I once had a problem that seemed to manifest itself similarly to what you describe. It turned out to be a misindexing of the diffraction origin by +/- 1 due to a slightly incorrect beam center. You can use the pointless "centre" option to do a search for the correct center. There's an example of the command here: https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Pointless
I don't know HKL3000 very well, but in xds you would then use the INDEX_ORIGIN parameter to specify the correct origin, and reintegrate your data. -Tom On Fri, Sep 28, 2018 at 4:11 AM Zhang Foggy <foggyc...@gmail.com> wrote: > Dear All, > > Sorry for the off-topic. > > I recently collected a set of data. The diffraction spots are extremely > sharp. However, When I used HKL3000 to scale it, I get a final resolution > at 3.1A with overall R-merge ~0.54 (R-merge in the highest 3.2A-3.1A shell: > 1.59). Then I solve the structure with final R value 0.19 and R free value > 0.24 although I know this Rmerge value is totally unacceptable, and the > density looks perfect. > > I also tried to collect other four set of data with different crystals. > unfortunately, all of them have same problem. > > I ask one of my friend who is an expert in HKL3000, but he had no idea > about it. Does anyone has suggestions? > > Here is the scale information for your review: > Space group: P43 (I also tried P1, the Rmerge value is still similar) > > Shell Lower Upper Average Average Norm. Linear Square > limit Angstrom I error stat. Chi**2 R-fac R-fac Rmeas > Rpim CC1/2 CC* > 50.00 6.67 11.6 0.9 0.3 1.165 0.191 0.284 0.198 > 0.052 0.975 0.994 > 6.67 5.30 4.5 0.5 0.3 0.952 0.317 0.313 0.329 > 0.086 0.971 0.993 > 5.30 4.63 7.3 0.7 0.5 0.961 0.293 0.297 0.304 > 0.081 0.975 0.994 > 4.63 4.21 7.0 0.8 0.6 0.986 0.369 0.358 0.382 > 0.101 0.969 0.992 > 4.21 3.91 5.6 0.8 0.6 1.040 0.522 0.491 0.541 > 0.142 0.955 0.988 > 3.91 3.68 4.6 0.9 0.7 1.064 0.718 0.669 0.746 > 0.203 0.929 0.981 > 3.68 3.49 3.5 0.9 0.8 1.092 1.059 0.986 1.101 > 0.299 0.882 0.968 > 3.49 3.34 2.6 0.9 0.8 1.092 1.382 1.298 1.438 > 0.395 0.829 0.952 > 3.34 3.21 2.1 0.9 0.8 1.084 1.543 1.489 1.614 > 0.468 0.772 0.933 > 3.21 3.10 1.6 0.9 0.8 1.070 1.591 1.669 1.680 > 0.529 0.645 0.885 > All reflections 5.0 0.8 0.6 1.048 0.538 0.487 0.559 > 0.153 > > Thank you. > > Liang > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
