I was wondering if it would be possible to implement in the abinitio modeling (since de beginning) the experimental data from X-Ray crystallography like we do with experimental distances constraint. As far as I am aware there is a molecular replacement protocol but it is used only with relax protocol.
I’ve talked with the expert in crystallography with Rosetta (Frank Dimaio), and it’s not currently possible to use crystallographic information during the ab initio protocol. Instead, he recommends running the ab initio protocol without crystallography information, and then use the resultant structures as starting points in standard molecular replacement protocols.
Here are some papers that also may be of use (although not ab inito specific):