Export Formats

Visual SmallMol supports the following export formats. Use the right tool for the format you need; each format is available from specific workflows below.

Supported formats

SDF (Structure-Data File)
Standard format for small-molecule 3D structures. Compatible with most chemistry software (e.g. PyMOL, RDKit, Schrödinger). Export from the SMILES to 3D viewer or after loading a structure in SDF Upload when the viewer supports SDF download.
PDB (Protein Data Bank format)
3D atomic coordinates. Use for small molecules or proteins in structural viewers and pipelines. Available from the 3D Viewer sidebar after loading or generating a structure in SMILES to 3D or SDF Upload.
PNG
Screenshot of the current 3D view. Use the Export PNG button in the viewer for presentations or reports. Available in SMILES to 3D and SDF Upload.
PDF
Property report with molecular weight, logP, TPSA, Lipinski rule of five, rotatable bonds, and formula. Download from Molecular Properties (single structure) or Batch SMILES (optional ZIP of PDFs per molecule).

Where to export from

Molecular Properties — PDF report (single SMILES/structure).
Batch SMILES — Table + CSV; optional ZIP of PDF reports.
SMILES to 3D — PDB, PNG; SDF when supported.
SDF Upload — PDB, PNG for the loaded structure.

Export · 3D Viewer · Molecular Properties · Batch Export Citation Generator