Is there a way to transfer the Maestro Workspace into PyMOL?

Yes. Starting with Suite 2010, you can transfer structures with their representation to PyMOL, via the PyMOL for Maestro panel (Maestro → PyMOL; Tools → View in PyMOL from Suite 2012). To ensure that Maestro can find PyMOL, set the environment variable PYMOL4MAESTRO to the top directory of the PyMOL installation. You must have an "incentive" version of PyMOL to use this capability.

Keywords: Maestro, PyMOL, display, PyMOLforMaestro, PyMOL for Maestro,

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