Cite PyMOL as "The PyMol Molecular Graphics System, Version #, Schrodinger, LLC."
Cite AxPyMOL, a variation on PyMOL, as "The AxPyMOL Molecular Graphics Plugin for PowerPoint, Version #, Shrodinger, LLC."
Cite PyMOL in the text of the paper as well. PyMOL's requested citation style doesn't include instructions for in-text citations. To cite the resource in the paper, simple cite PyMOL and the version number within the text of the paper.