Hi Jacob

Why is the choice between A and B?  Why not C?  A & B seem to be opposite extremes, what happens if you aim for a RMSbonds value in the middle, say 0.01?

Cheers

-- Ian

On 25 January 2016 at 21:23, Eleanor Dodson <[log in to unmask]> wrote:

What is the RMS difference between the coordinates! I bet not very much.

I simply cannot believe that RMS bonds can be 0.003 - surely the different chemistry for different residues would result in a bigger rms bonds than that? 

Another Q - that is an overall R factor - is there some B factor related effect which should show up more at ugh resolution. The B factor restraints in REFMAC are too tight I think anyway. 

Eleanor

On 25 January 2016 at 20:52, Keller, Jacob <[log in to unmask]> wrote:

Dear Crystallographers,

I seem to have an artistic situation on my hands: the decision between R and geometry.

Refinement strategy A:

R/Rfree: 0.084/0.156
RMSbonds: 0.025
RMSlengths: 2.1995

Refinement strategy B:

R/Rfree: 0.136/0.177
RMSbonds: 0.003
RMSlengths: 0.338

RSRZ scores or similar are not available in B, but there are 0 outliers in A.

Do I just flip a coin? I am inclined to go for B, since the data are twinned and are therefore somewhat less information-rich than normal, so should perhaps be guided by the geometrical book values more than normal, but the Rfree is fully 2% lower in A. Also, the R/Rfree gap is probably too big in A. Any advice/input on how to decide? Having been chastened by the recent "questionable structure" thread and the vitriol against PDB pollution, I am trying to be especially vigilant.

Jacob Keller


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Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: [log in to unmask]
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