheck
by Alex Brown 03 Oct '02

03 Oct '02

Hi. Does any one have any experience running either (or both) of these programs on Mac OS X/Darwin. Cheers, Alex.

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New to Modeller !!
by Urmi Doshi 02 Oct '02

02 Oct '02

Hi, I have just installed Modeller exactly the way as given in the User's Manual on an SGI Fuel. However, when I try running the command "mod model-default" which is a script file available with modeller, the error message I get is " 'mod' command not found". I am sure there's something silly that I am missing, but can't figure out. Is there any stack requirement for running MODELLER on SGI FUEl? Can anyone help me start using MODELLER ? - Urmi Doshi

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a bug?
by Kong Lesheng 02 Oct '02

02 Oct '02

Hi, When I use align2d to generate alignment, non-standard residues are always replaced by "G" even I have set "HETATM_IO=ON". So in the following modeling, the program will complain that sequence differences between structure and alignment. Everytime before I do modeling, I have to manually edit the alignment sequences. Could MODELLER automatically write non-standard residues as "." or other symbols which do not affect modeling? Thank you very much! With best regards, Lesheng

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Problems with modeling chimera
by Andersen, Kim Vilbour (KVA) 02 Oct '02

02 Oct '02

Hi I try to model a chimeric protein based on FAQ 4 To test the method I took a PDB file and cut it in two parts and then try to model the complete molecule again based on an FAQ 4 I get the error: fit2xyz_E> number of equivalent positions < 3: 0 recover__> ERROR_STATUS >= STOP_ON_ERROR: 1 1 As I understand it there are not enough overlapping residues in the alignment. But that is exactly the point, I try to model a chimeric protein based on the independent fragments exactly as in FAQ 4. What is wrong? Does the templates have to be overlapping, and is FAQ 4 wrong? All files are attached Thanks in advance Kim ------------------------------------------------------------------------ Kim Vilbour Andersen, PhD Senior Scientist Maxygen Agern Allé 1 DK-2970 Hørsholm Denmark <<model.top.gz>> <<align.pir.gz>> <<1GR3_A2.pdb.gz>> <<1GR3_A1.pdb.gz>> Tel: +45 7020 5550 Direct: +45 4517 8473 Mobile: +45 2637 3727 Fax: +45 7020 5530 E-mail: kva(a)maxygen.dk http://www.maxygen.dk/ ------------------------------------------------------------------------

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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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