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[modeller_usage] cyclic peptide modeling



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!