On Thu, Jul 3, 2014 at 7:50 AM, Nat Echols <nathaniel.ech...@gmail.com> wrote:
> On Thu, Jul 3, 2014 at 6:53 AM, Dirk Kostrewa <kostr...@genzentrum.lmu.de> > 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
