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Thanks all for your comments! ************************************************ Yamei Yu On Jul 5, 2014, at 5:10 AM, Nat Echols <[log in to unmask]> wrote: > On Thu, Jul 3, 2014 at 7:50 AM, Nat Echols <[log in to unmask]> wrote: > On Thu, Jul 3, 2014 at 6:53 AM, Dirk Kostrewa <[log in to unmask]> wrote: > yes - unfortunately, in my hands, phenix.xtriage reads the XDS_ASCII.HKL intensities as amplitudes, producing very different output statistics, compared both to the XDS statistics and to an mtz file with amplitudes created from that XDS file. > > This is incorrect. It does read it correctly as intensities - the confusion probably arises from the fact that Xtriage internally converts everything to amplitudes immediately, so that when it reports the summary of file information, it will say "xray.amplitude" no matter what the input type was (the same will also be true for Scalepack and MTZ formats). However, the data will be converted back to intensities as needed for the individual analyses. Obviously this isn't quite ideal either since the original intensities are preferable but for the purpose of detecting twinning I hope it will be okay. In any case the incorrect feedback confused several other users so it's gone as of a few weeks ago, and the current nightly builds will report the true input data type. (The actual results are unchanged.) > > Tim: I have no reason to think we handle unmerged data poorly; I'm not sure who would have told you that. In most cases they will be merged as needed upon reading the file. I'm a little concerned that you're getting such different results from Xtriage and pointless/aimless, however. Could you please send me the input and log files off-list? Dirk, same thing: if you have an example where XDS and Xtriage are significantly in disagreement, the inputs (and logs) would be very helpful. In both cases, I suspect the difference is in the use of resolution cutoffs and absolute-scaled intensities in Xtriage versus other programs, but I'd like to be certain that there's not something broken. > > I stand corrected: unmerged XDS files (but not other formats) were not being handled appropriately in Xtriage; this was fixed several weeks ago, so the nightly builds should behave as expected. > > -Nat