Is the rms xyz displacement equivalent to an rmsd??
yes. it is in fact a better name than "rms deviation", although i think
'root-mean-square distance' is even better, as it says exactly what you
calculate.
think of it like this, the formula for rmsd is:
RMSD = square-root [ SUM(atoms) { (x1-x2)^2 + (y1-y2)^2 + (z1-z2)^2 } / Natoms
]
now, "(x1-x2)^2 + (y1-y2)^2 + (z1-z2)^2" is the Square of the Distance between
two equivalenced atoms in structure 1 and 2; adding them for all pairs of
equivalenced atoms and dividing by the number of atoms gives you the Mean
Squared Distance; finally, taking the square root yields the Root-Mean-Square
Distance, or RMSD
so, people, can we all please stop calling rmsd "rms deviation" - it really is
an "rms distance" (or "rms displacement"). you could argue that the formula
gives some kind of rms coordinate deviation, but in that case you ought to
divide by 3*Natoms instead.
(having said that, the term "RMS B displacement" sounds positively silly!)
--dvd
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Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED]
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