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Re: Problem to modeller



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