A plugin for UCSF Chimera to calculate and visualize Q-scores in 3D cryo-EM maps.
Practical Notes:
- Q-scores are now reported in EMDB validation reports. Expected_Q scores are not shown, but can be helpful to interpret the score; see tutorial for more details.
- EMDB reports Q-scores calculated with sigma=0.4, which are ~0.1 lower than Q-scores calculated with the default sigma=0.6; this is mainly to allow comparison across all cryo-EM maps in the EMDB which go up to a highest of ~1Å resolution.
- When using this plugin, Q-scores are usually compared to the expected_Q score. Sigma=0.4 should be used when the map is 1.5Å resolution and higher, otherwise either sigma is ok, and the expected_Q score will be reported for either sigma=0.4 or sigma=0.6. Using sigma=0.6 may be more beneficial when approaching ~4Å resolution maps.
- If using Google Drive: when calculating Q-scores with multiple processes, the process fails if the map and model files are on a Google Drive path. Fix is in the works.
- A video that shows how to genreate a color key for displaying Q-scores on a model ribbon: https://www.youtube.com/watch?v=lxy3reAXLKI
More details:
- (2020) Measurement of atom resolvability in cryo-EM maps with Q-scores Nature Methods, BioRXiv
- (2020) Resolving individual atoms... Cell Research
- (2021) Validation, analysis and annotation of cryo-EM structures Acta Cryst. Sect. D.
- (2022) Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future Biophysical Reviews