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Re: [modeller_usage] Modeller multiple alignment

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
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