Versions Compared

Old Version 19

changes.mady.by.user Chunhong Yoon

Saved on

compared with

New Version 20

changes.mady.by.user Chunhong Yoon

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Type "psocake" on your terminal to open up the GUI. For crystallography, we will need to open it in sfx mode (-m):

Code Block
languagepython
$ sit_setup nightly-2016070620160717 # (Optional) To get the bleeding edge version, use the nightly build
$ psocake -m sfx

...

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
languagepython
##############################################################
# Available area detectors: 
#  ['DscCsPad']
#######################('CxiDs1.0:Cspad.0', 'DscCsPad', '')
#######################################

2)  You can specify the experiment parameters as command line arguments in psocake using the psana-style experiment run string:

...

The default setting will analyze run 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: 3
  • Number of events to process: 30
The CXIDB filename being generated is file is generated in the output directory in the following format: <experiment name>_<4-digit run number>.cxi (i.e., /reg/d/psdm/cxi/cxitut13/scratch/<username>/psocake/r0010/cxitut13_0010.cxi) 

Two virtual powder patterns will also be generated in the run directory:
1) cxitut13_0010_maxHits.npy: Maximum pixel values for hits found
2) cxitut13_0010_maxMisses.npy: Maximum pixel values for misses
If the hit finding parameters are good, cxitut13_0010_maxMisses.npy should not contain many Bragg spots. You can look at these images by using the "Load image" button in the Image Control panel.

Jumping to interesting images based on the number of peaks

...

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 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.

Future plans

 

  • More Polygon mask shapes
  • More Better integration with logbook
  • Extend the crystallography analysis to XPP and MFX beamlines
  • cctbx-xfel support