Automatic PAIRed REFinement protocol

PAIREF is a tool for macromolecular crystallographers that performs the PAIRed REFinement protocol1) P.A. Karplus, K. Diederichs: "Linking crystallographic model and data quality." (2012) Science, 336(6084):1030-3. automatically to estimate the optimal high-resolution cutoff. It is developed in Python 2.7 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. REFMAC5 (part of the CCP4 Software Suite) is used for structure model refinement.

DOCUMENTATION GitHub PyPI

PAIREF screenshot PAIREF screenshot PAIREF screenshot

Installation and system requirements

PAIREF depends on the CCP4 Software Suite (it contains Computational Crystallography Toolbox with Python 2.7 and pip).

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 https://pairef.fjfi.cvut.cz/ and PyPI repository.

Example

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:

For detailed information about other program parameters, read the documentation available at http://pairef.fjfi.cvut.cz/docs.

Credits and contact

Please reference: 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: martin.maly@fjfi.cvut.cz.