hi
i need to create a mutant protein (ex.substitute a single amino acid)
is this possible with modeller?
which script file do i need, which input files?
i found on the website this script
# 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 HSD residues (neutral HIS):
MUTATE_MODEL RESIDUE_TYPE = 'HSD'
# 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'
but..how using it?
thanks frà
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