[phenixbb] The individual site refinement for Low resolution data (~3.8A)

Nathaniel Echols nechols at lbl.gov
Fri Mar 18 14:58:41 PDT 2011

On Fri, Mar 18, 2011 at 2:39 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
> I have no idea where you read this ("Phenix suggested "Individual site"
> refinement is only suitable for high or midi resolution data (<3.5A)") - I
> would never say this.
> With proper set of restraints (Ramachandran plot restraints, secondary
> structure restraints, reference model (if available) restraints) and weights
> (tight enough geometry) you can refine individual coordinates (as well as
> B-factors) at this resolution.

The documentation for the GUI says that individual_sites "is almost
always appropriate except at low-resolution (typically 3.5A or worse),
unless additional restraints (NCS, reference model, etc.) are used."
Which, in retrospect, was not the clearest way to state it, so I've
modified that sentence to sound less negative.

The intended message was the same as Pavel's - you usually need to add
more restraints to make coordinate refinement behave well at low
resolution.  However, I would recommend trying them in the opposite
order: a high-resolution reference model is ideal if available.  (You
should also use NCS restraints if NCS is present.)  The Ramachandran
restraints should only be used as a last resort, at the end of
refinement, and after you've fixed as many problems as possible
manually in Coot (with real-space refinement).


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