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??

>P1;ate1
sequence:ate1:1: :397: :ArATEs:Enterobacter_sp: :
MFQKVDAYAGDPILSLMER.....QRVAQAFAAVM*
>P1;3TAT
sequenceX:3TAT: :A: :A:ArATEc:Escherichia_coli: :
MFQKVDAYAGDPILTLMER.....QRVAKAFAAVM*

# Homology modelling by the MODELLER TOP

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