-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Excellent! Thank you Gerard,
Miguel Gerard DVD Kleywegt escribió: >> But my understanding is that Iain's procedure gives the rmsds of the >> _aligned_ C-alphas, whereas Jenny actually seems to be more interested >> in those that she excludes from the alignment. I may be wrong, but in >> these cases, I use lsqman (from DVD) or lsqkab (from ccp4) to superpose >> the proteins (using one as reference) according to a particular scheme >> (Jenny's 1-40,60-100) and then write a script to calculate the rmsds for >> the "interesting" 41-59 residues. There may be an easier way, which I'll >> be interested to learn about. > > hola miguel, > > i would use the rmsd command in lsqman, like so: > > read m1 m1.pdb > read m2 m2.pdb > expl m1 "a1-40 a60-100" m2 "a1 a60" > rmsd m1 a41-59 m2 a41 > > --gerard > > ****************************************************************** > 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. > ****************************************************************** > > - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: [EMAIL PROTECTED] www: http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Le travail est ce que l'homme a trouvé de mieux pour ne rien faire de sa vie. (Raoul Vaneigem) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) iD8DBQFGRDtWF6oOrDvhbQIRAiYIAJ9Zsh5KNyqzfWhz2WaaRYlRUfKXTwCeLQOK YtSKkl+Q4N3TF8MganziUDs= =TWIp -----END PGP SIGNATURE-----
