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Comparing structures with pymol and babel

To align structures using babel, the command is:

babel -ixyz structure1.xyz structure2.xyz -opdb out.pdb --align

Of course, you can change the output format to something else, e.g., xyz, and you can output to multiple files.

babel -ixyz structure1.xyz structure2.xyz -oxyz align.xyz --align -m

Then, you could, for example, load the structures into pymol and view the aligned structures.

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