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XRD2 Info for Users

Synchweb logbook - Data collection diagnostics and Autoproc output!

Data collections log and relevant files (e.g. ready to use .MTZ files) are directly accessible from the proposal "View All Data" page in Synchweb.
XRD2 data collections are automatically processed using Global Phasing data reduction pipeline "Autoproc".

The "View All Data" page gives you precious information about average diffraction limit of your crystals within each data acquisition. You can use the embedded raw diffraction image viewer or get fast and useful hints from the "Spots(Y)-Bragg(B)-Res(R) Vs Frame" plot (i.e. the graph shown on the right)

Pathological signs of radiation damage or crystal mis-centring can be easily spotted out from unstable trends in this graph!
This graph is populated on the fly while you collect data - keep an eye on it before you decide to trash your crystal!!!

Real data collections can be easily filtered using the "Full Collections" toggle (i.e. to exclude characterizations):

Summary of autoprocessing output can be expanded clicking on the "Auto Processing" grey bar.

The "Logs & Files" button allows to quickly download relevant "ready for electron density maps" files:

  • summary.html ...contains summary of relevant autoproc output statistics from core pipeline steps
  • truncate-unique.mtz ...contains merged and scaled intensities plus amplitudes, isotropic resolution cut, complete data to highest resolution
  • truncate-unique.table1 ...contains standard "Table 1" pubblication statistics
  • truncate-unique.stats ...contains complete statistics by resolution shells
  • staraniso_alldata.mtz ...contains merged and scaled intensities plus amplitudes, anisotropic resolution cut
  • staraniso_alldata-unique.mtz ...contains merged and scaled intensities plus amplitudes, anisotropic resolution cut, complete data to highest resolution
  • XDS_ASCII.HKL(.zip) ...is the final "raw XDS" output, available for rescaling through CCP4 Pointless+Aimless (using XDSIN card)
NB: "alldata" = up to the highest reosolution collected (i.e. up to the detector corners), "unique" = mtz completed with Rfree test-set column


Get a quick summary of data collections out of Synchweb

A compact summary table of data collections parameters and Autoproc results is available from the "Summary" button:

NB: A handy printable report of data collected during each visit can be downloaded from the "mx202xxxx" --> "Visits" --> "Download PDF Report" button:

Last Updated on Wednesday, 18 November 2020 13:31