Structure Utilities
Repair structures and compare conformational ensembles.
Results
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Method & evidence
Use one workspace for checksum-bound structure preparation with PDBFixer and collective pairwise RMSD analysis with the original pyRMSD QCP kernel.
Scope & limitations
- PDBFixer uses bundled standard templates and rejects operations that would require mutable remote CCD definitions.
- Missing-atom addition fails closed if PDBFixer would otherwise discard a retained chain composed entirely of unknown molecules.
- pyRMSD upstream bindings target Python 2; the service calls its unmodified QCP C++ kernel through a narrow Python 3 C ABI.
- GPU/CUDA calculators, trajectory formats, inferred correspondence, solvation, and molecular-mechanics minimization are outside this first release contract.
Interpreting results
- PDBFixer prepares coordinates for downstream modeling; repaired coordinates are computed structures, not experimental observations.
- RMSD measures coordinate difference after optimal rigid-body superposition and the declared atom selection. It does not measure stability, affinity, or function.
- Compare RMSD values only when atom correspondence, chain scope, structure preparation, and method identity are identical.
References
Input requirements & outputs
Input checks
- PDB input only; client file paths and remote PDB identifiers are not accepted
- Repair: up to 20 structures and 20 MB total input
- RMSD: 2–200 structures with identical ordered atom identities after selection
- Primary model and primary alternate location only for RMSD correspondence
Expected results
- Repaired structure Dataset — Publish each repaired PDB as a new immutable Artifact with source lineage, before/after counts, operations, and checksums.
- Pairwise RMSD evidence — Publish every structure pair, RMSD in Å, atom count, selection, atom-identity digest, and pyRMSD method identity.
- Native result — Keep the complete independently verified response as an immutable JSON Artifact.
