import-serial 0.8

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

List of all options:

$ ccp4-python -m import_serial --help

usage: import_serial [-h] --hklin HKLIN [--half-dataset HKL1 HKL2] [--wavelength WAVELENGTH]
                     [--spacegroup SPACEGROUP] [--cell a b c alpha beta gamma] [--cellfile CELLFILE]
                     [--streamfile STREAMFILE] [--reference REFERENCE] [--dmin D_MIN] [--dmax D_MAX]
                     [--nbins N_BINS] [--project PROJECT] [--crystal CRYST] [--dataset DATASET]

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, --HKLIN HKLIN
                        Specify merged mtz file from xia2.ssx or merged hkl file from CrystFEL
  --half-dataset HKL1 HKL2
                        CrystFEL only: two half-data-set merge files (usually .hkl1 and .hkl2)
  --wavelength WAVELENGTH, -w WAVELENGTH
                        Wavelength (only for data from CrystFEL)
  --spacegroup SPACEGROUP
                        Space group
  --cell a b c alpha beta gamma
                        Unit cell parameters divided by spaces, e.g. 60 50 40 90 90 90
  --cellfile CELLFILE   Cell file from CrystFEL
  --streamfile STREAMFILE
                        Stream file from CrystFEL
  --reference REFERENCE, --ref REFERENCE, --pdb REFERENCE, --cif REFERENCE, --mmcif REFERENCE
                        Reference file (PDB, mmCIF or MTZ) to provide spacegroup and unit cell
  --dmin D_MIN, --highres D_MIN
                        High-resolution cutoff
  --dmax D_MAX, --lowres D_MAX
                        Low-resolution cutoff
  --nbins N_BINS, --nshells N_BINS
                        Number of resolution bins
  --project PROJECT     Project name
  --crystal CRYST       Crystal name
  --dataset DATASET     Dataset name

Installation

This program is already distributed within CCP4 so it is not necessary to install it. You can get 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

Tests

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

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

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