MUTATE_MODEL -- mutate selected MODEL residues

RESIDUE_TYPE = <string:1>

'undefined'

new residue type

Description:

This command mutates the selected residues of the MODEL to the type specified by RESIDUE_TYPE. CHARMM 4-character residue type names are used (see library file $RESTYP_LIB). To select the residues for mutation, use PICK_ATOMS command. All the residues with at least one atom in the selected set 1 of atoms are mutated. To produce mutants, employ this command with SEQUENCE_TO_ALI and WRITE_ALIGNMENT. It is usually necessary to write the mutated sequence out and read it in before proceeding, because not all sequence related information about MODEL is changed by this command (e.g., internal coordinates, charges, and atom types and radii are not updated).

Example:

# Example for: MUTATE_MODEL

# This will read a PDB file, change its sequence a little, build new 
# coordinates for any of the additional atoms using only the internal
# geometry, and write the mutant PDB file.  It can be seen as primitive,
# but rapid comparative modeling for substitution mutants. For insertion 
# and deletion mutants, follow the standard comparative modeling procedure.

# Read the topology library with non-hydrogen atoms only:
READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib', TOPOLOGY_MODEL = 3
# To produce a mutant with all hydrogens, uncomment this line:
# READ_TOPOLOGY FILE = '$(LIB)/top.lib', TOPOLOGY_MODEL = 1

# Read the CHARMM parameter library:
READ_PARAMETERS FILE = '$(LIB)/par.lib'

# Read the original PDB file and copy its sequence to the alignment array:
READ_MODEL FILE = '1fas'
SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = '1fas', ALIGN_CODES = '1fas'

# Select the residues to be mutated: in this case all ASP residues:
PICK_ATOMS RES_TYPES = 'ASP'

# The second example is commented out; it selects residues '1' and '10'.
# SET SELECTION_SEARCH = 'SEGMENT', SELECTION_FROM   = 'ALL'
# PICK_ATOMS SELECTION_SEGMENT =  '1'  '1',  SELECTION_STATUS = 'INITIALIZE'
# PICK_ATOMS SELECTION_SEGMENT = '10' '10',  SELECTION_STATUS = 'ADD'

# Mutate the selected residues into HIS residues (neutral HIS):
MUTATE_MODEL RESIDUE_TYPE = 'HIS'

# Add the mutated sequence to the alignment arrays (it is now the second 
# sequence in the alignment):
SEQUENCE_TO_ALI ADD_SEQUENCE = on, ALIGN_CODES = ALIGN_CODES '1fas-1'

# Generate molecular topology for the mutant:
GENERATE_TOPOLOGY SEQUENCE = '1fas-1'

# Transfer all the coordinates you can from the template native structure
# to the mutant (this works even if the order of atoms in the native PDB 
# file is not standard):
TRANSFER_XYZ

# Build the remaining unknown coordinates for the mutant:
BUILD_MODEL INITIALIZE_XYZ = off

# Write the mutant to a file:
WRITE_MODEL FILE = '1fas-1.atm'