Format conversion
Converts a structure between SDF, PDB, mmCIF, MOL2 and SMILES, with nothing invented — no 3D coordinates generated, no geometry changed. Use when a downstream tool or an external program needs a different file format than what's saved.
Format conversion
What it does
Takes one saved structure and rewrites it in a different file format: PDB, SDF, MOL2, mmCIF, or SMILES.
Nothing about the molecule changes — no 3D coordinates are generated, no geometry is altered. If the input has 3D coordinates, they carry over. If it doesn't, the output doesn't gain any. This is a pure rewrite, not a computation.
Choosing a target format
- PDB — the traditional format most structural tools read
- SDF — the standard small-molecule interchange format
- mmCIF — the modern macromolecular format RCSB uses by default
- MOL2 — carries atom-typing information PDB and SDF don't
- SMILES — a compact text string with no coordinates at all; useful for getting a molecule's connectivity out of a structure file
How the conversion is done
Open Babel, and only Open Babel — unlike 3D conformer generation, there is no engine choice here. Reading and writing these formats is deterministic: two engines converting the same file the same way would agree, so there is nothing for a dropdown to offer.
Input
One structure, saved as an SDF, PDB, or mmCIF. Other formats currently saved on this platform (bCIF in particular) aren't supported as input yet.
Important limitations
No 3D generation. Converting a flat (2D or no-coordinate) structure to a 3D-capable format like SDF doesn't add coordinates — the file just declares itself in that format while still being flat. Use 3D conformer generation first if an actual 3D geometry is needed.
A file that doesn't match its claimed format is refused, not guessed at. If a PDB file is uploaded but tagged as SDF, the conversion fails with an explanation rather than silently producing garbage.