Re: [PyMOL] [External Email] 2 Molecules superposition

Hello, Under the plugin menu option there is an included default plugin "alignment" tool which will bring up an alignment GUI. Best, Franz From: Giuseppa Cefalu Sent: Saturday, January 11, 2025 11:21 PM To: PyMOL-users@lists.sourceforge.net Subject: [External Email][PyMOL] 2 Molecules superpos

Re: [PyMOL] 2 Molecules superposition

I usually open the second molecule after pymol has loaded first molecule by just dropping the file on the window. Afterwards I used align Command: https://pymolwiki.org/index.php/Align Super command is also useful: https://pymolwiki.org/index.php/Super Also after loading 2 molecules you can use Al

Re: [PyMOL] Running pymol without launching window in batch

Apart from others' reply, I believe pymol will run .pml files while python will run .py files. Regards, Saurabh Gayali -- *Saurabh Gayali* Business Analyst [Excelra], Former Research Scientist [IGIB] saurabh.gay...@gmail.com / +91 8800412916 Bang