Garib may have more to say, but the first point would be to always include the original data file as your input MTZ file for any cycle of refinement, whether you're using Refmac in CCP4 or phenix.refine. (In phenix.refine, if you assign the R-free data the first time you do refinement, it will produce a file containing all the information used in that cycle of refinement, including the new R-free flags and possibly any Hendrickson-Lattman coefficients, and you should use that file for all subsequent refinements.)
As for whether R-free takes twinning into account, I think it's fair to say that all the refinement programs that handle twinning will do this appropriately. Regards, Randy Read On 2 Mar 2012, at 08:01, arka chakraborty wrote: > Hi all, > > I will like to know, as a follow up of what Prof. Randy Read said, what > should be done to do the refinement against the measured data and not the > detwinned F( which refmac outputs in the mtz after twin refinement), during > subsequent refinements. And also, I would like to know how to ensure that the > free R generated takes twinning into account if I am not using phenix. > > Thanks in advance, > > Regards, > > ARKO > > On Fri, Mar 2, 2012 at 12:44 PM, Randy J. Read <rj...@cam.ac.uk> wrote: > I'm worried when you say that you use the initial job's output MTZ. Refmac > replaces F with a detwinned F in the output file so you wouldn't be refining > against your measured data in the subsequent round. > > Best wishes > > Randy Read > > ---- > Randy J. Read > > On 2 Mar 2012, at 02:00, wtempel <wtem...@gmail.com> wrote: > > > Dear CCp4ers, > > A good morning to everyone. > > Today, I have a structure that I initially refined in space group P6522, > > 1mol/asu. > > Scaling stats (scalepack): 2.30-2.26A: Rsym=99.9%; <I>/<sigma> > 3 > > 2.61-2.55A: Rsym=39.6%, <I>/<sigma> > 10 > > 50.00-6.13: Rsym=6.4% > > Some mild anisotropy in the resolution limits is apparent on the > > diffraction images. Say, visible spots at 2.2A in one direction, 2.6A in > > the other. > > Rfree, using data to 2.3A, was stuck in mid-30%s. The map appears like 3.5A > > resolution, with some difference density for loops that cannot be > > interpreted with reasonable geometry. > > Rsym is very similar for data scaled in P3, in all resolution shells. > > Xtriage does not suggest merohedral twinning. > > Nevertheless, I extended my free flags in sftools from P6522 to P32 and > > cad'd them to amplitudes merged in spacegroup P32. Correspondingly, I > > expanded my model to a homotetramer and ran Refmac with amplitude based > > twinning. (Would this be a reasonable input to twin refinement?) > > From the output coordinates: > > REMARK 3 TWIN DETAILS > > REMARK 3 NUMBER OF TWIN DOMAINS : 4 > > REMARK 3 TWIN DOMAIN : 1 > > REMARK 3 TWIN OPERATOR : H, K, L > > REMARK 3 TWIN FRACTION : 0.269 > > REMARK 3 TWIN DOMAIN : 2 > > REMARK 3 TWIN OPERATOR : -K, -H, -L > > REMARK 3 TWIN FRACTION : 0.171 > > REMARK 3 TWIN DOMAIN : 3 > > REMARK 3 TWIN OPERATOR : K, H, -L > > REMARK 3 TWIN FRACTION : 0.258 > > REMARK 3 TWIN DOMAIN : 4 > > REMARK 3 TWIN OPERATOR : -H, -K, L > > REMARK 3 TWIN FRACTION : 0.302 > > Does this establish twinning versus underestimated symmetry? And what do I > > need to know about my free-R? Did refmac assign a new flag? Whereas the > > output file's flags are all 1s and 0s, the input file had 0 ... 19. During > > the first run, Rfree dropped to <28%. But on a subsequent run, Rfree was > > stuck >30% when I used the initial job's output MTZ. > > Many thanks in advance for your helpful comments. > > Wolfram Tempel > > > > > > -- > > ARKA CHAKRABORTY > CAS in Crystallography and Biophysics > University of Madras > Chennai,India > ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
