> Bernhard's thought experiment is a good one,
I picked it up from Ianprobably posted earlier
BR
> (1). Can I say the X-ray weighting is optimal when it yields the smallest
> Rfree, meanwhile RMS-Z(bonds) is smaller than "0.85 - 0.146*resolution"
> (angles also maybe)?
The weighting is optimal when the free likelihood is maximised with
respect to the weights, or equivalently when the negative
> (2). Why RMS-Z(bonds) should be lower than that for low resolution data
and higher for high resolution? Or why high-resolution can allows more
outliers?
Imagine torsion angle refinement only, at low resolution: The bond
lengths are fixed to target values, their rmsd will be zero.
Imagine free r
Hi Ian:
Thanks a lot! I have 2 questions:
(1). Can I say the X-ray weighting is optimal when it yields the smallest
Rfree, meanwhile RMS-Z(bonds) is smaller than "0.85 - 0.146*resolution"
(angles also maybe)?
(2). Why RMS-Z(bonds) should be lower than that for low resolution data
and higher for
The automatic weighting feature in the latest
releases of refmac is pretty good. However, if you are setting the
X-ray weighting factor manually, typical targets for rms bond
angles are 1.0-2.0 degrees and rms bond lengths of 0.01-0.02 A.
On 9/21/2010 3:54 PM,
To give credit where it is due I should perhaps have explained that
the formula for RMS-Z(bonds) that I quoted was derived from an
analysis of re-refinements from the PDB-REDO project
(http://www.cmbi.ru.nl/pdb_redo), not from the PDB itself. PDB-REDO
itself uses the LLfree optimisation method tha
Hi Hailiang
The short answer is that the optimal X-ray weighting factor minimises
Rfree, or better -LLfree.
However this is tricky to carry out in practice since it means you
have to run several jobs adjusting the weight manually each time to
find the optimum. Also, ideally the same procedure sh
Hi all:
I have a question about deciding an ideal "Weight matrix" value in REFMAC.
When I change it from 0.1 to 0.001, the bond distance rmsd changes from
0.075 to 0.008, while the R changes from 0.26 to 0.33 (resolution 3.2A).
Now I am not sure what is the best balance based on these numbers. Are
