Re: 'sequence not read in'

[Andras Fiser <>]

there is no "sequenceX" entry type in the alignment, csak "sequence" or
"structureX"

Andras

> Á¶º´°ü wrote:
> 
> Hi modellers..
> 
> Today, i met this message from modeller....but i can not understand
> why this occurs....
> i retrived 3TAT.pdb file from www.pdb.org and prepared ate1.ali file
> from ClustalW in PIR format...
> The related files and log file are below....
> why modeller give me the 'sequence not read in' message??
> 
> Byung-Kwan
> 
> - ate1.ali file
> >P1;ate1
> sequence:ate1:1: :397: :ArATEs:Enterobacter_sp: :
> MFQKVDAYAGDPILSLMER.....QRVAQAFAAVM*
> >P1;3TAT
> sequenceX:3TAT: :A: :A:ArATEc:Escherichia_coli: :
> MFQKVDAYAGDPILTLMER.....QRVAKAFAAVM*
> 
> - 3TAT.pdb
> 
> - ate1.top
> # Homology modelling by the MODELLER TOP
> 
> INCLUDE
> 
> SET OUTPUT_CONTROL = 1 1 1 1 1
> SET ALNFILE  = 'ate1.ali'
> SET KNOWNS = '3TAT'
> SET SEQUENCE  = 'ate1'
> SET ATOM_FILES_DIRECTORY =
> '/usr/bin/modeller6v1/examples/tutorial-model/atm/'
> SET STARTING_MODEL= 1
> SET ENDING_MODEL= 5
> SET RAND_SEED  = '76077'
> SET MD_LEVEL = 'refine1'
> 
> 
> CALL ROUTINE = 'model'
> - ate1.log
> 
>                          MODELLER 6v1, 17 Jan 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 localhost 2.2.18-10
> i686
> Date and time of compilation         : 01/24/2002 16:28:15
> Job starting time (YY/MM/DD HH:MM:SS): 2002/09/03  13:59:14.415
> 
> TOP_________>   105  705 SET ALNFILE  = 'ate1.ali'
> 
> TOP_________>   106  706 SET KNOWNS = '3TAT'
> 
> TOP_________>   107  707 SET SEQUENCE  = 'ate1'
> 
> TOP_________>   108  708 SET ATOM_FILES_DIRECTORY = './:'
> 
> TOP_________>   109  709 SET STARTING_MODEL = 1
> 
> TOP_________>   110  710 SET ENDING_MODEL = 5
> 
> TOP_________>   111  711 SET RAND_SEED  = '76077'
> 
> TOP_________>   112  712 SET MD_LEVEL = 'refine1'
> 
> TOP_________>   113  713 CALL ROUTINE = 'model'
> 
> TOP_________>   114  398 CALL ROUTINE = 'getnames'
> 
> TOP_________>   115  508 STRING_IF STRING_ARGUMENTS = MODEL
> 'undefined', OPERATION;
>                        = 'EQ', THEN =     'STRING_OPERATE OPERATION =
> CONCATENA;
>                       TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT =
> MODEL'
> 
> TOP_________>   116  509 STRING_IF STRING_ARGUMENTS = CSRFILE
> 'undefined', OPERATI;
>                       ON = 'EQ', THEN =     'STRING_OPERATE OPERATION
> = CONCATE;
>                       NATE, STRING_ARGUMENTS = SEQUENCE .rsr,  RESULT
> = CSRFILE;
>                       '
> 
> TOP_________>   117  510 STRING_OPERATE OPERATION =
> 'CONCATENATE',                ;
>                          STRING_ARGUMENTS = SEQUENCE '.sch',  RESULT =
> SCHFILE
> 
> TOP_________>   118  511 STRING_OPERATE OPERATION =
> 'CONCATENATE',                ;
>                         STRING_ARGUMENTS = SEQUENCE '.mat',  RESULT =
> MATRIX_FI;
>                       LE
> 
> TOP_________>   119  512 SET ROOT_NAME = SEQUENCE
> 
> TOP_________>   120  513 RETURN
> 
> TOP_________>   121  399 CALL ROUTINE = 'homcsr'
> 
> TOP_________>   122  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  ate1.ali
> 
> Dynamically allocated memory at         amaxbnd [B,kB,MB]:
> 7974421    7787.521     7.605
> openf5__224_> Open       11  OLD  SEQUENTIAL  ate1.ali
> 
> Read the alignment from file       : ate1.ali
> Total number of alignment positions:   397
> 
>   #  Code        #_Res #_Segm PDB_code    Name
> -------------------------------------------------------------------------------
>   1       3TAT     397      1        3TAT ArATEc
>   2       ate1     397      1        ate1 ArATEs
> TOP_________>   123  107 CHECK_ALIGNMENT
> 
> check_a_343_> >> BEGINNING OF COMMAND
> check_a_337E> Structure not read in:        1
> recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1
> 
> Dynamically allocated memory at          finish [B,kB,MB]:
> 7974421    7787.521     7.605
> Starting time                                            : 2002/09/03
> 13:59:14.415
> Closing time                                             : 2002/09/03
> 13:59:15.159
> Total CPU time [seconds]                                 :       0.70

-- 
    ,
Andras Fiser, PhD            # phone: (212) 327 7216
The Rockefeller University   # fax:   (212) 327 7540 
Box 270, 1230 York Avenue    # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras