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
bkill [number] # stops unwanted job

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	weak powder
17	221.0	1.2686	weak powder
18	221.0	1.2686	weak powder
19	221.0	1.2686	weak powder
20	221.0	1.2686	strong powder
21	171.0	1.2686	strong powder	shadow
22	171.0	1.2686	strong powder	shadow
23	171.0	1.2686	strong powder	shadow
24	171.0	1.2686	strong powder	shadow
25	171.0	1.2686	strong powder	shadow
26	171.0	1.2686	strong powder	shadow
27	171.0	1.2686	strong powder	shadow
31	570.9	1.2686	Dark
71	271.0	1.2966	weak powder
72	131.0	1.2966	weak powder	shadow
73	131	1.2966	strong powder	shadow

Some conclusions:

• Run 31 was the dark run. We'll use the average and standard deviation for further processing. Tutorial students can take result from the instructor's directory:

/reg/d/psdm/cxi/cxi84914/scratch/nksauter/initial_dark/e157/r0031/000/out/avg-r0031.pickle
/reg/d/psdm/cxi/cxi84914/scratch/nksauter/initial_dark/e157/r0031/000/out/stddev-r0031.pickle

• We are interested in getting the Zn anomalous signal from thermolysin, therefore we'll discard runs 71-73 collected at 1.2966 Angstroms, lower energy than the Zn K-edge at 9659 eV or 1.2836 Angstroms. See the X-ray handbook.

• We'll also discard run 16 as the diffraction was relatively weak and the unique detector distance would require separate detector calibration.

• We'll accept runs 17-20 ("calibration17"), and runs 21-27 ("calibration21").

Prepare to mask out the untrusted pixels

We'll now calculate dark-subtracted averages.

for m in 17 18 19 20 21 22 23 24 25 26 27; \
 do echo $m; cxi.lsf -c ~/myrelease/cxi84914/mkavg_e157.cfg \
 -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e157/ \
 -i /reg/d/psdm/cxi/cxi84914/xtc/e157 -q psanacsq -s -p 8 -x 157 -r ${m} -t 0; done

This repeats exactly the same averaging calculations as before, except the dark average from run 31 is subtracted. The dark image to be subtracted (along with its std deviation) is defined in the configuration file mkavg_e157.cfg.