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To find the Bragg peaks on the image, set the "Algorithm" to “Droplet” in the Peak Finder panel. Details of the peak finding algorithm is given here: Hit and Peak Finding Algorithms#Twothreshold"Dropletfinder"
Examine the peaks found by zooming in/out with the middle mouse scroll (or a two finger slide on a Mac touchpad). Notice that the Bragg peaks are composed of 2 to 6 connected pixels. Setting the radius to 2 sets a 5x5 cyan boundary around the Bragg peaks (radius x 2+1 = 5). Change the following values in the Peak Finder panel.
  • Set npix_min: 2
  • Set npix_max: 5
  • radius: 2

Hover the mouse pointer over the Bragg peaks to study the intensities. The sum of the Bragg peak pixels are above 400 ADUs. Set the following values:

  • Set atot_thr: 400

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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.
Once you are happy with the detector geometry and indexing parameters, you can click "Launch indexing”.
  • Run(s): 10
  • Sample name: lysozyme
  • Queue: psanaq 
  • CPUs: 24
  • Keep CXI images: Off

If you would like to save the detector images in the .cxi file, turn on "Keep CXI images". Only set this to true, if you anticipate that you will want to reindex this run. Otherwise, it's just a total waste of your precious disk space.

As with peak finding, you can launch indexing jobs on multiple runs by specifying runs in the Run(s) field.

Indexing will take some time to complete. If successful, you should see a stream file in: /reg/d/psdm/cxi/cxitut13/scratch/<username>/psocake/r0010/cxitut13_10.stream

 

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.
Once you are satisfied with indexing all your runs, please remember to backup your .cxi files in the /res directory of your experiment. The scratch folder will get wiped after few months (Data Retention Policy).
The stream file is small enough to transfer back to your institute for post-processing (CrystFEL tutorial) and phase retrieval (PHENIX).
For phase retrieval, you can use Phenix and CCP4 by sourcing the following lines:

 

Code Block
languagebash
# Phenix
source /reg/common/package/phenix/phenix-1.10.1-2155/phenix_env.sh
# CCP4
source /reg/common/package/ccp4/ccp4-7.0/bin/ccp4.setup-sh

 

Bug/Comments:

Please send bug reports/comments:

yoon82@slac.stanford.edu