Hi,
I have some problems making a disulphide bridge in MODELLER. Any help would be greatly appreciated.
Thanks,
Thijs Beuming
My script:
# 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 176 and 185: self.patch(residue_type='DISU', residues=(self.residues['176'], self.residues ['185']))
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 = '~/NTProject2005/NEW_TCA/MODELLER'
a = mymodel(env, alnfile = '~/NTProject2005/NEW_TCA/MODELLER/ molpharm.pir', # alignment filename knowns = '2A65-clean', # codes of the templates sequence = 'hNET') # 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
The error:
Traceback (most recent call last): File "model_hNET_xray2.py", line 26, in ? a.make() # do the actual homology modeling File "/softlib/exe/ia64/pkg/modeller/8v2/dist/modlib/modeller/ automodel/automodel.py", line 100, in make self.homcsr(exit_stage) File "/softlib/exe/ia64/pkg/modeller/8v2/dist/modlib/modeller/ automodel/automodel.py", line 334, in homcsr self.generate_method(self, aln) File "/softlib/exe/ia64/pkg/modeller/8v2/dist/modlib/modeller/ automodel/generate.py", line 24, in transfer_xyz mdl.create_topology(aln) File "/softlib/exe/ia64/pkg/modeller/8v2/dist/modlib/modeller/ automodel/automodel.py", line 483, in create_topology self.special_patches(aln) File "model_hNET_xray2.py", line 10, in special_patches self.patch(residue_type='DISU', residues=(self.residues['176'], File "/softlib/exe/ia64/pkg/modeller/8v2/dist/modlib/modeller/ model.py", line 543, in __getitem__ ret = modutil.handle_seq_indx(self, indx) File "/softlib/exe/ia64/pkg/modeller/8v2/dist/modlib/modeller/util/ modutil.py", line 117, in handle_seq_indx raise TypeError TypeError