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
List of all options:
.. code ::
$ 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:
.. 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
Tests
-----
.. code ::
$ 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 <mailto:martin.maly@soton.ac.uk>`_
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"description": "import_serial\n=============\n\nCalculate statistics of serial MX data from xia2.ssx or CrystFEL and import them to CCP4.\n\nRequirements: ccp4-python from CCP4 8.0 or later (it includes CCTBX)\n\nExample of usage:\n\n.. code ::\n\n $ 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\n $ 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\n\nList of all options:\n\n.. code ::\n\n $ ccp4-python -m import_serial --help\n \n usage: import_serial [-h] --hklin HKLIN [--half-dataset HKL1 HKL2] [--wavelength WAVELENGTH] \n [--spacegroup SPACEGROUP] [--cell a b c alpha beta gamma] [--cellfile CELLFILE]\n [--streamfile STREAMFILE] [--reference REFERENCE] [--dmin D_MIN] [--dmax D_MAX]\n [--nbins N_BINS] [--project PROJECT] [--crystal CRYST] [--dataset DATASET] \n \n Calculate statistics of serial MX data from xia2.ssx or CrystFEL and import them to CCP4\n \n optional arguments:\n -h, --help show this help message and exit\n --hklin HKLIN, --HKLIN HKLIN\n Specify merged mtz file from xia2.ssx or merged hkl file from CrystFEL\n --half-dataset HKL1 HKL2\n CrystFEL only: two half-data-set merge files (usually .hkl1 and .hkl2)\n --wavelength WAVELENGTH, -w WAVELENGTH\n Wavelength (only for data from CrystFEL)\n --spacegroup SPACEGROUP\n Space group\n --cell a b c alpha beta gamma\n Unit cell parameters divided by spaces, e.g. 60 50 40 90 90 90\n --cellfile CELLFILE Cell file from CrystFEL\n --streamfile STREAMFILE\n Stream file from CrystFEL\n --reference REFERENCE, --ref REFERENCE, --pdb REFERENCE, --cif REFERENCE, --mmcif REFERENCE\n Reference file (PDB, mmCIF or MTZ) to provide spacegroup and unit cell\n --dmin D_MIN, --highres D_MIN\n High-resolution cutoff\n --dmax D_MAX, --lowres D_MAX\n Low-resolution cutoff\n --nbins N_BINS, --nshells N_BINS\n Number of resolution bins\n --project PROJECT Project name\n --crystal CRYST Crystal name\n --dataset DATASET Dataset name\n\n\nInstallation\n------------\n\nThis program is already distributed within CCP4 so it is not necessary to install it. You can get the latest code from GitHub:\n\n.. code ::\n\n $ ccp4-python -m pip install https://github.com/MartinMalyMM/import_serial/archive/master.zip --no-deps --upgrade --user\n\nor from PyPI:\n\n.. code ::\n\n $ ccp4-python -m pip install import_serial --no-deps --upgrade --user\n\nTests\n-----\n\n.. code ::\n\n $ cd test\n $ ccp4-python -m pytest -vv -s\n\nTest data are available in a separate repository: https://github.com/MartinMalyMM/import_serial_test_data\n\nDeveloped by Martin Maly, University of Southampton, `martin.maly@soton.ac.uk <mailto:martin.maly@soton.ac.uk>`_\n",
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