Usage - command line

Scatterkit can be used directly from the command line (cli). Using cli instead of a Jupyter notebook can sometimes be more comfortable, particularly for lengthy analysis. The cli in particular is handy because it allows for updating the analysis results during the run. You can specify the number of frames after the output is updated with the -concfreq flag. See below for details.

Note that in this documentation, we almost exclusively describe the use of scatterkit from the python interpreter, but all operations can be equivalently performed from the cli.

scatterkit saxs -s water_nvt.tpr \
                -f water_nvt.xtc \
                -atomgroup 'resname SOL'

The SAXS profile has been written in a file named sq.dat in the current directory. The written file starts with the following lines

head -n 20 sq.dat

For lengthy analysis, use the concfreq option to update the result during the run

scatterkit saxs -s water_nvt.tpr \
                -f water_nvt.xtc \
                -atomgroup 'resname SOL' \
                -concfreq '10'

The general help of scatterkit can be accessed using

scatterkit -h

Package-specific page can also be accessed from the cli

scatterkit saxs -h