On 09/27/2016 04:29 AM, Josh Bullock wrote: > I was wondering, how does IMP handle crosslinks when there are multiple > copies of the same subunit (created in IMP using the create_clone() > function) ?

Ambiguity *should* be handled automatically.

> If an inter-subunit crosslink is satisfied in IMP with an > intra-crosslink, does this stop the crosslink from contributing to the > scoring ?

The restraint doesn't statically pick one interaction and freeze that; rather (as I far as I understand it) each possible interaction is a minimum on the restraint's energy surface, so the assignment can change during a simulation.

> Also, experimentally it is possible to clarify which crosslinks are > definitely intra-subunit (via SDS-PAGE). However there doesn't seem to > be any way to flag this on a crosslink in IMP, unless I'm missing > something ... ?

That I don't know, but Riccardo would.

Ben