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You can jump to other events to see if your peak parameters are well tuned. Once you are happy, let's launch the peak finder on our the cluster.

The output directory on the peak finder panel should already be automatically set to: /reg/d/psdm/cxi/cxitut13/scratch/<username>/psocake

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The default setting will analyze run 10 on psanaq with 24 CPUs. Number of events to process set to 0 analyzes all the events.
Click "Launch peak finder”. For this demo, let's analyze only 30 events with 2 CPUs
  • Run(s): 10
  • CPUs: 32
  • Number of events to process: 30
Note: You can launch peak finding jobs on multiple runs, e.g. Run(s) 1,10:13 will launch peak finding on runs 1, 10, 11, and 13.
The CXIDB file is generated in the output directory in the following format: <experiment name>_<4-digit run number>.cxi (i.e., /reg/d/psdm/cxi/cxitut13/scratch/<username>/psocake/r0010/cxitut13_0010.cxi) 

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This should load a plot of all the peaks found so far per event. Click "Refresh" to update the plot even if your batch job is still running.

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It is often the case at the beginning of a beamtime that the detector distance to the interaction point (coffset) is not well known, and we can use the Diffraction Geometry panel to find this distance.
  • In the diffraction geometry panel, set "Detector distance" to 156mm. 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).
  • Try drawing a resolution ring on top of the water ring by using “Resolution (pixels)” field. If your detector distance is correct, the crystallographic resolution ring should display 3.2A.

Jumping to indexed images

Once you have completed indexing a run, you may want to look at the indexed events.

In the small data panel, type the CXIDB filename:

  • filename: /reg/d/psdm/cxi/cxitut13/scratch/<username>/psocake/r0010/cxitut13_0010.cxi
  • dataset: /entry_1/result_1/index
You can click on the red marker in the plot to jump to the corresponding events.

Bug/Comments:

Please send bug reports/comments to Chuck:

yoon82@slac.stanford.edu