LB67 Thermolysin

A short tutorial for processing thermolysin data from LB67 with a gain mask applied. The data for this tutorial is at /reg/d/psdm/cxi/cxi84914/xtc/e350. Config files and phil files are available at /reg/d/psdm/cxi/cxi84914/scratch/cctbx-tutorial/lb67thermolysin.

IMPORTANT. Throughout this tutorial and in the config and phil files referenced, we are using $USER to represent your username. This will substitute your username in the command line, but not in the phil or config files. Be sure to replace $USER with your username in the config and phil files.

Preparation

First off, use mod_average to make a dark from LB67 run 24. Copy dark.cfg from /reg/d/psdm/cxi/cxi84914/scratch/cctbx-tutorial/lb67thermolysin into your myrelease folder. Then, from the myrelease folder, submit the averaging job:

cxi.lsf -c dark.cfg -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages -x cxi84914 -r 24 -s -q psanacsq -p 6 -i /reg/d/psdm/cxi/cxi84914/xtc/e350

You can track the progress of your job using a command like this:

tail -f /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/r0024/000/stdout/sNN.out

Get information about beamtime:

cxi.print_pickle /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/r0024/000/out/avg-Ds1-r0024.pickle

Detector format version: CXI 8.2
DISTANCE 378.0042
DETECTOR_ADDRESS CxiDs1-0|Cspad-0
SIZE1 1765
SIZE2 1765
TIMESTAMP 2014-03-06T00:05Z19.502
CCD_IMAGE_SATURATION 16383
SATURATED_VALUE 16383
64 active areas, first one:  [715, 439, 909, 624]
PIXEL_SIZE 0.11
BEAM_CENTER_Y 96.965825
BEAM_CENTER_X 96.99305
WAVELENGTH 1.75860511344
xtal_target None
DATA len=3115225 max=16383.000000 min=0.000000
SEQUENCE_NUMBER 0

Convert the gain map:

cxi.gain_map -o cxib6714_1.pickle -d 378 -w 1.81587210772 cxib6714_1.gain -f "CXI 8.2"

Test map and make an average:

cxi.lsf -c cxi84914/average.cfg -o /reg/d/psdm/cxi/cxi84914/scratch/brewster/averages -x cxi84914 -r 25 -s -q psanacsq -p 8 -i /reg/d/psdm/cxi/cxi84914/xtc/e350

Index:

cxi.lsf -c cxi84914/LB67-thermolysin.cfg -o /reg/d/psdm/cxi/cxi84914/scratch/brewster/thermolysin -p 16 -q psanacsq -r 25 -x cxi84914 -i /reg/d/psdm/cxi/cxi84914/xtc/e350