Page History
...
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 cxi06216cxitut13, run 2210, detector DscCsPad, event 11.
...
| Code Block | ||
|---|---|---|
| ||
$ psocake exp=cxi06216cxitut13:run=2210 -d DscCsPad -n 11 |
3) You can also use the -e and -r arguments for the experiment and the run number:
| Code Block | ||
|---|---|---|
| ||
$ psocake -e cxi06216cxitut13 -r 2210 -d DscCsPad -n 11 |
Don’t worry if you don’t remember these arguments. For argument options, use --help:
...
To save the user-defined mask, click on "Save user-defined mask" on the mask panel which will save the mask in the scratch folder. For this example, the mask will be saved here:
/reg/d/psdm/cxi/cxi06216cxitut13/scratch/<username>/psocake/r0022r0010/mask.npy (3D ndarray)
/reg/d/psdm/cxi/cxi06216cxitut13/scratch/<username>/psocake/r0022r0010/mask.txt (2D text)
You can load the user-defined mask using the "Load user-defined mask" button and selecting mask.npy.
...
You can jump to other events to see if your peak parameters are well tuned. Once you are happy, launch the peak finder on our cluster.
The output directory on the peak finder panel should already be automatically set to: /reg/d/psdm/cxi/cxi06216cxitut13/scratch/<username>/psocake
Since we are analyzing run 2210, /r0022 r0010 directory will be generated under the output directory.
The default setting will analyze run 22 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,
- CPUs: 23
- Number of events to process: 30
The CXIDB filename being generated is in the following format: <experiment name>_<4-digit run number>.cxi (i.e., cxi06216cxitut13_00220010.cxi)
Jumping to interesting images based on the number of peaks
Once you have submitted the peak finder job, let's plot the number of peaks found for each event.
In the small data panel, type the CXIDB filename:
- filename: /reg/d/psdm/cxi/cxi06216cxitut13/scratch/<username>/psocake/r0022r0010/cxi06216cxitut13_00220010.cxi
- metric_dataset: /entry_1/result_1/nPeaksAll
...
- In the indexing panel, set the PDB field to: /reg/d/psdm/cxi/cxi06216cxitut13/scratch/psocake/lys.cell
...
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.
- 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 3.4A.
Future plans
- More mask shapes
- More integration with logbook
- Extend the crystallography analysis to XPP and MFX beamlines
- cctbx-xfel support
Overview
Content Tools