[3dem] Paper Published: 3DEM Structure-Map Validation Recommendations

[Justin Flatt]

A new publication describes two percentile-based metrics: Q_relative_all 
and Q_relative_resolution. The publication presents a statistical 
analysis of Q-score and these new percentile based validation metrics.

Q_relative_all is a single value percentile, representing the overall 
quality of the model-map fitness. It is derived by comparing a model-map 
average Q-score to all model-map average Q-scores calculated for 3DEM 
structures in the PDB/EMDB. Higher Q_relative_all percentile values, 
infer higher quality in the model-map fitness.

Q_relative_resolution is a single value percentile, derived by comparing 
the average Q-score of a model-map with the Q-scores of other model-map 
entries of similar resolution. This metric was developed from the 
principle that average Q-score is correlated with map resolution. 
Q_relative_resolution percentile values close to 50% therefore represent 
a score that is commonly observed for entries in the PDB/EMDB of similar 
resolution, inferring model-map fitness is typical for an entry of a 
particular resolution. Notably low or high Q_relative_resolution 
percentiles may be helpful to guide further review of model-maps.

The EMDB has made these metrics available since Spring 2024 via 
emdatabank.org [2] and since the publication of the paper, the wwPDB is 
in the process of incorporating these metrics into wwPDB validation 
reports by providing the Q-score percentile slider for the assessment of 
model-map fitness of 3DEM entries. This validation enhancement will help 
depositors, reviewers and the community to improve the quality of data 
submissions and assist users to assess 3DEM data quality in the PDB and 
EMDB, wwPDB core archives.

  [1]_Examples of Q-score application in proteins and in nucleic acids 
adapted from: doi: 10.1107/S2059798325005923_

> Q-score as a reliability measure for protein, nucleic acid and 
> small-molecule atomic coordinate models derived from 3DEM maps
> Grigore Pintilie, Chenghua Shao, Zhe Wang, Brian P Hudson, Justin W 
> Flatt, Michael F Schmid, Kyle L Morris, Stephen K Burley, Wah Chiu
> (2025) _Acta Cryst_ D81: 410-422 doi: 10.1107/S2059798325005923 [1]


Links:
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[1] https://urldefense.com/v3/__https://doi.org/10.1107/S2059798325005923__;!!Mih3wA!DIZHHyCNnVS70bmGpD-s6N2SISpYi5mG9kBjCoRGPXaGDGeMwU9bsEmoxmMRITj64Zw12IVtswR_4f9h6a40a11u$ 
[2] https://urldefense.com/v3/__https://emdatabank.org__;!!Mih3wA!DIZHHyCNnVS70bmGpD-s6N2SISpYi5mG9kBjCoRGPXaGDGeMwU9bsEmoxmMRITj64Zw12IVtswR_4f9h6Ytb53wR$ 
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