distance restraint to symmetry related atom

als

I have a rigid body which is one half of a molecule. The other half is generated by symmetry elements. I shall refer to the symmetry generated elements as the prime, ie C2'.

Allowing the rigid body to refine I get reasonable bond distances within the rigid body, however between C4 and C2' I end up with a short ie. 1.2 A vs 1.45 A bond length.

Is there a way to use distance restrain to restrain the distance between an element and the symmetry generated copy, ie C4 and C2'?

johnsoevans

It is possible to apply restraints between different symmetry generated copies of an atom. You describe the specific atom as something like "O2 7 -1 1 1" where the four numbers refer to the symmetry operation used to generate the copy and the unit cell it sits in. You can find these labels from the distance and angle calculation.

However, it doesn't seem like this is what you want to do. If you have a rigid body that lies on a symmetry element then you have to consider if it's sensible to refine e.g. all the rotx/roty/rotz parameters. For example, imagine a triangle in the xy plane that lies on a 2 fold axis along a such that you define two sites (one apex on the two fold and one not). You could refine a rotation about x, but the rotation around z would have to be zero. If not you'd move the apex off the two fold axis destroying the rigid body.

als

Thanks John, that was helpful.