PyMOL is an open-source software that provides a way for users to view and study molecules. PyMOL has a specific citation style to use regardless of whether your paper is using APA (American Psychological Association), MLA (Modern Language Association) or Chicago-style citations. The citation is the same for any style, though you may want to note to a professor that PyMOL requires users to cite its system a certain way.
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.