Re: [modeller_usage] Disulfide bridge between residues into different monomers

Hi,

I am working on a decameric protein and want to create disulfide bridge between cysteines of adjacent monomers. I used the following script (model-disulfide.py):

# Homology modeling by the automodel class

from modeller import * # Load standard Modeller classes

from modeller.automodel import * # Load the automodel class

# Redefine the special_patches routine to include the additional disulfides

# (this routine is empty by default):

class MyModel(automodel):

def special_patches(self, aln):

# A disulfide between residues 8 and 45:

self.patch(residue_type='DISU', residues=(self.residues['14:A'],

self.residues['44:D']))

log.verbose() # request verbose output

env = environ() # create a new MODELLER environment to build this model in

# directories for input atom files

env.io.atom_files_directory = ['.', '../atom_files']

a = MyModel(env,

alnfile = 'twochain.ali', # alignment filename

knowns = 'em', # codes of the templates

sequence = 'query') # code of the target

a.starting_model= 1 # index of the first model

a.ending_model = 1 # index of the last model

# (determines how many models to calculate)

a.make() # do the actual homology modeling

First I tried making only one hydrogen bond between residue 14 of chain A and 44 of chain D but I am getting the following errors:-

H:\Modeller9.13\examples\automodel\Lysine Decarboxylase>mod9.13 model-disulfide.

'import site' failed; use -v for traceback

Traceback (most recent call last):

File "model-disulfide.py", line 26, in ?

a.make() # do the actual homology modeling

File "H:\Modeller9.13\modlib\modeller\automodel\automodel.py", line 97, in mak

self.homcsr(exit_stage)

File "H:\Modeller9.13\modlib\modeller\automodel\automodel.py", line 436, in ho

mcsr

self.make_initial_model(aln)

File "H:\Modeller9.13\modlib\modeller\automodel\automodel.py", line 450, in ma

ke_initial_model

self.generate_method(self, aln)

File "H:\Modeller9.13\modlib\modeller\automodel\generate.py", line 39, in tran

sfer_xyz

mdl.create_topology(aln)

File "H:\Modeller9.13\modlib\modeller\automodel\automodel.py", line 677, in cr

eate_topology

self.special_patches(aln)

File "model-disulfide.py", line 10, in special_patches

self.patch(residue_type='DISU', residues=(self.residues['14:A'],

File "H:\Modeller9.13\modlib\modeller\coordinates.py", line 254, in __getitem_

(self.offset, self.length, self.suffix))

File "H:\Modeller9.13\modlib\modeller\util\modutil.py", line 23, in handle_seq

_indx

int_indx = lookup_func(*args)

File "H:\Modeller9.13\modlib\modeller\coordinates.py", line 318, in _indxres

raise KeyError("No such residue: %s" % indx)

KeyError: 'No such residue: 44:D'

I even tried giving the residue information as: 14:A and 44:D, but still I am getting the same error (as above).

Just to inform you further my template does not have cysteines for the formation of disulfide bridges, so I also generated a mutant with cysteines and tried the patch.py script:

from modeller import *

from modeller.scripts import complete_pdb

env = environ()

env.io.atom_files_directory = ['../atom_files']

env.libs.topology.read(file='$(LIB)/top_heav.lib')

env.libs.parameters.read(file='$(LIB)/par.lib')

# Create the disulfide bond:

def patches(mdl):

mdl.patch(residue_type='DISU', residues=(mdl.residues['14:A'],

mdl.residues['44:D']))

# Read the sequence:

code = 'em-2.pdb'

mdl = complete_pdb(env, code, special_patches=patches)

# Create the stereochemical restraints

sel = selection(mdl)

mdl.restraints.make(sel, restraint_type='stereo', spline_on_site=False)

# Calculate the energy to test the disulfide:

sel.energy()

This is the error I got:

H:\Modeller9.13\examples\automodel\Lysine Decarboxylase>mod9.13 patch.py

'import site' failed; use -v for traceback

Traceback (most recent call last):

File "patch.py", line 19, in ?

mdl = complete_pdb(env, code, special_patches=patches)

File "H:\Modeller9.13\modlib\modeller\scripts\complete_pdb.py", line 39, in co

mplete_pdb

special_patches(mdl)

File "patch.py", line 15, in patches