SEQUENCE_TO_ALI -- copy MODEL sequence and coordinates to alignment

ADD_SEQUENCE = $\langle{\tt logical:1}\rangle$	off	whether to add the new sequences to the existing alignment
ALIGN_CODES = $\langle{\tt string:0}\rangle$	'all'	codes of proteins in the alignment
ATOM_FILES = $\langle{\tt string:0}\rangle$	''	complete or partial atom filenames
OUTPUT_DIRECTORY = $\langle{\tt string:1}\rangle$	''	output directory

Output:

NUMB_OF_SEQUENCES, ALIGN_CODES, ATOM_FILES

Description:

This command copies the sequence and coordinates of the MODEL to the alignment arrays.

If ADD_SEQUENCE is on the sequence is added to the sequences that are already in the alignment arrays, otherwise it becomes the only sequence in those arrays.

When sequence $i$ is added, the corresponding elements of ALIGN_CODES and ATOM_FILES are used to set the protein and PDB code fields in the alignment file, respectively.

Example: See COMPARE_ALIGNMENTS command.