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

In 2020, cryo-EM single particle analysis achieved true atomic resolution. The number of high resolution reconstructions continues to grow, increasing the importance of accurate determination of atomic coordinates. Here, a new Python package and program called Servalcat is presented that is designed to facilitate structure refinement. Servalcat implements a refinement pipeline, using REFMAC5, and map calculation for manual and automatic inspection. The unsharpened and unweighted maps from independent half-set reconstructions are taken as inputs and the noise in the Fourier coefficients is estimated. If a point group symmetry has been applied to the map during reconstruction, the asymmetric unit model is refined with appropriate symmetry constraints. Servalcat calculates a weighted Fo?Fc difference map which guides manual model rebuilding in real space, as is common practice in crystallography. The Fo ? Fc map helps visualisation of weak features including hydrogen densities. Although hydrogen densities are weak, they are stronger than in electron density maps produced by X-ray crystallography, and some hydrogen atoms are even visible at ～ 1.8 ? resolution.