Page History
...
- Starting psocake
- Mask making
- Peak finding
- Looking at peaks foundJumping to interesting images based on the number of peaks
Indexing crystals
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.
Type "psocake" on your terminal to open up the GUI:
| Code Block | ||
|---|---|---|
| ||
$ 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.
Note that available detector names will be printed on the terminal
...
once you
...
have typed in the experiment name and the run number.
| Code Block | ||
|---|---|---|
| ||
####################### # Available detectors: ['DscCsPad'] ####################### |
2) You can specify the experiment parameters as command line arguments in psocake using the psana-style experiment run string:
| Code Block | ||
|---|---|---|
| ||
$ psocake exp=cxi06216:run=22 -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 cxi06216 -r 22 -d DscCsPad -n 11 |
Don’t worry if you don’t remember these arguments. For argument options, use --help:
...
You can load the user-defined mask using the "Load user-defined mask" button and selecting mask.npy.
Peak finding
To find the Bragg peaks on the image, set the "Algorithm" to “Droplet” in the Peak Finder panel.
...
| Code Block | ||
|---|---|---|
| ||
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.
...
Overview
Content Tools