- modeller_usage - salilab.org

NOTE FOR BASH USERS
by Romain.Studer＠etu.unil.ch 01 May '03

01 May '03

NOTE FOR BASH USERS: I run modeller and it crashes with this message: "/bin/mod6v2: line 38: 1874 Segmentation fault (core dumped) $NICE ${EXECUTABLE} $STEERF >$LOGF" I used bash and I put the following command line in the .bashrc file as suggested in some messages of the mailing list: ulimit -S unlimited It appears that using the -s (lower case "s") solved the problem mentioned above. -S means Soft limitation and -s for stack maximum. The correct command is therefor: ulimit -s unlimited

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Restraints
by Anurag Sethi 29 Apr '03

29 Apr '03

Hi, I am modeling membrane proteins and I dont want a particular loop to enter in to the membrane. However as this loop is long (about 40 amino acids) and has nothing to model on (gap in template), it seems to form a sheet parallel to the transmembrane helices. This has to be avoided because the loop should not enter the membrane. My question is whether I can cause some restraints in Modeller by which any of the atoms in the loop donot have z-coordinate below a certain number. Thanks in advance, Anurag Sethi

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problem with files .top solve
by JP 24 Apr '03

24 Apr '03

when the files file.top or file.ali don`t have a last line in blank the process not run. always this files should have this last line in blank . thanks all.

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problem with files .top
by JP 24 Apr '03

24 Apr '03

(- suse linux 8.1 - modeller6v2 - file pdb is pdb1f4a.ent ) with file modelo1.top the process to run correctly INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'archivo.ali' SET KNOWNS = '1f4aC' SET SEQUENCE = 'sec1' SET STARTING_MODEL= 1 SET ENDING_MODEL = 1 CALL ROUTINE = 'model' ----------------------------------------------------------------------------------------------------- BUT with file modelo2.top the process not run INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'archivo.ali' SET KNOWNS = '1f4aC' SET SEQUENCE = 'sec1' SET STARTING_MODEL= 1 SET ENDING_MODEL = 1 CALL ROUTINE = 'model' and 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 2.4.19-4GB i686 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2003/04/23 11:53:47.784 TOP_________> 105 705 SET ALNFILE = 'archivo.ali' TOP_________> 106 706 SET KNOWNS = '1f4aC' TOP_________> 107 707 SET SEQUENCE = 'sec1' TOP_________> 108 708 SET STARTING_MODEL = 1 TOP_________> 109 709 SET ENDING_MODEL = 1 Dynamically allocated memory at finish [B,kB,MB]: 2200483 2148.909 2.099 Starting time : 2003/04/23 11:53:47.784 Closing time : 2003/04/23 11:53:50.734 Total CPU time [seconds] : 2.88 ---------------------------------------------------------------------------------------- which is a problem? which is a difference between the files modelo1.top and modelo2.top? is a bug the modeller? the files top to contain the same information but with file model2.top the process not run. thanks..

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optimize with a membrane protein
by jxs818＠bham.ac.uk 24 Apr '03

24 Apr '03

Hi All I am trying to model an membrane protein, and wondered how to turn off the optimize routine for selected parts of the protein. What I am really after is for Modeller to just do the sidechain replacement in the membrane domain and then do its normal job (whichs its very good at!) in the more variable loop regions. Cheers all John

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Superposer two protein structure
by Shiyong Liu 23 Apr '03

23 Apr '03

Dear all, When I do superpose two proteins , I don't know how to output the structures of the two proteins totally. In the default superpose.top script, the output command is WRITE_MODEL2 FILE = '2ctx.fit' . I want to output two structures in one file at the same time so that I can display them easily in one windows. Best regards, Shiyong Peking University

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problem with check_alignment
by JP 21 Apr '03

21 Apr '03

- Suse linux 8.1 my files are: me Top File bioinf@bioinf4:/usr/local/bin/modeller6v2/work> more modelo.top INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'alignment.ali' # alignment filename SET KNOWNS = '1f36A' # codes of the templates SET SEQUENCE = 'sec1' # code of the target SET ATOM_FILES_DIRECTORY = '/data1' SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model (determines how many models tocalculate) CHECK_ALIGNMENT CALL ROUTINE = 'model' # do homology modelling the files: bioinf@bioinf4:/usr/local/bin/modeller6v2/work> ls -al total 188 drwxr-xr-x 2 bioinf users 216 2003-04-21 14:31 . drwxrwxrwx 5 wwwrun root 120 2003-04-21 14:28 .. -rw-r--r-- 1 bioinf users 281 2003-04-21 14:29 alignment.ali -rw-r--r-- 1 bioinf users 643 2003-04-21 14:31 modelo.top -rw-r--r-- 1 bioinf users 175446 2003-04-21 14:29 pdb1f36.ent log file 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 2.4.19-4GB i686 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2003/04/21 14:31:58.119 TOP_________> 105 705 SET ALNFILE = 'alignment.ali' TOP_________> 106 706 SET KNOWNS = '1f36A' TOP_________> 107 707 SET SEQUENCE = 'sec1' TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = '/data1' TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 1 TOP_________> 111 711 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND check_a_335E> No alignment. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2200483 2148.909 2.099 Starting time : 2003/04/21 14:31:58.119 Closing time : 2003/04/21 14:32:01.072 Total CPU time [seconds] : 2.93 what is a problem?

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PSC Summer Workshop: Modeling from Protein Sequence to Structure
by Troy Wymore 21 Apr '03

21 Apr '03

Hello MODELLERs, The following workshop should be of interest to researchers subsribing to this list; especially those wanting to refine structures generated with MODELLER. *************************************************** PSC BIOMEDICAL INITIATIVE WORKSHOP 2003 MODELING FROM PROTEIN SEQUENCE TO STRUCTURE: COMPUTATIONAL TOOLS FOR STRUCTURE PREDICTION June 2-5 Application Deadline: April 30 Primary Instructor: Prof. Charles Brooks (Scripps) This workshop will introduce researchers to computational tools (the MMTSB Tool Set available at http://mmtsb.scripps.edu) aimed at predicting structure based on sequence alone, from identification of suitable homology templates, or through application of secondary-structure templated de novo folding, as well as refinement and energy calculations on "ensembles" of molecular structures. This freely available tool set comprises a perl-based library of applications that interface to the molecular modeling packages CHARMM and Amber, and the MONSSTER package for protein structure prediction. Participants in the workshop will be presented lectures on molecular modeling theory and practice, protein structure prediction, loop modeling and energy-based structure refinement. Advanced sampling methods such as replica-exchange molecular dynamics, as utilized in structure prediction algorithms, will be discussed. Practical tutorials exploring the use and application of the MMTSB tool set will focus on conventional molecular mechanics calculations of energy, minimization and dynamics as well as loop modeling and refinement using replica-exchange molecular dynamics and hierarchical protein structure prediction using de novo (or secondary structure templated) folding algorithms in the MONSSTER and CHARMM packages. Web-based servers for protein sequence alignment, secondary structure prediction and homology template identification will be discussed in the context of their utility to the overall structure prediction pipeline utilizing the MMTSB Tool Set. For specific details, including an electronic application form, see: http://www.psc.edu/biomed/training/workshops/2003/proteomics/index.html If you have any questions, please contact Nancy Blankenstein at blankens(a)psc.edu

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Problem to run modeller (problem v3)
by JP 17 Apr '03

17 Apr '03

(note: I have installed modeller6v2 in Linux Suse 8.1. When execute modeller with the examples , modeller execute correctly . If the files "model-default.top" and "alignment.ali" in the directory "tutorial-model" are copy in other directory and execute the process (mod6v2 model-default.top) run correctly obtain the new model for target sequence ) hi I have a problem to run modeller I create my alignment file (alignment.ali) and top file (model-default.top) ,but to run "mod6v2 model-default.top" the log file to show the not execute the process. and the log file no show errors. which can be the problem? the files are: alignment.ali C; A sample alignment in the PIR format; used in tutorial >P1;1f36A structureX:1f36:10 :A :98 :A : : : : VLTVSTVNSQDQVTQKPLRDSVKQALENYFAQLNGQDVNDLYELVLAEVEQPLLDMVMQYTRGNQTRAALMMGINRGTLRKKLKKYGMN* >P1;sec1 sequence:sec1:1 :A :89 :A : : : : VLTVSTVNSQAQVTQKPLRDSVKQALKNYFAQLNGQDVSDLYELVLAEVEQPLLDMVMQYTRGNQTRAALMMGINRGTLRKKLKKYGMN* model-default.top # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'alignment.ali' # alignment filename SET KNOWNS = '1f36A' # codes of the templates SET SEQUENCE = 'sec1' # code of the target SET ATOM_FILES_DIRECTORY = '/data1' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling model-default.log 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 2.4.19-4GB i686 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2003/04/17 14:05:48.759 TOP_________> 105 705 SET ALNFILE = 'alignment.ali' TOP_________> 106 706 SET KNOWNS = '1f36A' TOP_________> 107 707 SET SEQUENCE = 'sec1' TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = '/data1' TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 1 Dynamically allocated memory at finish [B,kB,MB]: 2200483 2148.909 2.099 Starting time : 2003/04/17 14:05:48.759 Closing time : 2003/04/17 14:05:51.710 Total CPU time [seconds] : 2.87 the log file no show errors and show that the process is not execute. which can be the problem? I need Help The modeller have other file where save logs? thanks...

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Problen to run modeller v2
by JP 16 Apr '03

16 Apr '03

I have the next problem, I execute "mod6v2 model-default.top" into directory "tutorial-model" and execute correctly but the execute the next file obtain error I have this alignment file: ******-----------------------**** my alignment file is: >P1;1ety structureX:1ety:6:B:98:B:::: VNSDVLTVSTVNSQDQVTQKPLRDSVKQALKNYFAQLNGQDVNDLYELVLAEVE QPLLDMVMQYTRGNQTRAALMMGINRGTLRKKLKKYGMN* >P1;sec1 sequence:sec1:1::93::::: VNSDVLTVSTVNSQAQVTQKPLRDSVKQALKNYFAQLNGQDVSDLYELVLAEVE QPLLDMVMQYTRGNQTRAALMMGINRGTLRKKLKKYGMN* *****------------------------------------------------------------------------** and the log file is: my log file is: Kind, OS, HostName, Kernel, Processor: 4, Linux bioinf4 2.4.19-4GB i686 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2003/04/16 11:55:50.106 TOP_________> 105 705 SET ALNFILE = 'alignment.ali' TOP_________> 106 706 SET KNOWNS = '1ety' TOP_________> 107 707 SET SEQUENCE = 'sec1' TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = '/data1' TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 1 TOP_________> 111 711 CALL ROUTINE = 'model' TOP_________> 112 399 CALL ROUTINE = 'getnames' TOP_________> 113 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 114 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 115 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 116 512 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 117 513 SET ROOT_NAME = SEQUENCE TOP_________> 118 514 RETURN TOP_________> 119 400 CALL ROUTINE = 'homcsr' 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 alignment.ali rdpir___270E> Error reading/processing file: alignment.ali recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2205269 2153.583 2.103 Starting time : 2003/04/16 11:55:50.106 Closing time : 2003/04/16 11:55:53.073 Total CPU time [seconds] : 2.91 ************----------------------------------------------****************************** My top file # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'alignment.ali' # alignment filename SET KNOWNS = '1ety' # codes of the templates SET SEQUENCE = 'sec1' # code of the target SET ATOM_FILES_DIRECTORY = '/data1' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling ################################ what is a problem?, I have some problem in alignment file..? Thaks...

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