Yes, LSQKAB does, but not the equivalent screw axis (which exists by Chasles theorem). I think a screw
axis may well be the best way to describe the rigid body movement which began the thread. A simple
distance and angle (2 numbers) are easier to understand, and often of more biological relevance, than
RT matrices, for example in the case of relative domain motions.
On Jun 20, 2012, at 5:20 PM, Mark J van Raaij 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 <[log in to unmask]> 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 ([log in to unmask])
>>>>
>>>> Institut de Biologia Molecular de Barcelona (IBMB-CSIC)
>>>>
>>>> Barcelona, Spain
>>>>
>>>>
>>>>
