Abstract
Structural determination of molecular complexes by cryo-EM requires large, often complex processing of the image data that are initially obtained. Here, TEMPy2, an update of the TEMPy package to process, optimize and assess cryo-EM maps and the structures fitted to them, is described. New optimization routines, comprehensive automated checks and workflows to perform these tasks are described.
Highlights
Structural determination of biological assemblies is paramount to understanding their function
Cryo-EM is experiencing an exponential growth in popularity, in particular owing to its ability to resolve large assemblies in an aqueous environment without the need for crystallization
The code is divided into subpackages, each targeted towards common tasks performed on EM maps and related structures: (i) the maps subpackage handles the creation and manipulation of maps; (ii) the protein subpackage handles the manipulation of structural data and its comparison to maps; (iii) the math subpackage handles operations such as geometric transforms used on atomic structures as well as maps; (iv) the assembly subpackage deals with the optimization of multiple structures within a map; (v) the graphics module contains routines to generate plots from the data produced by various analyses
Summary
Structural determination of biological assemblies is paramount to understanding their function. Cryo-EM is experiencing an exponential growth in popularity, in particular owing to its ability to resolve large assemblies in an aqueous environment without the need for crystallization This has allowed large structures to be resolved quickly, with the recent coronavirus spike-protein structure determinations being a salient example (Wrapp et al, 2020). Despite the so-called ‘resolution revolution’ (Kuhlbrandt, 2014), many of the recently solved structures of biological assemblies still suffer from having a resolution that is far from near-atomic, especially in peripheral and flexible regions of the structure, where it may be difficult to unambiguously place side chains, backbone or even entire subunits. Include -TEMPy, ‘local fit optimizer’ and ‘local fit quality estimation’, among others
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