I agree with Petr. For a rigid body displacement the RMSD is not much use as a descriptor. Such a displacement can be described by a translation along and rotation around a direction, or rotation-translation matrices. These will allow someone else to reproduce the displacement, but the RMSD will not. I liked the FIT program of Guoguang Lu for this type of calculation and still use some C code based on it. Not sure where the original went though.
On Jun 20, 2012, at 9:31 AM, James Holton wrote: > Because sometimes it is important to know how much the structure moved > relative to the unit cell, such as before and after a round of > refinement. > > -James Holton > MAD Scientist > > On Tue, Jun 19, 2012 at 3:34 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 >> >> >>
