On 9/30/22 2:50 PM, Franceschini Ghilardi, Amanda (BIDMC - Lijun Sun - General Surg SF) via modeller_usage wrote: > I am trying to model a heptamer (homomultimer), but the structure > generated is wrong because there are many clashes and it looks > completely different from the template. How can I solve this issue?
This is generally caused by an incorrect alignment. You should carefully check your modeling alignment to ensure that it seems reasonable; in particular, many alignment tools don't do a great job aligning multi-chain targets and templates. (You may need to align the chains individually and then combine the alignment manually.)
> def special_restraints(self, aln): > # Constrain the A and B chains to be identical (but only restrain > # the C-alpha atoms, to reduce the number of interatomic distances > # that need to be calculated): > s1 = Selection(self.chains['A']).only_atom_types('CA') > s2 = Selection(self.chains['B']).only_atom_types('CA') > s3 = Selection(self.chains['C']).only_atom_types('CA') > s4 = Selection(self.chains['D']).only_atom_types('CA') > s5 = Selection(self.chains['E']).only_atom_types('CA') > s6 = Selection(self.chains['F']).only_atom_types('CA') > self.restraints.symmetry.append(Symmetry(s1, s2, 1.0))
I assume you are attempting to force all 6 chains to adopt the same conformation, but you have only added a single restraint (between selections s1 and s2, i.e. the A and B chains). One way to achieve this would be to add additional symmetry restraints between s1&s3, s1&s4, etc.
Ben Webb, Modeller Caretaker