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Automatic PAIRed REFinement protocol

Project description

Automatic PAIRed REFinement protocol

PAIREF is a tool for macromolecular crystallographers that performs the PAIRed REFinement protocol [1] automatically to estimate the optimal high-resolution cutoff. It is developed in Python and can be installed as a module into the Computational Crystallography Toolbox. It provides graphical and command-line interface that executes all the needed calculations. Parameters of refinement can be specified in detail to put all the calculations under full control of the user. Obtained results are presented as plots and tables in HTML log file. PAIREF supports REFMAC5 (part of the CCP4 Software Suite) and phenix.refine (part of the PHENIX) for structure model refinement.

README_images/example_gui.gif README_images/example_head.gif README_images/example_free_work.gif
[1]P.A. Karplus, K. Diederichs: “Linking crystallographic model and data quality.” (2012) Science, 336(6084):1030-3.

Installation and system requirements

PAIREF depends on the CCP4 Software Suite or PHENIX. Both contain the Computational Crystallography Toolbox with Python and pip). PAIREF works with both Python 2 and Python 3.

PAIREF can be easily installed running command cctbx.python -m pip install pairef --user --no-deps in terminal (GNU/Linux, macOS) or CCP4Console (Windows). More information are available in documentation. Check also the PAIREF homepage at and PyPI repository.


To run paired refinement of a model (previously refined at 1.81 Å) for a series of cutoffs (1.7, 1.6, and 1.5 Å), execute a following command:

cctbx.python -m pairef --XYZIN model_1-81A.pdb --HKLIN data_1-5A.mtz --HKLIN_UNMERGED data_1-5A_unmerged.mtz -i 1.81 -r 1.7,1.6,1.5

For detailed information about other program parameters, read the documentation available at

Credits and contact

Please refer: M. Maly, K. Diederichs, J. Dohnalek, P. Kolenko: Paired refinement under the control of PAIREF (2020) IUCrJ 7

PAIREF is developed by Martin Malý in collaboration of Czech Technical University, Czech Academy of Sciences, and University of Konstanz. In case of any questions or problems, please do not hesitate and write us:

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pairef-1.3.9.tar.gz (1.2 MB view hashes)

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