Hi Ian,
Yes, I guess my rule does work as you say. If, starting the day from (Rwork = 20, Rfree = 30) abbreviate (20,30), you do something to get (18,29), yes this means that that something was a bare minimum acceptable thing to do. If you do something to get (16,29) (decreased R by 4, Rfree by 1), then I would immediately suspect that that thing that was done introduced excessive over-fitting. If you do something to get (18,28) (decreased R by 2, Rfree by 2), then I would say that the thing that was done was a good thing. Yes, other arbitrary linear combinations could work. Not great analysis of this method was performed. I considered that it came to a question of what degree of over-fitting is acceptable. In practice, this rule stopped endless additions of water molecules and further alternate conformations, and for that purpose the precise point seemed unimportant. However, I also used this rule to determine preferred parameters for BFAC and the matrix weight. Do you think this is a bad rule, and can you point me to a better rule? Replying to BR: >> This rule of thumb has proven successful in providing a defined end point >>for building and refining a structure. >Hmmm. I always thought things like no more significant explainable >(difference) density define endpoints > >in model building and not R-values. This strategy has proven successful in >nailing ligand structures where > >R-value rules of thumb were used to define the end points. Of course, there are other rules. One has to explain all significant residual density. But this tends to be a finite task. The above rule was not applicable to building active sites, or other things that would be discussed directly in a paper. The problem I attempt to address is endless fiddling with features of every-diminishing importance. Apologies if I have missed a recent relevant thread, but are lists of rules of thumb for model building and refinement? Anthony Anthony Duff Telephone: 02 9717 3493 Mob: 043 189 1076 -----Original Message----- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Wednesday, 27 October 2010 12:53 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] diverging Rcryst and Rfree [SEC=UNCLASSIFIED] Anthony, Your rule actually works on the difference (Rfree - Rwork/2), not (Rfree - Rwork) as you said, so is rather different from what most people seem to be using. For example let's say the current values are Rwork = 20, Rfree = 30, so your current test value is (30 - 20/2) = 20. Then according to your rule Rwork = 18, Rfree = 29 is equally acceptable (29 - 18/2 = 20, i.e. same test value), whereas Rwork = 16, Rfree = 29 would not be acceptable by your rule (29 - 16/2 = 21, so the test value is higher). Rwork = 18, Rfree = 28 would represent an improvement by your rule (28 - 18/2 = 19, i.e. a lower test value). You say this criterion "provides a defined end-point", i.e. a minimum in the test value above. However wouldn't other linear combinations of Rwork & Rfree also have a defined minimum value? In particular Rfree itself always has a defined minimum with respect to adding parameters or changing the weights, so would also satisfy your criterion. There has to be some additional criterion that you are relying on to select the particular linear combination (Rfree - Rwork.2) over any of the other possible ones? Cheers -- Ian On Tue, Oct 26, 2010 at 6:33 AM, DUFF, Anthony <a...@ansto.gov.au> wrote: > > > 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:ccp...@jiscmail.ac.uk] On Behalf Of Artem > Evdokimov > Sent: Tuesday, 26 October 2010 1:45 PM > To: CCP4BB@JISCMAIL.AC.UK > 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.) > <hofkristall...@gmail.com> 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:ccp...@jiscmail.ac.uk] On Behalf Of Artem > Evdokimov > Sent: Monday, October 25, 2010 6:36 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] diverging Rcryst and Rfree > > > > http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg04677.html > > 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 <rjo...@purdue.edu> 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 > > > >
