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...sed -e "s,FS,Flex,g"|sed -e "s,DMIN,$dmin,g"|sed -e "s,NEG,$neg,g"|sed -e "s,TAG,$tag,g"` ...sed -e "s,FS,Flex,g"|sed -e "s,DMIN,$dmin,g"|sed -e "s,NEG,$neg,g"|sed -e "s,TAG,$tag,g"`

dxtbx.image_average -v -a avg.pickle -m max.pickle -s stddev.pickle -n 64 $data/*.cbf.bz2 ...t for the average, maximum and standard deviation images using -a, -m and -s. -v means verbose output, and we specify 64 cores for averaging using -n.

...sigma cutoffs are set to 1.5 in scaling and post-refinement steps while it's set to -3.0 so we can include negative values in the merged reflection set.

...an save the content of the output to any file name - in this tutorial, let's save it to thermolysin.phil.

| <code>input.path</code> || None || Path(s) to the integrated data — a folder, several folders, or individual files; ...e>filter.outlier.min_corr</code> || 0.1 || Minimum correlation of an image's intensities to the reference model; images below this are rejected. Only ap

...in the latest phenix installers. The only missing package is DIALS. Here's how to get ''cctbx.xfel'' configured from an existing Phenix installation.

* [[Cppxfel Indexing | Indexing with ''cppxfel'']] - cppxfel's own indexing algorithm, TakeTwo

...rameters, followed by the line <code>COMMANDS</code>, after which the task(s) for ''cppxfel'' to complete are listed. In this case, ''cppxfel'' should <

...ion. ''cctbx.xfel'' uses masks and pedestals deployed into the experiment’s calibration store using the LCLS program calibman [https://confluence.slac. ...tions using powder rings can be done manually using ''cctbx.xfel'' or LCLS's calibman tool [https://confluence.slac.stanford.edu/display/PSDM/Calibratio

dials.import file.h5 (the h5 will have 1000's of images in it)

...ference geometry is supplied, copy its refined local frames onto the image's detector hierarchy node-by-node (the hierarchies must match in shape). If F | <code>input.glob</code> || None || Wildcard path(s) for large multi-file datasets (e.g. <code>*.cbf</code>). May be given mult

...e high-speed readoff. This can be seen in the _sXX_ part of XTC filenames (s for stream). These streams are written to the FFB filesystem located at /re

''cctbx.xfel'''s current native file formats, image pickles and integration pickles, are mai ...he hood these are serialized python dictionaries, but for general users it's sufficient to know that the blob of data consists of name/value pairs. The

-i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -s -p 8 -x 239 -r 16 -t 0 -i /reg/d/psdm/cxi/cxi84914/xtc/e240 -q psanacsq -s -p 8 -x 240 -r 16 -t 0

On SLAC's interactive nodes, this takes just over 6 minutes. To avoid problems with r Here, in addition to hot, update and build, there's a command called 'base', which downloads a python and needed packages and c

...tion package.] Winter, G., Waterman, D. G., Parkhurst, J. M., Brewster, A. S., Gildea, R. J., Gerstel, M., Fuentes-Montero, L., Vollmar, M., Michels-Cla ...h in serial crystallography with DIALS geometry refinement.] Brewster, A. S., Waterman, D. G., Parkhurst, J. M., Gildea, R. J., Young, I. D., O'Riordan

...e detector geometry and experimental parameters to be present in the image’s header. Generally this consists of detector distance, wavelength, pixel si Usage: cxi.image2pickle [-v] [-c] [-s] [-w wavelength] [-d distance] [-p pixel_size] [-x beam_x] [-y beam_y] [-o

-i /reg/d/psdm/cxi/cxi84914/xtc/e157 -q psanacsq -s -p 8 -x 157 -r 16 -t 0 * -s funnel all streams for the run into one node (takes longer, but necessary f

....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 ...sed by the beamline operator to a format usable to cctbx.xfel. First, let's extract some useful information from one of the dark averages:

...>_iso statistics. <i>CC</i>_1/2 is defined as Pearson's correlation coefficient between two sets, such that for each unique refl ...mputational resources. Therefore, it is recommended to merge data on SLAC's interactive nodes.