If you have unmerged data try running it through pointless/aimless/ctruncate. That analyses twin fractions very carefully and with that twin law you should see some evidence of 6 fold symmetry but less pronounced than for the 3 and 2 fold symmetry operators..
Eleanor On 11 June 2015 at 01:03, Mengbin Chen <mengb...@sas.upenn.edu> wrote: > Thank you Jacob and Ethan! > > I haven't put water molecules into the density blob, which aren't many out > there, but I fitted the ligands in already. Molbrobity statistics are not > yet great, since there are 13.5% rotamer outliers. > > Will adjust the models manually, and try refmac and TLS refinement. > > Thanks again for your insightful suggestions! > > Best, > Mengbin > > On Wed, Jun 10, 2015 at 6:16 PM, Ethan A Merritt <merr...@u.washington.edu > > wrote: > >> On Wednesday, 10 June, 2015 17:35:25 Mengbin Chen wrote: >> > Hello everyone, >> > >> > I am refining a 2.5 angstrom structure whose phase is solved by >> molecular >> > replacement with a search probe determined by SAD with 3 angstrom >> > resolution. While I am able to see densities of a bunch of water >> molecules >> > and ligands in the MR solved structure, which means that the phase is >> > correct, the Rfree gets stuck at ~27%. >> >> Why do you think this is a problem? >> It is true that turning on twin refinement is expected to yield lower >> R factors, and thus 27% in the presence of twin refinement is worse than >> 27% without twin refinement. But having said that, Rfree = 0.27 is still >> not so horrible. >> >> If the starting point for your MR solution was a 3A model, >> there may have been errors in sidechain placement or even >> backbone conformation that can be corrected now that you >> have higher resolution data. Don't assume that the starting >> model was perfect. >> >> You say that you can see density for a bunch of waters and ligands. >> Are these in your refinemed model yet? >> >> What does Molprobity (or coot or phenix) say about the quality of >> your sidechain rotamers? >> >> Have you tried adding a TLS description? >> >> Ethan >> >> >> > The crystal belongs to P3221 and has >> > a twinning fraction of 19%, according to Xtriage. Currently I've been >> > sticking to Phenix for refinement, and twin law (-h, -k, l) has been >> > applied. >> > >> > I was wondering if the CCP4 community would have any suggestions of how >> to >> > refine this twinned structure, such as softwares to use, tricky >> strategies >> > to choose, etc. I really appreciate any recommendations you would come >> up >> > with my situation! >> > >> > Thank you in advance! >> > >> > Best, >> > Mengbin >> > >> > >> -- >> Ethan A Merritt >> Biomolecular Structure Center, K-428 Health Sciences Bldg >> MS 357742, University of Washington, Seattle 98195-7742 >> >> > > > -- > Mengbin Chen > PhD Candidate > Christianson Laboratory > Department of Chemistry > University of Pennsylvania > 231 S. 34th Street, #323 > Philadelphia, PA 19104 USA > Phone: (215)898-2227 > Email: mengb...@sas.upenn.edu >
