Geometry-based validation tools similar to those used in X-ray crystallography can be used to highlight implausible modeling choices and guide modeler toward more native-like structures. The CaBLAM method, which only uses Cα atoms, is suitable for low-resolution structures from cyro-EM.A way to compute the difference density map has been formulated for cyro-EM. Cross-validation using a "free" map, comparable to the use of a free R-factor, is also available. Other methods for checking model-map fit include correlation coefficients, model-map FSC, confidence maps, CryoEF (orientation bias check), and TEMPy SMOC.