[modeller_usage] question on mutate monomers script

[Andrew Voronkov <>]

Dear Modeller users, 
I am trying to mutate several aminoacids in the PDB file. I ve used the scrtipt (mutate.py) attached for this, but I get the error given below. What can be the problem? 
As I understand I need only PDB file for this script execution. 
Do I need to write path to the libraries in the explicit way or it should get it from the environment setup? I haven't specified the full path. 

Sincerely yours, 
Andrew 



:~/Mutate> mod9v7 mutate.py 
'import site' failed; use -v for traceback 
warning: Non-ASCII character '\xe2' in file mutate.py on line 11, but no encoding declared; see http://www.python.org/peps/pep-0263.html for details 
File "mutate.py", line 11 
env.libs.topology.read(file=’$(LIB)/top_heav.lib’) 
^ 
SyntaxError: invalid syntax 
edward@29:~/Mutate> 




Скачать присоединенный файл (mutate.py):
# Example for: selection.mutate() 
# 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. 
from modeller import * 
env = environ() 
env.io.atom_files_directory = ['.', '../atom_files'] 
# Read the topology library with non-hydrogen atoms only: 
env.libs.topology.read(file=’$(LIB)/top_heav.lib’) 
# To produce a mutant with all hydrogens, uncomment this line: 
#env.libs.topology.read(file=’$(LIB)/top_allh.lib’) 
# Read the CHARMM parameter library: 
env.libs.parameters.read(file=’$(LIB)/par.lib’) 
# Read the original PDB file and copy its sequence to the alignment array: 
code = ’1ijy’ 
aln = alignment(env) 
mdl = model(env, file=code) 
aln.append_model(mdl, atom_files=code, align_codes=code) 
# Select the residues to be mutated: in this case all ASP residues: 
sel = selection(mdl).only_residue_types(’ASP’) 
# The second example is commented out; it selects residues ’1’ and ’10’. 
#sel = selection(mdl.residues[’1’], mdl.residues[’10’]) 
# Mutate the selected residues into HIS residues (neutral HIS): 
sel.mutate(residue_type=’ASN’) 
# Add the mutated sequence to the alignment arrays (it is now the second 
# sequence in the alignment): 
aln.append_model(mdl, align_codes=’1ijy-1’) 
# Generate molecular topology for the mutant: 
mdl.clear_topology() 
mdl.generate_topology(aln[’1ijy-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): 
mdl.transfer_xyz(aln) 
# Build the remaining unknown coordinates for the mutant: 
mdl.build(initialize_xyz=False, build_method=’INTERNAL_COORDINATES’) 
# Write the mutant to a file: 
mdl.write(file=’1ijy-1.atm’)