On Fri, Oct 3, 2014 at 11:17 AM, PC <patrick.coss...@inbox.com> wrote:
> Sorry its me again. Can someone tell me where I can find the code for
> the align command?
> It seems the RMSD differs from other online tools I found.
>
Are you running it with default arguments? If you do this:
align object1, object2
it does an iterative procedure where it throws out the most disagreeable
atoms and re-runs superposition. The final RMSD will be calculated without
these atoms (but it should print out the intermediate results), and is
always much lower. If you want it to keep the original alignment with all
atoms, do this:
align object1, object2, 0, 0
(the zeros specifying the number of refinement cycles, I think)
-Nat
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