[phenixbb] Phenix.refine bonds/angles rmsd
PAfonine at lbl.gov
Wed Apr 14 23:46:07 PDT 2010
> Just a thought, but running the default "phenix.refine" command is
> going to refine individual atomic coordinates and ADPs, unless you
> specify otherwise.
where ADPs can be refined as individual isotropic or individual
anisotropic. Plus, it will refined occupancies in some cases:
> At 3.3A are you sure you have enough data to model all of these
Most of the time at 3.3A you can refine individual ADPs and coordinates.
Just use tighter restraints. Of course it's case dependent and in each
case you need to see what would work best.
> Even with heavy restraints, i'm not sure individual coordinate
> refinement is feasible.
Why? I've see such a case only once, when refining against 60% complete
neutron data at 3A resolution where the model contained all H/D
explicitly present (not riding) -:)
> Perhaps doing a rigid-body refinement of multiple groups with grouped
> ADPs would yield better results. You could even model in TLS groups.
It is always good to use TLS, at 1.7A or at 6A resolution (slides 30-36):
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