Dear Pavel,
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).
Greetings,
John
Cc
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
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, Pavel