Is part of your question based there being many ways to superimpose
structures, which there are?

JPK

On Tue, Jun 19, 2012 at 5:34 PM, Petr Leiman <petr.lei...@epfl.ch> wrote:
> Would anyone be kind enough to explain what kind of information does the
> "RMSD" for two not-yet-superimposed structures transmit?
>
> If two structures are indeed identical but are apart spatially, then it is
> more appropriate to calculate the COM and the inertia tensor for both
> structures and report the displacement and the rotation (moleman or moleman2
> do just that, right?). Reporting "RMSD" in this case does not seem to make
> sense because the same RMSD describes an infinite number of spatial
> configurations of the two structures.
>
> If two structures are not identical, one HAS to superimpose them, i.e. to
> move all (or selected) atoms to be as close in space as possible and only
> then calculate the RMSD for the superimposed or all atoms.
>
> Thank you in advance,
>
> Petr
>
> --------------------
> Petr Leiman
> EPFL
> BPS-415
> CH-1015 Lausanne
> Suisse
>
> On Jun 19, 2012, at 5:04 PM, Claudia Millán Nebot wrote:
>
> Hello everyone :)
>
> I would like to know if it exist some tool that allows to calculate RMSD
> between 2 pdbs that are identic, but just displaced in space. It should not
> make a superposition, beause if this is the case it will just say that RMSD
> is 0 .
> I know is not such a difficult problem in terms of scripting, but i was
> wondering if there are tools already.
>
> Claudia Millán (cmn...@ibmb.csic.es)
>
> Institut de Biologia Molecular de Barcelona (IBMB-CSIC)
>
> Barcelona, Spain
>
>
>



-- 
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
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