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One "rule of thumb" based on R and R-free divergence that I impress onto crystallography students is this: If a change in refinement strategy or parameters (eg loosening restraints, introducing TLS) or a round of addition of unimportant water molecules results in a reduction of R that is more than double the reduction in R-free, then don't do it. This rule of thumb has proven successful in providing a defined end point for building and refining a structure. The rule works on the differential of R - R-free divergence. I've noticed that some structures begin with a bigger divergence than others. Different Rmerge might explain. Has anyone else found a student in a dark room carefully adding large numbers of partially occupied water molecules? Anthony Anthony Duff Telephone: 02 9717 3493 Mob: 043 189 1076 ________________________________ From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Artem Evdokimov Sent: Tuesday, 26 October 2010 1:45 PM To: [log in to unmask] Subject: Re: [ccp4bb] diverging Rcryst and Rfree Not that rules of thumb always have to have a rationale, nor that they're always correct - but it would seem that noise in the data (of which Rmerge is an indicator) should have a significant relationship with the R:Rfree difference, since Rfree is not (should not be, if selected correctly) subject to noise fitting. This rule is easily broken if one refines against very noisy data (e.g. "that last shell with Rmerge of 55% and <I/sigmaI> ratio of 1.3 is still good, right?") or if the structure is overfit. The rule is only an indicative one (i.e. one should get really worried if R-Rfree looks very different from Rmerge) and it breaks down at very high and very low resolution (more complete picture by GK and shown in BR's book). Since selection of data and refinement procedures is subject to the decisions of the practitioner, I suspect that the extreme divergence shown in the figures that you refer to is probably the result of our own collective decisions. I have no proof, but I suspect that if a large enough section of the PDB were to be re-refined using the same methods and the same data trimming practices, the spread would be considerably more narrow. That'd be somewhat hard to do - but may be doable now given the abundance of auto-building and auto-correcting algorithms. Artem On Mon, Oct 25, 2010 at 9:07 PM, Bernhard Rupp (Hofkristallrat a.D.) <[log in to unmask]> wrote: And the rationale for that rule being exactly what? For stats, see figures 12-23, 12-24 http://www.ruppweb.org/garland/gallery/Ch12/index_2.htm br From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Artem Evdokimov Sent: Monday, October 25, 2010 6:36 PM To: [log in to unmask] Subject: Re: [ccp4bb] diverging Rcryst and Rfree http:[log in to unmask] as well as some notes in the older posts :) As a very basic rule of thumb, Rfree-Rwork tends to be around Rmerge for the dataset for refinements that are not overfitted. Artem On Mon, Oct 25, 2010 at 4:10 PM, Rakesh Joshi <[log in to unmask]> wrote: Hi all, Can anyone comment, in general, on diverging Rcryst and Rfree values(say>7%) for structures with kind of low resolutions(2.5-2.9 angstroms)? Thanks RJ