EDIT_ALIGNMENT -- edit overhangs in alignment

EDIT_ALIGN_CODES = <string:0>	'last'	codes of proteins in the alignment to be edited
BASE_ALIGN_CODES = <string:0>	'rest'	codes of proteins in the alignment to be used as the base
MIN_BASE_ENTRIES = <integer:1>	1	minimal number of templates in EDIT_ALIGNMENT
OVERHANG = <integer:1>	0	un-penalized overhangs in protein comparisons
HETATM_IO = <logical:1>	off	whether to read HETATM coordinates
WATER_IO = <logical:1>	off	whether to read water coordinates
HYDROGEN_IO = <logical:1>	off	whether to read hydrogen coordinates
ATOM_FILES_DIRECTORY = <string:1>	'./'	input atom files directory list (e.g., 'dir1:dir2:dir3:./:/')

Description:

This command edits the overhangs in the alignment.

EDIT_ALIGN_CODES specifies the alignment codes for the alignment entries whose overhangs are to be cut; in addition, all or last can be used.

BASE_ALIGN_CODES specifies the alignment codes for the alignment entries that are used to determine the extent of the overhangs to be cut from the edited entries; in addition, all or rest (relative to EDIT_ALIGN_CODES) can be used.

The same entries can be cut and used for determining the base.

The base of the alignment is determined by the first and last alignment positions that have at least MIN_BASE_ENTRIES entries that started by that position, beginning from the first and last alignment positions, respectively.

The cuts are shortened by OVERHANG residues respectively, so that reasonably short terminii can be easily modeled ab initio if desired.

The HETATM_IO, WATER_IO, HYDROGEN_IO, and ATOM_FILES_DIRECTORY keywords also apply because the beginning and ending residue numbers for the `structure' entries in the alignment are renumbered automatically by reading the appropriate atom files.

Example:

# Example for: EDIT_ALIGNMENT

# Read an alignment, write it out in the 'PAP' format, with overhangs cut.

SET OUTPUT_CONTROL = 1 1 1 1 0

# Cut overhangs in the last sequences that are longer than 3 residues
# relative to the longest remaining entry in the alignment:

SET EDIT_ALIGN_CODES = 'last'
SET BASE_ALIGN_CODES = 'rest', MIN_BASE_ENTRIES = 1
SET OVERHANG = 3

READ_ALIGNMENT FILE = 'toxin.ali', ALIGN_CODES = 'all', ALIGNMENT_FORMAT = 'PIR'
WRITE_ALIGNMENT FILE = 'toxin.pap', ALIGNMENT_FORMAT = 'PAP'
EDIT_ALIGNMENT
WRITE_ALIGNMENT FILE = 'toxin-1.pir', ALIGNMENT_FORMAT = 'PIR'
WRITE_ALIGNMENT FILE = 'toxin-1.pap', ALIGNMENT_FORMAT = 'PAP'