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Automatic PAIRed REFinement protocol

Planned event: PAIREF webinar

We are pleased to announce the webinar on paired refinement in macromolecular crystallography to be held on March 23, 2021, from 3 PM (CET) to 4 PM (CET). This protocol provides an accurate estimation of the high-resolution cutoff to the diffraction data. The “PAIREF webinar” will be a free virtual event for up to 300 participants. The meeting will be recorded. Participants are assumed to have installed CCP4 or PHENIX software. Feel free to contact us with your data.

Please register here to receive your Zoom link.

All the instruction for the tutorial are available on this page.

We will cover:

  1. Introduction to paired refinement.
  2. Installation of PAIREF for CCP4 and/or PHENIX users.
  3. Short tutorial (files will be provided).
  4. Discussion.

PAIREF is a tool for macromolecular crystallographers that performs the PAIRed REFinement protocol1) 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. PAIREF supports REFMAC5 (part of the CCP4 Software Suite) and phenix.refine (part of the PHENIX) for structure model refinement.


PAIREF screenshot PAIREF screenshot PAIREF screenshot

Installation and system requirements

PAIREF depends on the installation of the CCP4 Software Suite or PHENIX (both contain Computational Crystallography Toolbox with Python 2.7.

PAIREF can be easily installed running the 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 the 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

Example cases

Example runs presented in our scientific paper Paired refinement under the control of PAIREF (2020) in IUCrJ 7 are available online and can be downloaded from Zenodo:

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: