Motivation

Electron cryo-microscopy (cryo-EM) is an important and rapidly developing field of structural biology. Thanks to numerous advancements in instrumentation and data processing software, the number of structures determined by cryo-EM is growing rapidly and the resolution of cryo-EM maps is improving dramatically. Computational tools for the analysis of 3D reconstructions and atomic model refinement are also undergoing rapid development. It is likely that current refinement software can provide improved models compared to those determined previously. This site makes available updated versions of existing cryo-EM models automatically obtained using the latest version of phenix.real_space_refine.

Scripts performing the tasks (curation, statistics, re-refinement) are available on the CryoEMRErefine GitHub page.

Procedure

Hover over the boxes in the figure to see a more detailed description in the shaded frame.

re-refinement procedure

Literature

List of publications for tools that were used to perform the CERES computations:

  • CERES webserver:
    Liebschner, D.; Afonine, P. V.; Moriarty, N. W.; Poon, B. K.; Chen, V. B.; Adams, P. D. CERES : A Cryo-EM Re-Refinement System for Continuous Improvement of Deposited Models. Acta Cryst. D 2021, 77 (1), 48–61 https://doi.org/10.1107/S2059798320015879
  • Program to perform refinements in real-space: phenix.real_space_refine
    Afonine, P. V.; Poon, B. K.; Read, R. J.; Sobolev, O. V.; Terwilliger, T. C.; Urzhumtsev, A.; Adams, P. D. Real-Space Refinement in PHENIX for Cryo-EM and Crystallography. Acta Cryst. D 2018, 74 (6), 531–544. https://doi.org/10.1107/S2059798318006551
    Documentation for phenix.real_space_refine
  • Program to generate ligand restraints: eLBOW
    Moriarty, N. W.; Grosse-Kunstleve, R. W.; Adams, P. D. Electronic Ligand Builder and Optimization Workbench ( ELBOW ): A Tool for Ligand Coordinate and Restraint Generation. Acta Cryst. D 2009, 65 (10)1074–1080 https://doi.org/10.1107/S0907444909029436
    Documentation for phenix.elbow
  • Metrics for the validation of cryo-EM maps and models
    Afonine, P. V.; Klaholz, B. P.; Moriarty, N. W.; Poon, B. K.; Sobolev, O. V.; Terwilliger, T. C.; Adams, P. D.; Urzhumtsev, A. New Tools for the Analysis and Validation of Cryo-EM Maps and Atomic Models. Acta Cryst. D 2018, 74 (9), 814–840. https://doi.org/10.1107/S2059798318009324