To build a model of a cyclic protein, you must do two things:

  1. Disable the default patching, which would create a C and N terminus.
  2. 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 .ini file.

from modeller import *
from modeller.automodel import *

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:
                   residues=(self.residues[-1], self.residues[0]))

# 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