Setting Up Access to PyMOL on Windows

Both Maestro and Canvas can open PyMOL directly. To do so, PyMOL must be installed and the location communicated to the application.

Maestro uses the following sources to find an installation of PyMOL, in the order given:

  1. The PYMOL4MAESTRO environment variable, if it points to an executable file.

  2. A file named pymol4maestro.bat, pymolwin.exe, or pymol.bat, in any of the following locations:

    • The location specified by the PYMOL4MAESTRO environment variable
    • The Schrödinger software installation
    • The pymol folder in the Schrödinger software installation
    • The location specified by the $PYMOL_PATH environment variable

  3. The registry, if PyMOL is installed on Windows with an installer.

  4. C:\Program files\pymol\pymol

  5. The pymol folder in the same folder as the folder containing the Schrödinger software installation (i.e. parallel to the installation, not inside it).

  6. The pymol executable found in the PATH environment variable

See Setting Environment Variables on Windows for instructions on setting environment variables.