EMDA: A Python package for Electron Microscopy Data Analysis

An open-source Python library EMDA for cryo-EM map and model manipulation is presented with a specific focus on validation. The use of several functionalities in the library is presented through several examples. The utility of local correlation as a metric for identifying map-model differences and unmodeled regions in maps, and how it is used as a metric of map-model validation is demonstrated. The mapping of local correlation to individual atoms, and its use to draw insights on local signal variations are discussed. EMDA's likelihood-based map overlay is demonstrated by carrying out a superposition of two domains in two related structures. The overlay is carried out first to bring both maps into the same coordinate frame and then to estimate the relative movement of domains. Finally, the map magnification refinement in EMDA is presented with an example to highlight the importance of adjusting the map magnification in structural comparison studies.

Automated summary

This article presents an open-source Python library called EMDA, which focuses on the validation of cryo-EM map and model manipulation. The library's functionalities are demonstrated through several examples, including the use of local correlation as a metric for identifying map-model differences and unmodeled regions. The mapping of local correlation to individual atoms and its insights on local signal variations are discussed. In addition, the likelihood-based map overlay and map magnification refinement in EMDA are demonstrated to emphasize their importance in structural comparison studies.