SDF to PDB Converter
PDB is the lingua franca of molecular viewers. Convert an SDF record when you need to open it in PyMOL, Chimera or an online viewer.
When PDB is the right target
Molecular graphics tools — PyMOL, ChimeraX, VMD, Jmol — all read PDB natively. They also read SDF, but PDB is the format they were designed around, and it is what most structure-alignment and contact-analysis scripts expect.
What changes
- Atom records become
HETATMentries with element and coordinate columns. - Bond orders are not represented — PDB has no bond block, so tools perceive them from distances.
- Residue and chain identifiers are assigned generically.
Multi-record SDF
Each SDF record becomes a separate model in the PDB file, so a small library can be inspected as multiple frames in a viewer.