I replied in too great a rush - it is the Rfree, or the Rfree-Rwork gap, that would go up a lot if a structure originally refined at low resolution with targeting to an external high-resolution one was re-refined without that targeting.
Gerard. -- On Fri, Apr 04, 2014 at 04:55:03PM +0100, Gerard Bricogne wrote: > Dear Nat and Tim, > > On Fri, Apr 04, 2014 at 08:18:06AM -0700, Nat Echols wrote: > > On Fri, Apr 4, 2014 at 1:57 AM, Tim Gruene <[email protected]> > > wrote: > > > > > A more up-to-date reason is that programs calculate R values very > > > differently. If you take a PDB file refined with program X and put it > > > into program Y you easily get discrepancies greater than 5%. > > > > > > > This is actually pretty rare - usually it's only 1-2% at most. > > Discrepancies like 16.5% versus 30.9% usually indicate that there's > > something wrong or misleading in the annotation of the entry, and often > > mean that you can't even reproduce the R-factor with the specified program. > > > > -Nat > > It could also be that such a structure is the result of a refinement > against low-ish resolution data that was restrained by "targeting" it to > another similar structure that was refined against higher-resolution data, > so as to retain the good local geometry of the latter in spite of the > shortage of data at low resolution. This is perfectly legitimate, and was > first done by Oliver Smart in BUSTER under the acronym of "LSSR", outlined > in an ACA 2008 Abstract then fully described in Acta Cryst. D68, 368-380 > (2012). A similar feature has also become available in REFMAC and PHENIX. > > The problem is that the deposition process is very likely to have lost > track of the recourse to that method, so that the outcome of the refinement > cannot be reproduced from the deposited data in an automated environment > such as the EDS server. > > This may not be the case with the structure Tim was mentioning, but it > provides an opportunity to point out that the use of some recent approaches > to improving refinement at low resolution may need further attention at the > deposition stage to ensure reproducibility of the results from the deposited > information. > > > With best wishes, > > Gerard.
