[phenixbb] Anisotropic B-factors with Trucated Data
jrhelliwell at gmail.com
Sat Aug 1 09:51:07 PDT 2015
I appreciate your reply, thankyou.
And what would you use firstly to monitor success (an Rfree drop presumably but how much is of a drop is significant?) and second to guard against 'over fitting' eg (restraining the aniso Bij?).
PDB Redo use a Hamilton Rfactor test algorithm to judge if aniso can sensibly be applied. That seems to me the ideal check (Hamilton).
Emeritus Prof John R Helliwell DSc_Physics
FInstP FRSC FRSB Fellow of the ACA
Emeritus Member of the British Biochemical Society
School of Chemistry, University of Manchester, M13 9PL, UK.
On 1 Aug 2015, at 17:23, Pavel Afonine <pafonine at lbl.gov> wrote:
> Dear John,
>> 1.7 Angstrom resolution seems to me awfully low for thinking about anisotropic protein model refinement! Ie in terms of number of diffraction data to model parameters.
> in refinement we use restraints that contribution is added with variable weights:
> Ttotal = Tdata + w * Trestraints .
> One can think of Trestraints being "observations" added to the actual data in different amounts depending on choice of the weight w.
> This is exactly why we can still refine individual coordinates or isotropic B-factors at "macromolecular" resolutions like 2-6A or so. If we think of this in terms of data/parameters ratio counted as Nreflections vs Natoms*(4xyz+1B) (that is without restraints) that would be impossible but restraints do the trick.
> Likewise, we can still refine anisotropic B-factors at resolutions beyond 1-1.2A. I agree 1.7A is a bit low(ish) but in favorable cases (data is very good and comes from a crystal that can diffract to a higher resolution) might be worth a try.
> All the best,
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