import-serial 0.3

Import diffractio data from serial macromolecular crystallography

Calculate statistics of serial MX data from xia2.ssx or CrystFEL and import them to CCP4.

Requirements: ccp4-python from CCP4 8.0 or later (it includes CCTBX)

Example of usage:

$ ccp4-python -m import_serial --hklin 116720-721.lst-asdf-scale.hkl --half-dataset 116720-721.lst-asdf-scale.hkl1 116720-721.lst-asdf-scale.hkl2 --spacegroup P21 --cell 39.4 78.5 48.0 90 97.94 90
$ ccp4-python -m import_serial --hklin 116720-721.lst-asdf-scale.hkl --spacegroup P21 --cell 39.4 78.5 48.0 90 97.94 90 --nbins 20 --dmin 1.65 --project protein --dataset 01

Test data are available in a separate repository: https://github.com/MartinMalyMM/import_serial_test_data

List of all options:

$ ccp4-python -m import_serial --help

usage: ccp4-python -m import_serial [-h] --hklin hklin_file [--spacegroup spacegroup]
                                    [--cell cell_a cell_b cell_c cell_alpha cell_beta cell_gamma]
                                    [--half-dataset hkl1 hkl2] [--project PROJECT]
                                    [--crystal CRYST] [--dataset DATASET] [--dmax D_MAX]
                                    [--dmin D_MIN] [--nbins N_BINS]

Calculate statistics of serial MX data from xia2.ssx or CrystFEL and import them to CCP4

optional arguments:
  -h, --help            show this help message and exit
  --hklin hklin_file, --HKLIN hklin_file
                        Specify merged mtz file from xia2.ssx or merged hkl
                        file from CrystFEL
  --spacegroup spacegroup
                        Space group
  --cell cell_a cell_b cell_c cell_alpha cell_beta cell_gamma
                        Unit cell parameters divided by spaces, e.g. 60 50 40
                        90 90 90
  --half-dataset hkl1 hkl2
                        CrystFEL only: two half-data-set merge files (usually
                        .hkl1 and .hkl2)
  --project PROJECT     Project name
  --crystal CRYST       Crystal name
  --dataset DATASET     Dataset name
  --dmax D_MAX, --lowres D_MAX
                        Low-resolution cutoff
  --dmin D_MIN, --highres D_MIN
                        High-resolution cutoff
  --nbins N_BINS, --nshells N_BINS
                        Number of resolution bins

Installation:

The latest code from GitHub:

$ ccp4-python -m pip install https://github.com/MartinMalyMM/import_serial/archive/master.zip --no-deps --upgrade --user

or - from PyPI:

$ ccp4-python -m pip install import_serial --no-deps --upgrade --user

Test:

$ cd test
$ ccp4-python -m pytest -vv -s

Developed by Martin Maly, University of Southampton, [e-mail]