I am not sure I understood what you are asking. But let me explain my question a little further.
If two structures are not identical, then the RMSD is a good enough parameter to describe the superposition: this many atoms were used in the superposition and they can be moved in such a way that this rmsd is achieved. The final result is just one global minimum or a finite number of local minima that all have the same RMSD. If two structures are identical and the "RMSD" is calculated without moving either of them, the number of configurations that have the same RMSD is infinite. Petr On Jun 20, 2012, at 12:38 AM, Jacob Keller wrote: > 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 <[email protected]> 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 ([email protected]) >> >> Institut de Biologia Molecular de Barcelona (IBMB-CSIC) >> >> Barcelona, Spain >> >> >> > > > > -- > ******************************************* > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > email: [email protected] > *******************************************
