Your TOP file calls CHECK_ALIGNMENT without there being any alignment in
memory, that is why you get the "check_a_335E> No alignment" error
message. It is actually not necessary to call CHECK_ALIGNMENT if the
'model' routine is going to be called; this routine already executes the
CHECK_ALIGNMENT command after the modeling alignment is read in.
Best,
Roberto
--
Roberto Sanchez, Assistant Professor
Structural Biology Program, Department of Physiology & Biophysics
Mount Sinai School of Medicine
Box 1677, 1425 Madison Avenue, New York, NY 10029
phone +1 (212) 659 8648, fax +1 (212) 849 2456
http://physbio.mssm.edu/~sanchez/
-----Original Message-----
From:
[">mailto:] On Behalf Of JP
Sent: Monday, April 21, 2003 2:47 PM
To:
Subject: problem with check_alignment
- Suse linux 8.1
my files are:
me Top File
bioinf@bioinf4:/usr/local/bin/modeller6v2/work> more modelo.top
INCLUDE # Include the predefined TOP
routines
SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log
file
SET ALNFILE = 'alignment.ali' # alignment filename
SET KNOWNS = '1f36A' # codes of the templates
SET SEQUENCE = 'sec1' # code of the target
SET ATOM_FILES_DIRECTORY = '/data1'
SET STARTING_MODEL= 1 # index of the first model
SET ENDING_MODEL = 1 # index of the last model
(determines how many models tocalculate)
CHECK_ALIGNMENT
CALL ROUTINE = 'model' # do homology modelling
the files:
bioinf@bioinf4:/usr/local/bin/modeller6v2/work> ls -al
total 188
drwxr-xr-x 2 bioinf users 216 2003-04-21 14:31 .
drwxrwxrwx 5 wwwrun root 120 2003-04-21 14:28 ..
-rw-r--r-- 1 bioinf users 281 2003-04-21 14:29
alignment.ali
-rw-r--r-- 1 bioinf users 643 2003-04-21 14:31 modelo.top
-rw-r--r-- 1 bioinf users 175446 2003-04-21 14:29 pdb1f36.ent
log file
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 2.4.19-4GB i686
Date and time of compilation : 07/16/2002 11:42:16
Job starting time (YY/MM/DD HH:MM:SS): 2003/04/21 14:31:58.119
TOP_________> 105 705 SET ALNFILE = 'alignment.ali'
TOP_________> 106 706 SET KNOWNS = '1f36A'
TOP_________> 107 707 SET SEQUENCE = 'sec1'
TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = '/data1'
TOP_________> 109 709 SET STARTING_MODEL = 1
TOP_________> 110 710 SET ENDING_MODEL = 1
TOP_________> 111 711 CHECK_ALIGNMENT
check_a_343_> >> BEGINNING OF COMMAND
check_a_335E> No alignment.
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]:
2200483 2148.909 2.099
Starting time : 2003/04/21
14:31:58.119
Closing time : 2003/04/21
14:32:01.072
Total CPU time [seconds] : 2.93
what is a problem?