Hi Murpholino, "how much red my idxref should show" has several answers, on several levels. E.g. 1) less than black 2) as little as possible 3) as much as necessary / unavoidable
The plot is supposed to give you diagnostic information about your data - it reveals ice rings, secondary lattices and the like. However, its appearance is not strictly correlated with the data quality. With the default setting (0.5) of MINIMUM_FRACTION_OF_INDEXEX_SPOTS, as long as the number of indexed spots is larger than the number of un-indexed spots, XDS would automatically continue with DEFPIX INTEGRATE CORRECT. However, if the black fraction is less than MINIMUM_FRACTION_OF_INDEXEX_SPOTS, the user should at least notice that there may be problems. Some such problems can be fixed (e.g. wrong geometry specification in XDS.INP), but if no obvious reasons for failure of indexing can be found, s/he may just continue data processing with JOB= DEFPIX INTEGRATE CORRECT . Often this will result in good processing. Your plots all look good to me. That some of them are "red at higher diffraction angle" might indicate that IDXREF's single orientation and/or cell (in XPARM.XDS) just cannot predict all observed reflections of the data set accurately (enough); this is why INTEGRATE performs additional refinement, every DELPHI-sized batch of data. Hope this helps, Kay On Fri, 22 Jun 2018 23:41:03 -0500, Murpholino Peligro <[email protected]> wrote: >As the wiki says "The right side of the tab shows the indexed (black) and >not-indexed (red) reflections of SPOT.XDS ><https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php?title=SPOT.XDS&action=edit&redlink=1> >." > >I have a few data sets to contrast this. >https://drive.google.com/file/d/1HKEq8Lb4promCv7NgW0p0Foxd36kypMI/view?usp=sharing >https://drive.google.com/file/d/1DBF0OCSW2gyE9qCCxdHA7XNc9sxMQ4fE/view?usp=sharing >https://drive.google.com/file/d/1FjxA9Y9DBs3cBBN0Ysrpya2z6_D7hZtf/view?usp=sharing >https://drive.google.com/file/d/1CPY4o7yYgn9t_5bGXhl0H8LBtfDNqGFB/view?usp=sharing >https://drive.google.com/file/d/1td0wOzMO3cbgatQAZBXI4j9-6vZOs1kn/view?usp=sharing >https://drive.google.com/file/d/108qni5odYoQFyo4VbofB1UIElZ3yr8Kk/view?usp=sharing >https://drive.google.com/file/d/1jxBy0uQ4QMcLjvK5yi5crOQIRUrlk06F/view?usp=sharing >https://drive.google.com/file/d/1D4KNxcx2EtDSKUNmj1H4vwIO2KpiOrOH/view?usp=sharing > >As you can see some have more or less red. >What magic keywords you use in XDS.INP to solve this? >Should I worry? (particularly for #4 and #6...) > > >Thanks > >######################################################################## > >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
