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MODELLER 6v2, 17 Feb 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 bioinf4 2.4.4-4GB i686
Date and time of compilation : 05/24/2002 09:27:23
Job starting time (YY/MM/DD HH:MM:SS): 2002/10/17 15:00:00.125
TOP_________> 105 705 SET ALNFILE = '1f4h-so34a0.ali'
TOP_________> 106 706 SET ATOM_FILES_DIRECTORY = '/home/jpalacio/fasta'
TOP_________> 107 707 SET KNOWNS = '1f4hD'
TOP_________> 108 708 SET SEQUENCE = 'so34a0'
TOP_________> 109 709 SET STARTING_MODEL = 1
TOP_________> 110 710 SET ENDING_MODEL = 1
TOP_________> 111 711 CALL ROUTINE = 'model'
TOP_________> 112 399 CALL ROUTINE = 'getnames'
TOP_________> 113 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined',
OPERATION;
= 'EQ', THEN = 'STRING_OPERATE OPERATION =
CONCATENA;
TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL'
TOP_________> 114 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined',
OPERATI;
ON = 'EQ', THEN = 'STRING_OPERATE OPERATION =
CONCATE;
NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT =
CSRFILE;
Dynamically allocated memory at amaxseq
[B,kB,MB]: 2205269 2153.583 2.103
openf5__224_> Open 11 OLD SEQUENTIAL 1f4h-so34a0.ali
openf5__224_> Open 13 OLD SEQUENTIAL /home/jpalacio/fasta/pdb1f4h.ent
rdpir___270E> Error reading/processing file: 1f4h-so34a0.ali
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish
[B,kB,MB]: 2205269 2153.583 2.103
Starting time :
2002/10/17 15:00:00.125
Closing time :
2002/10/17 15:00:03.672
Total CPU time [seconds] : 3.36
----------------------
teha align file is:
>P1;1f4hD
structureX:1f4h: :D:: ::::
ITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITVN*
>P1;so34a0
sequence:so34a0: : : : ::: 0.00: 0.00
KFNSRAGVLQRGDVENPGVAQLNRLGEHPLFASWRNSEEARTGSPFLQVGSLNGKWDAPCSGALNEGPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITVN*
--------------------------
the top file:
# Homology modelling by the MODELLER TOP routine 'model'.
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file
SET ALNFILE = '1f4h-so34a0.ali' # alignment filename
SET ATOM_FILES_DIRECTORY = '/home/jpalacio/fasta'
SET KNOWNS = '1f4hD' # codes of the templates
SET SEQUENCE = 'so34a0' # code of the target
SET STARTING_MODEL= 1 # index of the first model
SET ENDING_MODEL = 1 # index of the last model
# (determines how many models to
calculate)
CALL ROUTINE = 'model' # do homology modelling
----------------------------