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 > > ---------------------------- >