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1) There are four parameters required to uniquely identify an image at LCLS. Type the (1) experiment name, (2) run number, (3) detector name, and (4) event number in the Experiment Parameters panel.

For this tutorial, we will look at experiment cxitut13, run 10, detector DscCsPad, event 4411.

Note that available detector names will be printed on the terminal once you have typed in the experiment name and the run number. 

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Code Block
languagepython
$ psocake exp=cxitut13:run=10 -d DscCsPad -n 4411 -m sfx

Or you can also use the -e and -r arguments for the experiment and the run number:

Code Block
languagepython
$ psocake -e cxitut13 -r 10 -d DscCsPad -n 4411 -m sfx

To check psocake version:

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Click "Launch peak finder”. You can check the status of launched jobs by typing "bjobs" in your Terminal. This will display the job ID and the status amongst other information.
A logfile of the peak finding is also saved under the same directory, .<jobID>.log. Note the "." in front of the logfile name.
If the status stays in PEND or SUSP mode for awhile, then you may want to kill the jobs. To kill a batch job, type "bkill <jobID>". For more information, please refer to: Submitting Batch Jobs
Click "Refresh" in Small Data panel to see the progress. You should see a red plot showing event number vs number of peaks found. When peak finding finishes, the plot will turn blue.
Note: You can launch peak finding jobs on multiple runs when you are ready to analyze the entire experiment, e.g. Run(s) 1,10:13 will launch peak finding on runs 1, 10, 11, and 13.

...

Once you have submitted the peak finder job, let's plot the number of peaks found for each event .by clicking the "Refresh" button. The refresh button will sometimes not work if your .cxi file is busy writing.

In the small data panel, In the small data panel, you should see the CXIDB filename:

  • filename: /reg/d/psdm/cxi/cxitut13/scratch/<username>/psocake/r0010/cxitut13_0010.cxi
  • dataset: /entry_1/result_1/nPeaksAll

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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.Note: If you already have indexed the crystals, you can jump to the indexed patterns by using:
  • dataset: /entry_1/result_1/index

Indexing crystals

First things first, crystal indexing requires an accurate detector geometry. Latest CXI geometry files can be found here: Geometry history

...

Code Block
languagebash
source /reg/g/cfel/crystfel/crystfel-dev/setup-sh
CFDEPDIR=/reg/g/cfel/dependencies
export PATH=${CFDEPDIR}/bin:$PATH

...

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 experiment parameters diffraction geometry panel, set Event Number to 44."Detector distance" to 156mm. 
  • In the indexing panel, tick "Indexing on".

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  •  If indexing succeeds, the integrated (predicted) peaks will be marked with magenta circles. These triple rings represent the integration radius

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  • . 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

Hopefully, you have indexed this diffraction pattern. Notice that the unitcell parameters are a bit off compared to what is expected. Let's load a CrystFEL unitcell file to help the indexer along.

  • In the Indexing panel, set the PDB field to:  /reg/d/psdm/cxi/cxitut13/scratch/<username>/psocake/lys.cell
  • Set Indexing Method field to: dirax-axes-cell
Code Block
languagebash
CrystFEL unit cell file version 1.0
lattice_type = tetragonal
centering = P
unique_axis = c
a = 77.05 A
b = 77.05 A
c = 37.21 A
al = 90 deg
be = 90 deg
ga = 90 deg
You should notice that the reindexed result will match the known unit cell parameters more closely.
  • /<runNumber>/.temp.geom).

Indexing panel uses CrystFEL to index the diffraction patterns, so the input parameters in the indexing panel should be familiar to you if you've used indexamajig before.

CrystFEL geometry: This geometry file is automatically converted from our psana geometry to CrystFEL geometry for you. Feel free to look inside .temp.geom. If you have a CrystFEL geometry file that you know is good, you can simply type it in. Psocake will never modify this file even if you change the "detector distance" in the diffraction geometry panel. (Just don't name your geometry .temp.geom, it will get overridden). You can also deploy the CrystFEL geometry as a psana geometry by clicking "Deploy CrystFEL geometry" in the indexing panel.

Integration radii: These 3 numbers define the radius of two concentric rings about each Bragg spot. Inner ring is used to integrate the Bragg spot and the outer ring is used to estimate the background. Try adjusting these numbers and see what is being integrated on screen. It should be large enough to fit a Bragg spot inside the inner ring.

PDB: If you have a CrystFEL unitcell, you can constrain the indexing algorithms to look for this unit cell.

Indexing method: Default is mosflm-noretry, dirax. "retry" is used to speed up mosflm (it can take few seconds).

Tolerance: These 4 numbers define how much wriggle room you want for indexing. 5, 5, 5 are the tolerance level for unitcell axes a, b, c. 1.5 is the tolerance level for the angles alpha, beta, gamma.

Extra CrystFEL parameters: You can enter extra parameters for indexamajig in this field. It will be appended at the end of the command line, e.g. --profile will turn on the processing timing information.

Let's try to index another diffraction pattern at event 44.

  • In the experiment parameters panel, set Event Number to 44.
  • You should see the magenta triangle appear again. Wait few seconds and hopefully you will have indexed another pattern.

Hopefully, you have indexed this diffraction pattern. Notice that the unitcell parameters are a bit off compared to what is expected. Let's load a CrystFEL unitcell file to help the indexer along.

  • In the Indexing panel, set the PDB field to: /reg/d/psdm/cxi/cxitut13/scratch/psocake/lys.cell
Code Block
languagebash
CrystFEL unit cell file version 1.0
lattice_type = tetragonal
centering = P
unique_axis = c
a = 77.05 A
b = 77.05 A
c = 37.21 A
al = 90 deg
be = 90 deg
ga = 90 deg
You should notice that the reindexed result will match the known unit cell parameters more closely
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
    • : 24
    • Keep CXI images: On

    Psocake saves the detector images of only the hits in the .cxi file. It is likely that you may want to reindex these files to optimize the indexing rate. If you anticipate that you have finalized the indexing parameters, set 'Keep CXI images' to Off. It will delete If you would like to save the detector images in the your .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 which will free up your precious disk space for doing other things.

    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