Apparently I had missed some subtle considerations...
Yet, I confess am not fully convinced: is it so wrong to speak of
how much
different structures DEVIATE from each other ? I do not see what
prevents
you from defining the correct underlying probability distribution.
That
interatomic distances can be used to quantify deviations does not
hurt me so
much.
Thank you anyway...
Philippe Dumas
IBMC-CNRS, UPR9002
15, rue René Descartes 67084 Strasbourg cedex
tel: +33 (0)3 88 41 70 02
[EMAIL PROTECTED]
-----Message d'origine-----
De : Ed Pozharski [mailto:[EMAIL PROTECTED]
Envoyé : Tuesday, April 08, 2008 3:56 PM
À : Philippe DUMAS
Cc : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] Help with Superpose results
RMS deviation refers to the variance of a random variable - it is a
characteristic of the underlying probability distribution. When you
superpose two different structures, you are looking at the DISTANCE
between atoms, not the DEVIATION in their position. In fact, for
individual atoms you can't even say root-mean-square, it's just plain
distance. The core argument is that you are looking at two
structures
that represent different underlying probability distributions, and so
it's definitely not the rms deviation you are calculating, but rms
distance (rms over all the atoms in the structure). HTH,
Ed.
On Tue, 2008-04-08 at 11:07 +0200, Philippe DUMAS wrote:
Although this is not a very important issue..., I am a bit
surprised by
Gerard's insistance for a 'stop calling rmsd "rms deviation"'.
Isn'it a
general term in statistical studies, valid for distances separating
homologous atoms as well as for any other factor (B factors for
example) ?
Philippe Dumas
IBMC-CNRS, UPR9002
15, rue Rene Descartes 67084 Strasbourg cedex
tel: +33 (0)3 88 41 70 02
[EMAIL PROTECTED]
-----Message d'origine-----
De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] la part de
Gerard DVD Kleywegt
Envoye : Monday, April 07, 2008 7:20 PM
A : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] Help with Superpose results
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
******************************************************************
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]
******************************************************************
The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
******************************************************************
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion
arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /
