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Loading Molecules


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.

See Also

loading.txt · Last modified: 2013/08/19 21:00 (external edit)