TEMPy is an object-oriented Python library designed to help the user in the analysis of structures of macromolecular assemblies, especially in the context of 3D electron microscopy density maps. It is designed with a set of functionalities that assess the goodness-of-fit between a given atomic model and a density map or between two maps using a variety of different scoring functions.It can also generate various ensembles of alternative fits, which has been shown to be useful in assessing a model fit and find other models with good density fit. In the future, TEMPy will also include a suite of functions for density ﬁtting.
For the use of plotting TEMPy uses matplotlib but this optional.
- 1. Installation on Linux & Mac OSX
- 2. How to use TEMPy
- 3. Parser for Structure Instance
- 4. Class to define and manipulate protein structures
- 5. Map Parser
- 6. Density Map Generation
- 7. Density Map Instance Informations
- 8. Read Rigid Body Files in Flex-EM format
- 9. Parser for Transformation Matrices
- 10. Generation an Ensemble of Structure Instance
- 11. Scoring Functions
- 12. Clustering multiple fits in a cryoEM map
- 13. Consensus Scoring of multiple fits in a cryoEM map
- 14. Plotting and Output Functions
- 15. Vector
- 16. Multi-component Fitting: Gamma-tempy
This software is made available under GPL V3, together with some additional documentation.
Download the latest version here.
Copyright © 2015 Birkbeck College University of London.
Authors: Maya Topf, Daven Vasishtan, Arun Prasad Pandurangan, Irene Farabella, Agnel-Praveen Joseph, Harpal Sahota
If you use TEMPy, please cite:
Farabella, I., Vasishtan, D., Joseph, A.P., Pandurangan, A.P., Sahota, H. & Topf, M. TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits. (2015). J. Appl. Cryst. 48, 1314-1323, link.