[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

RE: Problem to modeller



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: 
> []On">mailto:]On Behalf Of Juan
> Palacios
> Sent: Thursday, October 17, 2002 2:11 PM
> To: 
> 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
>
> ----------------------------
>
>