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)
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Dec 05 2013 - 08:00:02 PST
