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!