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]<mailto:[email protected]>) Institut de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona, Spain
