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