COLOR_ALN_MODEL -- color MODEL according to alignment

Description:

This command colors MODEL according to a given alignment between MODEL and a sequence. MODEL has to be the first protein in the alignment. The second protein can be any sequence, with or without known structure. The MODEL can be displayed on the screen, colored by `the fourth parameter' and inspected for the structural context of deletions and insertions. This is useful in optimizing the alignment for comparative modeling. The isotropic temperature factors in MODEL are set as follows:

• 0, for those regions that have residues in both MODEL and the sequence (blue in RASMOL; light green in QUANTA);
• 1, for the two residues that span regions occurring in the sequence but not in MODEL (green in RASMOL; pink in QUANTA);
• 2, regions that occur in MODEL but are deleted from the sequence (red in RASMOL; bright green in QUANTA).

Example:

# Example for: COLOR_ALN_MODEL

# Two demos: 
#
# 1) Use a given alignment to color a structure according to 
#    insertions and deletions in a pairwise alignment.
#
# 2) Superpose two 3D structure and do (1).

# Demo 1:

READ_MODEL FILE = '1nbt'
READ_ALIGNMENT FILE = 'toxin.ali', ALIGN_CODES = '1nbt' '1fas', ;
               REMOVE_GAPS = on
COLOR_ALN_MODEL
WRITE_MODEL FILE = '1nbt-1.clr'

# Demo 2:

READ_MODEL FILE = '1nbt', MODEL_SEGMENT = '1:A' '66:A'
SEQUENCE_TO_ALI ALIGN_CODES = '1nbt', ATOM_FILES = ALIGN_CODES
READ_MODEL FILE = '1fas', MODEL_SEGMENT = '1:' '61:'
SEQUENCE_TO_ALI ADD_SEQUENCE = on, ALIGN_CODES = ALIGN_CODES '1fas', ;
                ATOM_FILES = ALIGN_CODES
ALIGN GAP_PENALTIES_1D= -600 -400
MALIGN3D GAP_PENALTIES_3D= 0 3.0
WRITE_ALIGNMENT FILE = 'color_aln_model.pap', ALIGNMENT_FORMAT = 'PAP'

READ_MODEL FILE = '1nbt', MODEL_SEGMENT = '1:A' '66:A'
COLOR_ALN_MODEL
WRITE_MODEL FILE = '1nbt-2.clr'