Dear Users,
I want to use modeller to model the cyclopeptide. Before
sending question
here, I checked the mail-list and found other people had
asked similar
questions. However, when I tried to solve my own problem
based on the
suggestion, I still could not get my problem resolved.
I have attached the script as following:
# Homology modeling by the automodel class
from modeller.automodel import *
# Load standard Modeller classes
env = environ() # create a new MODELLER environment to
build this model
in
# directories for input atom files
env.io.atom_files_directory =
'/home/rileiyu/model/single/atom'
# Disable default NTER and CTER patching
env.patch_default=False
class mymodel(automodel):
def special_patches(self, aln):
# Link between residues 22 and 1 to make chain
cyclic:
self.patch(residue_type='LINK',
residue_ids=('22:', '1:'))
a = mymodel(env,
alnfile = 'single', # alignment filename
knowns = 'mii', # codes of the templates
sequence = 'cmii',) # code of the target
a.make() # do the actual homology modeling
But when I started to model my cyclopepetide the problem
appeared as:
Traceback (most recent call last):
File "model.py", line 21, in ?
a.make() # do the actual homology modeling
File
"/home/rileiyu/share/modeller9v7/modlib/modeller/automodel/automodel.py",
line 98, in make
self.homcsr(exit_stage)
File
"/home/rileiyu/share/modeller9v7/modlib/modeller/automodel/automodel.py",
line 427, in homcsr
self.make_initial_model(aln)
File
"/home/rileiyu/share/modeller9v7/modlib/modeller/automodel/automodel.py",
line 441, in make_initial_model
self.generate_method(self, aln)
File
"/home/rileiyu/share/modeller9v7/modlib/modeller/automodel/generate.py",
line 25, in transfer_xyz
mdl.create_topology(aln)
File
"/home/rileiyu/share/modeller9v7/modlib/modeller/automodel/automodel.py",
line 659, in create_topology
self.special_patches(aln)
File "model.py", line 13, in special_patches
self.patch(residue_type='LINK', residue_ids=('22:',
'1:'))
TypeError: patch() got an unexpected keyword argument
'residue_ids'
Can anyone here give me more suggestions please?
Very appreciated for your help!