Regarding what Eleanor said: The program “labelit,” available within Phenix from command line, can check automatically for higher space groups.
In the labelit documentation/homepage it mentions the command: labelit.check_pdb_symmetry [pdb coordinate file] [data=mtz file] JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eleanor Dodson Sent: Tuesday, June 30, 2015 1:55 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Rfree below Rwork 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 <g...@globalphasing.com<mailto:g...@globalphasing.com>> 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 g...@globalphasing.com<mailto:g...@globalphasing.com> * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033<tel:%2B44-%280%291223-353033> * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889<tel:%2B44-%280%291223-366889> * * * ===============================================================
