8. References

8.1. Moorhen and Coot

https://github.com/moorhen-coot/Moorhen

Casañal, A, Lohkamp, B and Emsley, P. Current developments in Coot for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data. Protein Sci. 29(4): 1069–1078. 2020.

8.2. Servalcat

Yamashita, K, Palmer, C M, Burnley, T, Murshudov, G. N. Cryo-EM single particle structure refinement and map calculation using Servalcat. Acta Cryst D77, 1282-129, 2021.

Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM. Nicholls, RA, Tykac M, Kovalevskiy, O, & Murshudov, GN Acta Cryst D74, 492-505, 2018.

8.3. CCP-EM

Burnley, T, Palmer, CM & Winn M. Recent developments in the CCP-EM software suite. Acta Cryst D73, 469-47, 2017

CCP-EM Pipeliner: https://gitlab.com/ccpem/ccpem-pipeliner

8.4. RELION

Rosenthal P and Henderson R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology,333(4):721–745, October 2003.

Scheres SHW. Classification of Structural Heterogeneity by Maximum-Likelihood Methods. In Cryo-EM, Part B: 3-D Reconstruction, volume 482 of Methods in Enzymology, pages 295–320. 2010.

Scheres SHW. A Bayesian view on cryo-EM structure determination. Journal of Molecular Biology, 415(2):406–418, January 2012. doi:10.1016/j.jmb.2011.11.010.

Scheres SHW. RELION: Implementation of a Bayesian approach to cryo-EM structure determination. Journal of Structural Biology, 180(3):519–530, December 2012. doi:10.1016/j.jsb.2012.09.006.

Scheres SHW and Chen S. Prevention of overfitting in cryo-EM structure determination. Nature methods, 9(9):853–854, September 2012. doi:10.1038/nmeth.2115.

Shaoxia Chen, Greg McMullan, Abdul R. Faruqi, Garib N. Murshudov, Judith M. Short, Sjors H. W. Scheres, and Richard Henderson. High-resolution noise substitution to measure overfitting and validate resolution in 3d structure determination by single particle electron cryomicroscopy. Ultramicroscopy, 135:24–35, December 2013. doi:10.1016/j.ultramic.2013.06.004

8.5. em_placement

Read, R. J, Millan, C, McCoy, A. J. & Terwilliger, T. C. (2023). Likelihood-based signal and noise analysis for docking of models into cryo-EM maps. Acta Cryst D79, 271-280.

Millan, C, McCoy, A. J, Terwilliger, T. C. & Read, R. J. (2023). Likelihood-based docking of models into cryo-EM maps. Acta Cryst D79, 281-289.