Dear Smith, when you expand to P1, pointless should suggest the space group you expanded from, unless you fiddled with the data after expansion.
Regards, Tim On 07/01/2015 04:43 AM, Smith Liu wrote: > If both the PDB and mtz for the pdb have been assigned to P1 space group for > some reason, can this lead to Rwork higher than Rfree during refinement? > > > > If after converting my PDB and mtz to P1 space group, and I have forgotten > what is the original space group for my PDB and mtz before conversion to P1 > space group, is any method which can recover the original space group for my > PDBand mtz, so that in the following refine Rwork would be lower than Rfree? > > > Smith > > > > > > > > > At 2015-07-01 01:55:22, "Eleanor Dodson" <[email protected]> wrote: > > I suppose if I was the referee for this structure and your FreeR is so close > to the Rfactor I would ask you to ensure you had the right space group - is > the 6 fold NCS actually 2 fold NCS with a crystallographic 3 fold.. > Cases occur where R32 is indexed as C2.. > > > Certainly if the Rfree set is assigned randomly to reflections which are > symmetry equivalents then you see this phenomena of Rfree = Rfactor > > > Eleanor > > > On 30 June 2015 at 18:26, Gerard Bricogne <[email protected]> wrote: > Dear Wolfram, > > I have a perhaps optimistic view of the effect of high-order NCS > on Rfree, in the sense that I don't view it as a "problem". People > have agonised to extreme degrees over the "difficulty" of choosing a > free set of reflections that would produce the expected gap between > Rwork and Rfree, and some of the conclusions were that you would need > to hide almost half of your data in some cases! > > I think it is best to remember that the idea of cross-validation > by Rfree is to prevent overfitting, i.e. ending up with a model that > fits the amplitudes too well compared to how well it determines the > phases. In the case of high-order NCS (in your case, the U/V ratio > that the old papers on NCS identified as the key quantity to measure > the phasing power of NCS would be less than 0.1!) the phases and the > amplitudes are so tightly coupled that it is simply impossible to fit > the amplitudes without delivering phases of an equally good quality. > In other words there is no overfitting problem (provided you do have > good and complete data) and the difference between Rfree and Rwork is > simply within the bounds of the statistical spread of Rfree depending > on the free set chosen. > > You are lucky to have 6-fold NCS, so don't let any reviewer > convince you that it is a curse, and make you suffer for it :-) . > > > With best wishes, > > Gerard. > > -- > > On Tue, Jun 30, 2015 at 12:58:44PM -0400, wtempel wrote: >> Hello, >> my question concerns refinement of a structure with 6-fold NCS (local >> automatic restraints in REFMAC) against 2.8 A data. The size of my free set >> is 1172 selected in thin resolution shells (SFTOOLS) and corresponding to >> 4.3 % of reflections. >> A refmac run of 10 cycles of TLS and 10 cycles of CGMAT starts out at >> Rfree/Rcryst 0.271/0.272. After the 10th TLS cycle I have 0.227/0.224. Yes, >> Rfree < Rcryst. At the end of CGMAT I have 0.2072/0.2071. >> I understand that NCS stresses the independence assumption of the free set. >> Am I correct in believing that Rfree *may* be smaller than Rcryst even in >> the absence of a major mistake? My hope is that the combined wisdom of >> ccp4bb followers can point out my possible mistake, suggest tests that I >> may perform to avoid them and, possibly, arguments in defense of a >> crystallographic model with Rfree < Rcryst. >> Many thanks, >> Wolfram Tempel > > > -- > > =============================================================== > * * > * Gerard Bricogne [email protected] * > * * > * Global Phasing Ltd. * > * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * > * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * > * * > =============================================================== > > -- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A
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