Localization of macromolecules in cryo-electron tomograms is one of the key procedures to unravel structural features of imaged macromolecules. Positions of localized molecules are further used for structural analysis by single particle procedures such as fine alignment, averaging and classification. Accurate localization can be furthermore used to generate molecular atlases of whole cells.
A webserver for the localize module in the PyTom package. Localize.pytom is a free website and open to all users and there is no login requirement. The server accepts tomograms as they are imaged and reconstructed by Cryo-Electron Tomography (CET) and returns densities and coordinates of candidate-macromolecules in the tomogram.
Offers a platform for subtomograms analysis. TomoMiner is an open source software which consists of a set of methods for (i) large-scale subtomogram ranking (ii) template matching, (iii) averaging, and (iv) aligning. This application is able to handle more than 100 000 subtograms in a row. It aims to complement other existing approaches for analysis and exists as a standalone application or as a cloud-based implementation, called TomoMinerCloud, using Amazon AWS.
Provides the essential tools for the analysis of subtomograms obtained by cryo electron tomography. PyTom covers a processing pipeline of tomogram reconstruction, localization of macromolecular complexes in tomograms, fine alignment of subtomograms extracted at these locations and their classification. PyTom is mostly written in Python making it fairly easy to add new functionality as well as to customize existing methods for specific purposes. The package is mainly developed in the Förster lab at the Max Planck Institute for Biochemistry, but developers are highly encouraged to contribute to PyTom on an open source basis.
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