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Dear ansuman,

'rmsd' stands for 'root mean square deviation', i.e. in the context of
your first question you must sum the _square_ of the atomwise deviations
and then take the square root.

question two: I contradict: residues ARE static in this context: a
crystallographic structure model corresponds to the average of all
asymmetric units in the crystal, hence the resulting coordinates
represent an average value and therefore are to be considered static.
The fact that we assume that between two asymmetric units certain
deviations from the average will occur is modelled by the (isotropic /
anisotropic) ADP and the occupancy, respectively, but nevertheless,
the model that you use for calculating an rmsd is a static one. This
may be the reason why there is not one answer to your question two,
but may give rise to a longish discussion.

Best,
Tim

On 06/23/2013 02:50 PM, ansuman biswas wrote:
> Dear all, I have 2 queries regarding RMSD calculation and 
> interpretation.
> 
> 1. When 2 residue stretches are superposed using CCP4 superpose,
> the log file shows the atomwise-deviations between matched residue
> pairs. How to find the total deviation/RMSD between a specified
> residue pair - should the RMSDs of the individual atoms be summed
> over, or is there some other formula?
> 
> 2. Residues are not static; this dynamic nature is evident from 
> variations (for a given residue; by variations, I mean that the 
> residues don't superpose completely) when multiple chains of the
> same structure (from multiple chains in AU of a PDB, or from
> different PDBs) are superposed. My question is: is there an RMSD
> cut-off below which the variation can be considered as thermal
> fluctutation, and above which they can be said to be a different
> 'conformation' or 'state'?
> 
> Thanking all, regards, ansuman
> 

- -- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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