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.

• MOL format for loading of individual small molecule structures.

• SDF format for loading of multiple small molecule structures.

• MOL2 format for loading systems containing both small molecules and proteins.

• XYZ variants, including multimodel XYZ.

PyMOL also has limited support for

• ChemDraw3D CC1 and CC2.

• The old Macromodel MMD/MMOD format.

• Amber and Gromacs trajectory files, through the VMD plugin architecture.

Incentive PyMOL Builds also support the following proprietary formats:

• MOE Molecular Operating Environment (Chemical Computing Group)

• MAE Maestro (Schrödinger, LLC)

Molecular structures can be loaded into PyMOL in the following ways:

• via Menus
  • File Menu: Open
    

• Plugin Menu: PDB Loader Service
  

• via PyMOL Commands
  • load imports structures from disk.

    load 1vgc.pdb
    load 1nb6.pdb
    load 1fjf.pdb

  • fetch imports structures directly from the Protein Data Bank.

    fetch 1vgc 1nb6 1fjf

• 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

• via Python using cmd.load.

fetch | load