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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 |