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
Thijs Beuming wrote: > 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']))
According to your output, you are running Modeller 8v2. But this script you have written is intended for Modeller 9v1. Either upgrade to 9v1, or look in the 8v2 manual (http://salilab.org/modeller/8v2/manual/node124.html) for the old way to patch residues.
> env.io.atom_files_directory = '~/NTProject2005/NEW_TCA/MODELLER'
Neither Python nor Modeller will expand '~' in path names. You can use Python's os.path module to do this (http://www.python.org/doc/2.3.5/lib/module-os.path.html) or Modeller will expand environment variables such as ${HOME}.
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Thijs Beuming