Hello,
 
I havealigned two sequences and want to modelise one of them. I applied to my file all the previous suggestions evoqued in the archive (SET OUTPUT_CONTROL = 1 1 1 1 1, corrected the format of my PIR alignement). Yet I still get the same error message.
When I try to check my alignement, i also get this message.
 
Does any body have any idea?
 
 
here is the output
 
TOP_________>   109  749 SET ALNFILE = 'ali.pir'
 
TOP_________>   110  750 SET KNOWNS = '1ayx'
 
TOP_________>   111  751 SET SEQUENCE = 'KPB1'
 
TOP_________>   112  752 SET STARTING_MODEL = 1
 
TOP_________>   113  753 SET ENDING_MODEL = 5
 
TOP_________>   114  754 CALL ROUTINE = 'model'
 
TOP_________>   115  419 CALL ROUTINE = 'getnames'
 
TOP_________>   116  534 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION;
                       = 'EQ', THEN =     'STRING_OPERATE OPERATION = CONCATENA;
                      TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL'
 
TOP_________>   117  535 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI;
                      ON = 'EQ', THEN =     'STRING_OPERATE OPERATION = CONCATE;
                      NATE, STRING_ARGUMENTS = SEQUENCE .rsr,  RESULT = CSRFILE;
                      '
 
TOP_________>   118  536 STRING_OPERATE OPERATION = 'CONCATENATE',                ;
                         STRING_ARGUMENTS = SEQUENCE '.sch',  RESULT = SCHFILE
 
TOP_________>   119  537 STRING_OPERATE OPERATION = 'CONCATENATE',                ;
                        STRING_ARGUMENTS = SEQUENCE '.mat',  RESULT = MATRIX_FI;
                      LE
 
TOP_________>   120  538 SET ROOT_NAME = SEQUENCE
 
TOP_________>   121  539 RETURN
 
TOP_________>   122  420 CALL ROUTINE = 'homcsr'
 
TOP_________>   123  112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE;
                      NCE 
 
 
Dynamically allocated memory at         amaxseq [B,kB,MB]:        84067      82.097     0.080
openf5__224_> Open       20  OLD  SEQUENTIAL  ali.pir
 
Dynamically allocated memory at         amaxbnd [B,kB,MB]:      8049459    7860.800     7.677
openf5__224_> Open       20  OLD  SEQUENTIAL  ali.pir
 
Read the alignment from file       : ali.pir
Total number of alignment positions:   500
 
  #  Code        #_Res #_Segm PDB_code    Name
-------------------------------------------------------------------------------
  1       1ayx     446      1 glucoamlyse
  2       KPB1     394      1 alpha subun
TOP_________>   124  113 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER;
                      ATION = 'ne', THEN = 'GO_TO __ACCELRYS1'
 
TOP_________>   125  117 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