L498 Thermolysin
In this tutorial, we assume that we are handed an SFX dataset containing thermolysin diffraction, but are not told anything else. We will have to go through all the data runs, figure out which one is to be used for dark subtraction, and account for untrusted pixels and detector metrology. At this point, we will be prepared to integrate and merge the data. Finally, we will perform simple molecular replacement and ask whether there is any Zn signal in the anomalous difference Fourier.
Discovery of data collection parameters
Log in to pslogin.slac.stanford.edu, and then to psana. Carry through flags so that X-windows will work
ssh -YAC $USER@pslogin.slac.stanford.edu ssh -YAC psana
Go in to the working directory and source the package manager:
cd ~/myrelease sit_setup
Create a subdirectory for the 2014 tutorial files if not already done:
mkdir -p cxi84914
List out the thermolysin XTC files:
ls /reg/d/psdm/cxi/cxi84914/xtc/e157
Notice that there are numerous runs in the directory. Now we will create composite averages for each run. Grab this configuration file: mkdark.cfg and put it in your cxi84914 directory. For one run only:
cxi.lsf -c ~/myrelease/cxi84914/mkdark.cfg \ -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e157/ \ -i /reg/d/psdm/cxi/cxi84914/xtc/e157 -q psanacsq -s -p 8 -x 157 -r 16 -t 0
Take note:
- -c configuration file
- -o output directory (will be created)
- -i input files (directory containing the XTC streams)
- -q which batch queue to use
- -s funnel all streams for the run into one node (takes longer, but necessary for averaging)
- -p number of cores to use on the node
- -x which experiment number
- -r which run number
- -t which processing trial (auto increments from 0 if not given)
For all the runs in the thermolysin data set:
kinit aklog for m in 16 17 18 19 20 21 22 23 24 25 26 27 31 71 72 73; \ do echo $m; cxi.lsf -c ~/myrelease/cxi84914/mkdark.cfg \ -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e157/ \ -i /reg/d/psdm/cxi/cxi84914/xtc/e157 -q psanacsq -s -p 8 -x 157 -r ${m} -t 0; done
bjobs lists all your batch jobs; use this form for more information including other-user load:
bjobs -w -u all -q psanacsq
Some runs take up to 2 hrs wall time to average. Find the averages, view the max-composites, and list out header information:
ls /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e157/r*/000/out/*.pickle cctbx.image_viewer `find /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e157/r*/000 -name "max*.pickle"` for m in `find /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e157/r*/000 -name "max*.pickle"`; do echo $m; cxi.print_pickle $m; echo; done
Let's make a table of the results
Run | Distance | Wavelength | Diffraction | Comments |
16 | 271.0 | 1.2686 | Diffraction | Comments |
17 | 221.0 | 1.2686 | Diffraction | Comments |
18 | 221.0 | 1.2686 | Diffraction | Comments |
19 | 221.0 | 1.2686 | Diffraction | Comments |
20 | 221.0 | 1.2686 | Diffraction | Comments |
21 | 171.0 | 1.2686 | Diffraction | Comments |
22 | 171.0 | 1.2686 | Diffraction | Comments |
23 | 171.0 | 1.2686 | Diffraction | Comments |
24 | 171.0 | 1.2686 | Diffraction | Comments |
25 | 171.0 | 1.2686 | Diffraction | Comments |
26 | 171.0 | 1.2686 | Diffraction | Comments |
27 | 171.0 | 1.2686 | Diffraction | Comments |
31 | 570.9 | 1.2686 | Diffraction | Comments |
71 | 271.0 | 1.2966 | Diffraction | Comments |
72 | 131.0 | 1.2966 | Diffraction | Comments |
73 | 271.0xxxx | 1.2966 | Diffraction | Comments |