PyMOL understands a handful of common file formats for input of molecular structures, volumetric fields, and other information. PyMOL can also write a few formats as well as outputing images, geometries, and movies (in some cases).
The asterisk * below denotes formats that are supported through incorporation of the VMD Plugin Architecture. Much thanks to John Stone and the Theoretical and Computational Biophysics Group at UIUC for making it available under a suitable open-source license!
| Format | Load | Save |
|---|---|---|
| Molecular Structures | ||
| PDB | X | X |
| PDBx/mmCIF | X | X |
| CIF (small molecule) | X | |
| MOL2 | X | X |
| MOL | X | X |
| SDF | X | X |
| PKL | X | X |
| MAE | X | X (1.8.4) |
| MOE | X | |
| PQR | X | X |
| XYZ | X | X |
| PDBML | X | |
| PDBQT | X | |
| CML | X | |
| Trajectories & Topologies | ||
| TOP + Amber TRJ | X | |
| PDB + Gromacs TRJ, TRR, XTC, GRO, or G96* | X | |
| DCD* | X | |
| Volumetric Data | ||
| CCP4 | X | X (1.8.4) |
| XPLOR | X | |
| O (OMAP DSN6 BRIX) | X | |
| PHI | X | |
| DX | X | |
| Cube* | X | |
| MTZ | X | |
| Geometry | ||
| Raster3D | X | |
| VRML2 | X | |
| POV | X | |
| COLLADA | X | |
| Scripts & Annotated Structure Formats | ||
| PML | X | |
| P1M | X | |
| P5M | X | |
| Python | X | |
| Sessions | ||
| PSE | X | X |
| PSW | X | X |
| Images | ||
| PNG | X | |
See also the list of incomplete/unsupported Formats.