Thanks all for your comments! ************************************************
Yamei Yu On Jul 5, 2014, at 5:10 AM, Nat Echols <nathaniel.ech...@gmail.com> wrote: > 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
