[phenixbb] residue selection for rsrl?

Kevin Jude kjude at stanford.edu
Wed Nov 26 10:55:27 PST 2014

Hi Pavel, I've identified the root issue of my original problem - I am
using a reference model and the problematic side chains don't agree with
the reference.  Easy enough to fix.

Also I was using structure factors calculated by Buster, not realizing that
this file contained HL coefficients based on my model.  Phenix read these
coefficients and switched to MLHL; the resulting instability is probably
what led to the increase in Rfree.  Re-refinements using the ML target show
that the Rfree is essentially the same with and without RSR, to be expected
since the structure is about finished.

Best wishes

On Tue, Nov 25, 2014 at 7:27 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

>  Hi Kevin,
> real-space refinement is global: it does not work on selected atoms.
> I wonder why it results in increased Rfree.. Could you please send me
> files off list so I can investigate and perhaps suggest a solution?
> Thanks,
> Pavel
> On 11/25/14 12:59 PM, Kevin Jude wrote:
>  I am refining a structure at 2.9 Å resolution and have two side chains
> that keep moving out of density during reciprocal space refinement; both
> side chains should fit the resulting Fo-Fc density in favored rotamers.
> Turning on real-space refinement fixes this problem but leads to higher
> Rfree and poorer geometry overall.  Can I select a subset of residues for
> real space refinement while still performing reciprocal space refinement on
> the whole asymmetric unit?
>  Thanks for any help
> Kevin
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