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. ******************************************************************
