Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement

Descriptions are given of the maximum-likelihood gyre method implemented in Phaser for optimizing the orientation and relative position of rigid-body fragments of a model after the orientation of the model has been identified, but before the model has been positioned in the unit cell, and also the related gimble method for the refinement of rigid-body fragments of the model after positioning. Gyre refinement helps to lower the root-mean-square atomic displacements between model and target molecular-replacement solutions for the test case of antibody Fab(26-10) and improves structure solution with ARCIMBOLDO_SHREDDER.
This research was supported by the Wellcome Trust (Principal Research Fellowship to RJR, grant 082961/Z/07/Z) and by grant BB/L006014/1 from the BBSRC, UK. The research was facilitated by Wellcome Trust Strategic Award 100140 to the Cambridge Institute for Medical Research. MS and CM received financial support from CCP4 for a sabbatical in the group of RJR. CM is grateful to MINECO for her BES-2015- 071397 scholarship associated with the Structural Biology Maria de Maeztu Unit of Excellence. IU was supported by grants BIO2015-64216-P, BIO2013-49604-EXP and MDM2014-0435-01 (the Spanish Ministry of Economy and Competitiveness) and Generalitat de Catalunya (2014SGR997).