From: Jason Swails <>
Date: Thu, 05 Dec 2013 10:41:26 -0500

On Thu, 2013-12-05 at 15:22 +0000, John Smith wrote:
> I am sorry, I know I said it worked, it did but I just wanted to know
> which is more correct regarding rmsd line
> rmsd first (without any mask)
> OR
> rmsd first :1-431.C,CA,N (my protein has 431 residues)

Depends. The first does a fit on every atom, the second does a best-fit
on just the backbone. You have to decide which is better for your
study. (That's why there's an option in the first place)


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Dec 05 2013 - 08:00:02 PST
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