EXPAND_ALIGNMENT -- put all models into alignment

ROOT_NAME = $\langle{\tt string:1}\rangle$	'undf'	root of a filename for filename construction
FILE_ID = $\langle{\tt string:1}\rangle$	'default'	file id for filename construction
EXPAND_CONTROL = $\langle{\tt integer:5}\rangle$	9999 9999 1 10 0	for controlling EXPAND_ALIGNMENT
FILE_EXT = $\langle{\tt string:1}\rangle$	''	file extension for filename construction

Output:

alignment

Description:

ID1, ID2, ROOT_NAME, FILE_EXT, and FILE_ID are used to construct atom filenames for all the models (Section 2.1.4). Next, all the models are added to the alignment, using the last sequence in the input alignment as the guide. This allows easy multiple superposition of all the templates and models after comparative modeling.

Example:

# Example for: EXPAND_ALIGNMENT

# This will add models to the alignment.

READ_ALIGNMENT FILE = 'toxin.ali', ALIGN_CODES = '2ctx' '2abx'
EXPAND_ALIGNMENT EXPAND_CONTROL = 9999 9999 1 3 0, ;
                 ROOT_NAME = '2abx', FILE_ID = '.B', FILE_EXT = ''
WRITE_ALIGNMENT FILE = 'toxin-expand.ali'