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 <[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
>>>
>>>
>>>
