Hi all

 

We are trying to build a homotetramer model but having some difficulty maintaining symmetry.  I've read the previous posts but maybe someone can help me further - I'm new to Modeller and to Python.

 

I have imposed symmetry:

 

        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')

        self.restraints.symmetry.append(symmetry(s1, s2, 1.0))
        self.restraints.symmetry.append(symmetry(s1, s3, 1.0))
        self.restraints.symmetry.append(symmetry(s1, s4, 1.0))

 

but when I run automodel the molecular dynamics step pulls the monomers away from the template - so that although the subunits are identical, the symmetry is broken.

 

We can think of a few ways to get around this:

1) do no molecular dynamics, only minimisation (maybe someone can tell me how?)

2) run molecular dynamics only on selected regions of the model so that the core remains fixed in place (again, how would I do this?)

3) learn Python and write restraints using symmetry matrices (if someone has implemented something like this before I'd love to see their code!)

 

Looking forward to your input

Jean