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