Hi Jorge,
You are right align is only for proteins. You can use the Fit
<http://www.pymolwiki.org/index.php/Fit> command
Cheers,
Osvaldo.
On Tue, May 5, 2015 at 3:38 PM, Jorge Fernandez de Cossio Diaz <
cos...@cim.sld.cu> wrote:
How can I superimpose two small non-protein molecules in PyMol? I think
> that "align" is not working because it assumes that the molecules are
> proteins and contain residues.
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