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RE: problem with check_alignment



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?