Paired refinement in CCP4i2

P. Kolenko^1,2, M. Malý^1,2,3, S. McNicholas⁴

¹FNSPE, Czech Technical University in Prague, Břehová 7, 115 19 Praha, Czech Republic

²Institute of Biotechnology AS CR, v.v.i., Průmyslová 595, 252 50 Vestec near Prague, Czech Republic

³Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom

⁴Department of Chemistry, University of York, York YO10 5DD, United Kingdom

petr.kolenko@fjfi.cvut.cz

The final decision on the high-resolution diffraction limit can be based on results from paired refinement [1]. This routine is computationally demanding because it involves a lot of refinement cycles and multiple analyses of agreement between multiple models and data. The method was implemented in the program PAIREF [2,3]. Recently, we developed an algorithm that suggests the verdict on high-resolution diffraction limit of the data.

Program PAIREF is distributed within the CCP4 software suite [4]. It can be launched from the command line. This option provides the possibility to use two refinement engines: REFMAC5 [5] and phenix.refine [6]. The users of the CCP4 can launch the jobs in the i2 graphical interface (see Figure 1). The interface provides access to a comprehensive log file in HTML form.

Figure 1. The view of the PAIREF project window in CCP4i2.

1. P. A. Karplus & K. Diederichs, Science, 336, (2012), pp. 1030-1033.

2. M. Malý, K. Diederichs, J. Dohnálek, P. Kolenko, IUCrJ, 7, (2020), pp. 681-692.

3. M. Malý, K. Diederichs, J. Dohnálek, P. Kolenko, Acta Cryst. F77, (2021), pp. 226-229.

4. L. Potterton, J. Agirre, C. Ballard, K. Cowtan, E. Dodson et al., Acta Cryst. D74, (2018), pp. 68-84.

5. G. N. Murshudov, A .A. Vagin, E. J. Dodson, Acta Cryst. D53, (1997), pp. 240-255.

6. D. Liebschner, P. V. Afonine, M. L. Baker, G. Bunkóczi, V. B. Chen et al., Acta Cryst. D75, pp. 861-877.

This publication was supported by the MEYS CR (projects CAAS – CZ.02.1.01/0.0/0.0/16_019/0000778 and BIOCEV – CZ.1.05/1.1.00/02.0109) from the ERDF fund and by the GA CTU in Prague (SGS22/114/OHK4/2T/14) and by CCP4 / STFC (project 521862101).