Molecular Coordinate Representations

What scientific information is actually contained in a molecular coordinate file, and what must not be inferred silently?

Build the conceptual model first, then test the same idea through the linked scientific representation or tool.

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What scientific information is actually contained in a molecular coordinate file, and what must not be inferred silently?

Build the conceptual model first, then test the same idea through the linked scientific representation or tool.

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XYZ, PDB, molfile/SDF, MOL2, and CIF formats do not carry identical semantics. Coordinates may be explicit while bond records, unit conventions, model scope, or crystallographic metadata differ by format.