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 *******************************************
