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- Introduction to model quality assessment
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Walkthrough: Visualising validation metrics on structure
When evaluating a macromolecular structure on the PDBe website, the “Model quality” tab provides crucial insights into the model’s reliability.
On this tab, you can find the slider, which contains the visual indicators of clashscore, bond angles/lengths, sidechain rotamer outliers, and RSRZ outliers. These highlight steric clashes, geometric inconsistencies with expected values, and poor model-to-data fit. Along with other key data quality metrics.
Crucially, the 3D structure viewer on the right-hand side of the page offers a powerful way to visualise these metrics directly on the model. You can colour the residues in the structure based on validation criteria:
- “Issue count”: This option colours residues based on the total number of validation criteria they are an outlier, providing an immediate visual indication of problematic regions.
- “Specific issue”: Use the dropdown menu to select how the structure is colored. Selecting this allows you to colour the structure according to individual validation problems. This is invaluable for pinpointing specific types of errors. Examples of specific issues you can highlight include: bond lengths, bond angles, clashes, sidechain outliers, Ramachandran outliers, symmetry clashes, planarity deviations
By interactively exploring these visualisation options, you can quickly identify and focus on areas of the structure that require closer inspection due to validation flags.