What is a problem?? i need help...
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): 2002/10/17 15:00:00.125
TOP_________> 105 705 SET ALNFILE = '1f4h-so34a0.ali'
TOP_________> 106 706 SET ATOM_FILES_DIRECTORY = '/home/jpalacio/fasta'
TOP_________> 107 707 SET KNOWNS = '1f4hD'
TOP_________> 108 708 SET SEQUENCE = 'so34a0'
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 1f4h-so34a0.ali openf5__224_> Open 13 OLD SEQUENTIAL /home/jpalacio/fasta/pdb1f4h.ent rdpir___270E> Error reading/processing file: 1f4h-so34a0.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 : 2002/10/17 15:00:00.125 Closing time : 2002/10/17 15:00:03.672 Total CPU time [seconds] : 3.36
---------------------- teha align file is:
>P1;1f4hD structureX:1f4h: :D:: :::: ITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITVN* >P1;so34a0 sequence:so34a0: : : : ::: 0.00: 0.00 KFNSRAGVLQRGDVENPGVAQLNRLGEHPLFASWRNSEEARTGSPFLQVGSLNGKWDAPCSGALNEGPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITVN*
--------------------------
the 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 = '1f4h-so34a0.ali' # alignment filename SET ATOM_FILES_DIRECTORY = '/home/jpalacio/fasta' SET KNOWNS = '1f4hD' # codes of the templates SET SEQUENCE = 'so34a0' # code of the target 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
----------------------------
As the error message indicates there is a problem with the alignment file.
> rdpir___270E> Error reading/processing file: 1f4h-so34a0.ali > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
the first obvious thing that seems wrong is the structureX line of the template:
structureX:1f4h: :D:: ::::
It should specify the starting and ending positions corresponding to the sequence using the numbering in the PDB file. For both position the chain should be specified. In this case the line should look something like this (I'm making up the numbers):
structureX:1f4h:1:D:135:D::::
The MODELLER manual has a detailed section on the Alignment file format:
http://salilab.org/modeller/manual/node83.html#alignmentformat
I hope this helps.
Best,
Roberto
-- Roberto Sanchez, Assistant Professor Structural Biology Program, Department of Physiology & Biophysics and Institute for Computational Biomedicine, Mount Sinai School of Medicine Box 1677, 1425 Madison Avenue, New York, NY 10029 phone +1 (212) 659 8648, fax +1 (212) 849 2456 http://physbio.mssm.edu/~sanchez/
> -----Original Message----- > From: owner-modeller_usage@salilab.org > [mailto:owner-modeller_usage@salilab.org]On Behalf Of Juan > Palacios > Sent: Thursday, October 17, 2002 2:11 PM > To: modeller_usage@salilab.org > Subject: Problem to modeller > > > What is a problem?? > i need help... > > > 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): 2002/10/17 15:00:00.125 > > TOP_________> 105 705 SET ALNFILE = '1f4h-so34a0.ali' > > TOP_________> 106 706 SET ATOM_FILES_DIRECTORY = '/home/jpalacio/fasta' > > TOP_________> 107 707 SET KNOWNS = '1f4hD' > > TOP_________> 108 708 SET SEQUENCE = 'so34a0' > > 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 1f4h-so34a0.ali > openf5__224_> Open 13 OLD SEQUENTIAL > /home/jpalacio/fasta/pdb1f4h.ent > rdpir___270E> Error reading/processing file: 1f4h-so34a0.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 : > 2002/10/17 15:00:00.125 > Closing time : > 2002/10/17 15:00:03.672 > Total CPU time [seconds] : 3.36 > > ---------------------- > teha align file is: > > >P1;1f4hD > structureX:1f4h: :D:: :::: > ITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEA > VPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITVN* > >P1;so34a0 > sequence:so34a0: : : : ::: 0.00: 0.00 > KFNSRAGVLQRGDVENPGVAQLNRLGEHPLFASWRNSEEARTGSPFLQVGSLNGKWDAPCSGALNE > GPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITVN* > > > -------------------------- > > the 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 = '1f4h-so34a0.ali' # alignment filename > SET ATOM_FILES_DIRECTORY = '/home/jpalacio/fasta' > SET KNOWNS = '1f4hD' # codes of the templates > SET SEQUENCE = 'so34a0' # code of the target > 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 > > ---------------------------- > >
Try to drop the space before the > sign of >P1; in both lines it appears in the alignment file.
On Thu, 17 Oct 2002, Juan Palacios wrote:
> What is a problem?? > i need help... > > > 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): 2002/10/1715:00:00.125 > > TOP_________> 105 705 SET ALNFILE = '1f4h-so34a0.ali' > > TOP_________> 106 706 SET ATOM_FILES_DIRECTORY = '/home/jpalacio/fasta' > > TOP_________> 107 707 SET KNOWNS = '1f4hD' > > TOP_________> 108 708 SET SEQUENCE = 'so34a0' > > 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 1f4h-so34a0.ali > openf5__224_> Open 13 OLD SEQUENTIAL /home/jpalacio/fasta/pdb1f4h.ent > rdpir___270E> Error reading/processing file:1f4h-so34a0.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 : > 2002/10/1715:00:00.125 > Closing time : > 2002/10/1715:00:03.672 > Total CPU time [seconds] : 3.36 > > ---------------------- > teha align file is: > > >P1;1f4hD > structureX:1f4h: :D:: :::: > ITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITVN* > >P1;so34a0 > sequence:so34a0: : : : ::: 0.00: 0.00 > KFNSRAGVLQRGDVENPGVAQLNRLGEHPLFASWRNSEEARTGSPFLQVGSLNGKWDAPCSGALNEGPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITVN* > > > -------------------------- > > the 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= '1f4h-so34a0.ali' # alignment filename > SET ATOM_FILES_DIRECTORY = '/home/jpalacio/fasta' > SET KNOWNS = '1f4hD' # codes of the templates > SET SEQUENCE = 'so34a0' # code of the target > 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 > > ---------------------------- >
-
Juan Palacios -
Roberto Sanchez -
sasson iris