File Formats

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.

 
format.txt
 
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