At the present time, Open-Source PyMOL has support for the following molecular formats:
PDB format with support for various extensions for specifying connectivity, bond valences, multiple models, ensembles, and trajectories.
PyMOL also has limited support for
Incentive PyMOL Builds also support the following proprietary formats:
Molecular structures can be loaded into PyMOL in the following ways:
via PyMOL Commands
imports structures from disk.
via the command shell during program launch:
Unix: pymol 1vgc.pdb 1nb6.pdb 1fjf.pdb
Windows: "c:\program files\pymol\pymol\pymolwin.exe" +2 1vgc.pdb 1nb6.pdb 1fjf.pdb