Andreas Kowarsch wrote: > i also tried to run my skript to create a multiple alignment. > > top-file: > READ_MODEL FILE = '1HYZ.pdb', MODEL_SEGMENT 'FIRST:A''LAST:A' > SEQUENCE_TO_ALI ALIGN_CODES = '1HYZ' > > READ_MODEL FILE = '1BIS.pdb', MODEL_SEGMENT 'FIRST:B''LAST:B' > SEQUENCE_TO_ALI ALIGN_CODES = '1BIS',ADD_SEQUENCE = on > > READ_MODEL FILE = '1BIU.pdb', MODEL_SEGMENT 'FIRST:B''LAST:B' > SEQUENCE_TO_ALI ALIGN_CODES = '1BIU',ADD_SEQUENCE = on
To use SEQUENCE_TO_ALI to add sequence '1BIS' to an alignment, you should use SEQUENCE_TO_ALI ALIGN_CODES = ALIGN_CODES '1BIS',ADD_SEQUENCE = on and similar for 1BIU. Otherwise, you end up with only one sequence in the alignment.
> But my job don't terminate.... > it always made the same log file > > log-file: > Job starting time (YY/MM/DD HH:MM:SS): 2005/01/13 14:15:56.678 > > rdactio_534E> Command not recognized: > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
This usually means that your input file has odd line-end characters (e.g. you made it on a Windows box, but are running Modeller on Linux, or vice versa) or that you have tab characters in the file. Check it out in a text editor, and make sure the example files work for you.
Ben Webb, Modeller Caretaker