Hi Bernie, I agree with Herman. I think you will be all set if you simply change the "no" twin refinement option near the top of the Refmac interface to "intensity based" or "amplitude based" twin refinement. Refmac will determine the appropriate twin operators/fractions and refine.
Best, Chris > On Sep 17, 2014, at 14:19, "Santarsiero, Bernard D." <b...@uic.edu> wrote: > > Can someone point me to bulletpoint documentation on using the twin > refinement in CCP4? > > Here's what I did. > > 1. I'm in space group P3, and the see a very clean diffraction pattern > that looks like one single lattice. Very clean spots, so merohedral > twinning. > > 2. You can use various programs to estimate the twin fraction and select > various twin laws. > > 3. You run DETWIN in the UTILITIES section of DATA REDUCTION and > ANALYSIS. I have both intensities IMEAN and amplitudes FMEAN, and selected > amplitudes. The FMEAN changes to something like FMEAN_detw. You have to > select a twin fraction, but does it matter what the twin factor you assign > is? (It seems to get refined, or just estimated, in refinement?) > > 4. There are potentially 3 twin laws, so do you run DETWIN three times? > You can, in fact, get amplitudes that are FMEAN_detw_detw_detw. I've run > it once and three times, and seems to give the same result in REFMAC > refinement. > > 5. Select the Free R subset. Will uniqueify choose correctly? > > 6. In REFMAC, it looks for the F_detw amplitude, or you can select it. > Then it seems to select and test three twin laws, even if you only ran > DETWIN once, with one selected twin law. It tests if the twin laws give > low R(merge). If not, it tosses them out. It seems like the R(merge) > calculation depends on the starting model, and not just on the modified > Fobs data. It also seems like it tries to calculate the twin fraction, and > then refine the structure. Or, is it just giving an estimate, and I need > to go back to original data and rerun DETWIN? > > 7. I tried to work with intensities instead of amplitudes, and it can > blow up. I've also refined, got a good refinement (3 twin laws, each with > twin fraction around 0.1, Rcryst = 19%, Rfree = 21%), rebuilt one chain of > the structure, and it blows up, suggesting no twinning, but Rs around 35%. > > Does REFMAC refine the twin fraction? > Do I have to assign a twin fraction in DETWIN, or does it just set up the > relationships between reflections and amplitudes? > Should I try to work with intensities or amplitudes. The calculation is > presumably done on intensities, but seems to be more unstable using that > option. > > I haven't tried the PHENIX option. Just a quick step-by-step guide on what > to do would be useful. > > Thanks, > > Bernie > -- > Bernard D. Santarsiero > Research Professor > Center for Structural Biology > University of Illinois at Chicago > MC870 3070MBRB 900 South Ashland Avenue > Chicago, IL 60607-7173 USA > (312) 413-0339 (office) > (312) 413-9303 (FAX) > http://www.uic.edu/labs/bds > http://scholar.google.com/citations?user=fGauLBMAAAAJ
