[phenixbb] Rigid body refinement question

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Thu Apr 29 15:49:07 PDT 2010

> What if you do like this?
> "strategy=rigid_body+individual_sites" "sites.individual=chain A
> and resid 36" "sites.rigid_body=chain A" "sites.rigid_body=chain B"

During rigid-body refinement, the bonds/angles/dihedrals/nonbondeds
to the non-refined sites are not restrained. This could seriously
mess up the geometry.
In addition, rigid-body refinement and individual refinement will
only run alternatingly.
I'd be surprised if the parameter combination above did much good,
but you never know before you try it.
Simultaneous refinement of individual sites and (small) rigid bodies
with full use of restraints is on our long-term wish list.


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