PDB Structure — Water (.pdb)
The same water molecule in PDB format with fixed-column HETATM coordinate records and a CONECT bond record — for testing molecular-structure parsers and viewers and PDB/MOL conversion.
HEADER SAMPLE MOLECULE 01-JAN-26 0001
TITLE WATER (H2O) - PUBLISHED SAMPLE COORDINATES
REMARK 1 Sample fixture for parser testing, standard water geometry.
HETATM 1 O HOH A 1 0.000 0.000 0.000 1.00 0.00 O
HETATM 2 H1 HOH A 1 0.757 0.586 0.000 1.00 0.00 H
HETATM 3 H2 HOH A 1 -0.757 0.586 0.000 1.00 0.00 H
CONECT 1 2 3
MASTER 0 0 0 0 0 0 0 0 3 0 1 0
END
Specifications
- Format
- PDB (Protein Data Bank)
- Molecule
- H2O (water)
- Records
- HETATM, CONECT
- Atoms
- 3
What is a .pdb file?
A PDB file (.pdb, Protein Data Bank format) is a plain-text format for 3D molecular structures, using fixed-column ATOM and HETATM records for atom coordinates plus CONECT records for bonds. It is the classic format for proteins and small molecules in structural biology.
How to use this file
Use an example .pdb file to test molecular-structure parsers and viewers (PyMOL, Jmol, NGL), coordinate extraction, and PDB-to-mmCIF or PDB-to-MOL conversion.
How to use this file for testing
“PDB Structure — Water (.pdb)” is a deterministic Novus Examples fixture for Scientific data, Editor testing. Citation catalogs (BibTeX, RIS), chemistry structures (MDL Molfile, PDB), and gridded binary data (NetCDF, FITS) — for testing reference managers, molecule viewers, and scientific-data loaders.
Documented properties for this file: PDB (Protein Data Bank). Compare results against paired or grouped companions on this page when present (clean↔damaged, searchable↔scanned, or format twins) so scores stay reproducible across runs.
Download the file once, keep the path stable in CI or local scripts, and treat the spec table as the contract: dimensions, seeds, field lists, and roles are intentional. Corrupt or invalid samples are labelled as such — expect parsers to fail loudly rather than silently accept them.
Data fixtures document their exact quirks — delimiters, encodings, null handling, schema, and row counts — in the spec table. Point your parser or importer at the file and assert it handles the documented edge cases; clean and deliberately-messy siblings make before/after diffs straightforward.
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