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Re: 'sequence not read in'



Dear Byung-Kwan,

Please take a look at the list archives, where you will find multiple
examples 
of similar problems and answers how to solve it.

Best,
Bozidar



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 <http://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



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