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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