Metadata-Version: 2.1
Name: import-serial
Version: 0.4
Summary: Import diffractio data from serial macromolecular crystallography
Home-page: https://www.ccp4.ac.uk/
Author: Martin Maly
Author-email: martin.maly@soton.ac.uk
License: GNU Lesser General Public License v3 (LGPLv3)
Keywords: macromolecular crystallography,research
Classifier: Environment :: Console
Classifier: Environment :: Web Environment
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: MacOS
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Physics
License-File: LICENSE

import_serial
=============

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:

.. code ::

   $ 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:

.. code ::

   $ 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:

.. code ::

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

or - from PyPI:

.. code ::

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

Test:

.. code ::

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

Developed by Martin Maly, University of Southampton, `martin.maly@soton.ac.uk <mailto:martin.maly@soton.ac.uk>`_
