cctbx.xfel GUI/Merging Stats tab

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The Merging stats tab shows the merging statistics of each version of a dataset, read from the merging job's log, and the cosym embedding plot when the merge resolved an indexing ambiguity. The Merging Stats Sentinel re-reads the logs every 5 seconds while the tab is showing, so a merge that is still running fills in as it goes.

Back to cctbx.xfel GUI.

Selecting a dataset

  • Select dataset: the list of datasets; Active only (ticked by default) hides inactive ones.
  • Dataset version: All or a single version number. Only versions built with the dataset's current pipeline are listed; a version made before a stage was removed or detached is hidden.

Statistics page

For a single version, the plot shows the statistics by resolution shell, with resolution along the x axis:

  • % accepted (orange): the fraction of lattices accepted into each resolution shell,
  • Completeness (green) and CC1/2 (blue), as percentages on the left axis,
  • Multiplicity (red) and Merged I/sigI (purple) on the right axis.

With All versions selected, the plot shows how the merge improves with data: overall CC1/2 and overall multiplicity against the number of images, and resolution against the number of images, one point per version. This is the plot to watch during collection to decide when enough data have been collected.

The statistics are scraped from the merging log (the *main* file in the version folder), so they match the tables printed there. Nothing is shown for a version whose merge has not yet written its tables.

Cosym embedding page

When the merging stage ran modify_cosym to resolve an indexing ambiguity, it writes an embedding plot: each lattice is a point, and a successful resolution shows as well-separated clusters, one per indexing mode. A single blob means cosym could not separate the modes (too little signal in common between images, or no real ambiguity) and the merged data may be degraded by mis-indexed lattices. This page shows the plot for a single selected version; a selector appears when the job wrote more than one (one per plotting rank). The page explains when no plot is available.

Tips

  • Compare versions, or two datasets merged with different settings, by switching the selection; the plot is redrawn at the panel size, so enlarge the window for more detail.
  • If CC1/2 or completeness is poor in the outer shells, lower the resolution in the dataset's shared parameters (which creates no new version by itself; a new version is merged when further runs finish, or restart the merging job from the Jobs tab).
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