[phenixbb] Phenix.refine bonds/angles rmsd

Pavel Afonine PAfonine at lbl.gov
Wed Apr 14 23:46:07 PDT 2010

Hi Jason,

> 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 
> parameters?

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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