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 /
