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, they are calculated using this plugin.
- The default sigma is now 0.4 to match Q-scores calculated in the EMDB.
- Q-scores can be compared to Q_peak, Q_low_95%, and Q_high_95%, which are determined from other maps and models in the EMDB at similar reported resolution. See the recent BioRXiv for an explanation.
- 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.
- 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:
- (2025) Q-score as a reliability measure for protein, nucleic acid, and small molecule atomic coordinate models derived from 3DEM density maps BioRXiv
- (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