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: owner-modeller_usage@salilab.org [mailto:owner-modeller_usage@salilab.org] On Behalf Of JP Sent: Monday, April 21, 2003 2:47 PM To: modeller_usage@salilab.org 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?