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structure-validation

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Judges whether a macromolecular model (or a region of it) is reliable enough to build on, using resolution, R-free, B-factors, MolProbity geometry, and predicted-model confidence with Bio.PDB. Use when deciding if a structure or a specific region is trustworthy before docking/mechanism/measurement; reading resolution, R-work vs R-free and the R-free-minus-R-work overfitting gap; sanity-checking per-residue and mean B-factors; flagging clashscore, Ramachandran and rotamer outliers and cis non-proline peptides; validating a PREDICTED (AlphaFold/ESMFold) model via pLDDT bands and PAE before docking or molecular replacement; and interpreting cryo-EM global-vs-local resolution (FSC 0.143 half-map vs 0.5 map-model) or an NMR ensemble spread. Keywords validation, resolution, R-free, B-factor, MolProbity, clashscore, Ramachandran, rotamer, pLDDT, PAE, wwPDB, cryo-EM local resolution.

When to use

• deciding if a structure or region is trustworthy
• reading resolution and R-free metrics
• sanity-checking per-residue and mean B-factors
• flagging clashscore, Ramachandran, and rotamer outliers
• validating PREDICTED models via pLDDT and PAE
• interpreting cryo-EM global-vs-local resolution
• interpreting NMR ensemble spread

When not to use

• docking
• mechanism analysis
• measurement

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