[PyMOL] Protein Alignment

[Ecem G. <ece...@gm...>]

Dear all,

I have a question regarding the alignment tool of PyMOL. I would like to
align the binding sites of two different proteins with each other and get
the corresponding RMSD value. To do this, I selected the ligand and then
picked the residues within 8 A away from the ligand of interest for both
proteins, separately, using action>modify>around>residues within 8 A .
Then, I tried to align these two selections using action>align>to
selection. However, I got an error stating "ExecutiveAlign: mobile
selection must derive from one object only." How can I handle this? I
appreciate your feedback. Thanks in advance.

Kind regards