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Cryo-EM single-particle structure refinement and map calculation using Servalcat.

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Burnley, Tom 


In 2020, cryo-EM single-particle analysis achieved true atomic resolution thanks to technological developments in hardware and software. The number of high-resolution reconstructions continues to grow, increasing the importance of the accurate determination of atomic coordinates. Here, a new Python package and program called Servalcat is presented that is designed to facilitate atomic model refinement. Servalcat implements a refinement pipeline using the program REFMAC5 from the CCP4 package. After the refinement, Servalcat calculates a weighted Fo - Fc difference map, which is derived from Bayesian statistics. This map helps manual and automatic model building in real space, as is common practice in crystallography. The Fo - Fc map helps in the visualization of weak features including hydrogen densities. Although hydrogen densities are weak, they are stronger than in the electron-density maps produced by X-ray crystallography, and some H atoms are even visible at ∼1.8 Å resolution. Servalcat also facilitates atomic model refinement under symmetry constraints. If point-group symmetry has been applied to the map during reconstruction, the asymmetric unit model is refined with the appropriate symmetry constraints.



REFMAC5, Servalcat, cryo-EM, structure refinement, Algorithms, Cryoelectron Microscopy, Hydrogen, Macromolecular Substances, Models, Molecular, Single Molecule Imaging, Software

Journal Title

Acta Crystallogr D Struct Biol

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International Union of Crystallography (IUCr)