Alignment problem

18 Jul 2002


      Dear Bozidar,
I had problem when trying to get some a protein model.
What do I have to do? I used the PIR alignment format
also.
My Top file is:
INCLUDE                             # Include the
predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 1      # uncomment to
produce a large log file
SET ALNFILE  = 'alignment.seg.pap'      # alignment
filename
SET KNOWNS   = '1h9p'               # codes of the
templates
SET SEQUENCE = '1drg'               # code of the
target
SET ATOM_FILES_DIRECTORY = './:../atom_files' #
directories for input atom files
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
The alignment file seems to be ok:
Kind, OS, HostName, Kernel, Processor: 4, Linux
localhost.localdomain 2.4.18-6mdkenterprise i686
Date and time of compilation         : 07/05/2002
17:30:36
Job starting time (YY/MM/DD HH:MM:SS): 2002/07/18 
13:08:16.425
TOP_________>   105  705 SET ALNFILE  =
'alignment.seg.pap'
TOP_________>   106  706 SET KNOWNS   = '1h9p'
TOP_________>   107  707 SET SEQUENCE = '1drg'
TOP_________>   108  708 SET ATOM_FILES_DIRECTORY =
'./:../atom_files'
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;
                      '
TOP_________>   115  511 STRING_OPERATE OPERATION =
'CONCATENATE',                ;
                         STRING_ARGUMENTS = SEQUENCE
'.sch',  RESULT = SCHFILE
TOP_________>   116  512 STRING_OPERATE OPERATION =
'CONCATENATE',                ;
                        STRING_ARGUMENTS = SEQUENCE
'.mat',  RESULT = MATRIX_FI;
                      LE
TOP_________>   117  513 SET ROOT_NAME = SEQUENCE
TOP_________>   118  514 RETURN
TOP_________>   119  400 CALL ROUTINE = 'homcsr'
TOP_________>   120  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 
alignment.seg.pap
Dynamically allocated memory at         amaxbnd
[B,kB,MB]:      2560929    2500.907     2.442
openf5__224_> Open       11  OLD  SEQUENTIAL 
alignment.seg.pap
Read the alignment from file       : alignment.seg.pap
Total number of alignment positions:     0
#  Code        #_Res #_Segm PDB_code    Name
-------------------------------------------------------------------------------
  1       1h9p       0      1
  2       1drg       0      1
TOP_________>   121  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]:      2560929    2500.907     2.442
Starting time                                         
  : 2002/07/18  13:08:16.425
Closing time                                          
  : 2002/07/18  13:08:17.598
Frederico Moreno
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