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By the end of this tutorial, you will be able to find Bragg peaks and index crystal diffraction patterns and reduce the data to one stream file for structure determination.
Starting psocake
Make sure you have the psana environment setup (psana python Setup) before starting this tutorial. Also, check out a kerberos ticket by typing “kinit” which is needed for communicating with the experiment e-Log.
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$ psocake |
1) There are four parameters required to uniquely identify an image at LCLS. Type the experiment name, run number, detector name, and event number in the Experiment Parameters panel.
For this tutorial, we will look at experiment cxi06216, run 22, detector DscCsPad, event 11.
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Once you have submitted the peak finder job, let's look at the images that have Bragg peaksplot the number of peaks found for each event.
In the small data panel, type the CXIDB filename:
- filename: /reg/d/psdm/cxi/cxi06216/scratch/<username>/psocake/r0022/cxi06216_0022.cxi
- metric_dataset: /entry_1/result_1/nPeaksAll
"/entry_1/result_1/nPeaksAll" is an array containing number of peaks found for each event. Unfortunately the naming convention is cryptic, but it is how it is named inside a CXIDB file.
This should load a plot of all the peaks found so far per event. Click "Refresh" to update the plot if your batch job is still running.
You can click on the red marker in the plot to jump to the corresponding events. These lysozyme diffraction patterns have between 15 to 60 peaks.
Indexing crystals
Let's try to index the diffraction pattern at event 11.
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