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You can click on the red marker in the plot to jump to the corresponding events. These single crystal diffraction patterns of lysozyme seem to have between 15 to 60 peaks.

Indexing crystals

First things first, crystal indexing requires an accurate detector geometry. Latest CXI geometry files can be found here: Geometry historyDetector panels can manually adjusted using: calibman

Secondly, we need to know the diffraction geometry before we can index. It is often the case at the beginning of a beamtime that the detector distance to the interaction point (coffset) is not precisely known (We are talking about sub-millimetre precision), and we can use the Diffraction Geometry panel to find this distance.
  • In the diffraction geometry panel, set "Detector distance" to 156mm145mm. 
  • In the indexing panel, tick "Indexing on". If indexing succeeds, the integrated (predicted) peaks will be marked with magenta circles. These triple rings represent the integration radiusradii.  A A magenta triangle means wait. If indexing fails, you will see a magenta X.
  • If you see magenta circles and magenta unitcell appear, congratulations! You have indexed your first pattern using psocake.
  • Try incrementing this distance in 1mm step till the unit cell parameters are as close as possible to lys.cell. The optimum detector distance is around 158mm.
    Everytime the "Detector distance" value is changed by the user, psocake converts the psana geometry (in /reg/d/psdm/cxi/cxitut13/calib/CsPad\:\:CalibV1/CxiDs1.0\:Cspad.0/geometry/10-11.data) to a CrystFEL geom file (in /reg/d/psdm/cxi/cxitut13/scratch/<username>/psocake/<runNumber>/.temp.geom).

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