Beware do ing this - you may just find the coordinates are on a different
origin or a different symmetry equivalent.
Eleanor
On 20 June 2012 09:20, Mark J van Raaij <mjvanra...@cnb.csic.es> wrote:
> LSQKAB ("superpose" in CCP4i GUI) also outputs in its log-file the
> translation parameters and rotation matrix it used to superpose the
> structure.
>
>
>
> On 20 Jun 2012, at 07:34, Jeremy Tame wrote:
>
> > 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 <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
> >>>
> >>>
> >>>
>
