Import diffractio data from serial macromolecular crystallography
Project description
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: ccp4-python -m import_serial [-h] --hklin HKLIN [--spacegroup SPACEGROUP]
[--cell a b c alpha beta gamma] [--cellfile CELLFILE]
[--reference REFERENCE] [--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, --HKLIN HKLIN
Specify merged mtz file from xia2.ssx or merged hkl
file 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
--reference REFERENCE, --ref REFERENCE, --pdb REFERENCE, --cif REFERENCE, --mmcif REFERENCE
Reference file (PDB, mmCIF or MTZ) to provide
spacegroup and unit cell
--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
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, martin.maly@soton.ac.uk
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
import_serial-0.5.tar.gz
(16.7 kB
view hashes)