Difference between revisions of "LB67 Thermolysin"
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| − | + | 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/$USER/averages/r0024/000/stdout/sNN.out | ||
Get information about beamtime: | Get information about beamtime: | ||
| − | cxi.print_pickle /reg/d/psdm/cxi/cxi84914/scratch/ | + | cxi.print_pickle /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/r0024/000/out/avg-Ds1-r0024.pickle |
Detector format version: CXI 8.2 | Detector format version: CXI 8.2 | ||
Revision as of 16:20, 21 August 2014
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
