To build a model of a cyclic protein, you must do two things:
- Disable the default patching, which would create a C and N terminus.
- Use the LINK patching residue in the special_patches routine to link the last and first residues.
For example, the script below builds a cyclic model of 1fdx using 5fd1 as a template (alignment.ali is the example from the Modeller distribution).
⚠️ It is important that you get the residue order correct; the residues must be the last and first residue in the cyclic protein respectively (in the model, not the template). If in doubt, build a regular model first and look at the residue numbers and chain IDs in the final models or
from modeller import * from modeller.automodel import * log.verbose() env = Environ() # Disable default NTER and CTER patching env.patch_default = False class MyModel(AutoModel): def special_patches(self, aln): # Link between last residue (-1) and first (0) to make chain cyclic: self.patch(residue_type='LINK', residues=(self.residues[-1], self.residues)) # Use the new 'MyModel' class rather than 'AutoModel' a = MyModel(env, alnfile='alignment.ali', knowns='5fd1', sequence='1fdx') a.starting_model = a.ending_model = 1 a.make()