It does not matter. rmsd is going to give you a number no matter if the molecules are aligned or not. The thing is how you interpret the number, so discussing about alignment does not apply for implementation, only for interpretation. Correspondence does apply. If not addressed, fine with me :)<br>
<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Correspondence and rigid alignment are different questions.<br>

Correspondence is hard enough to solve that I figured it was clearly<br>
not being solved. Rigid alignment is trivial so it is not unreasonable<br>
to assume it is done (but unclear whether or not it is).<br>
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