Could somebody please point me to a program that calculates rmsd deviations and accounts for possible swapping of side chain orientations, namely 180° rotations for Tyr, Phe, Glu, Asp etc... My feeling is that lsqkab does not consider these alternative orientations / alternative atom naming. A plus would be if the program would also allow for the calculation of rmsd values without the calculation of the best superposition that is without reorienting the two molecules.
lsqman does all of this. the NOmenclature command makes sure that the ambiguous side-chain atoms of phe etc are named properly. subsequently, the FIx_atom_names command can fix the ambiguities by comparing two molecules and picking the atom naming that minimises the difference between the corresponding torsion angles. finally, the RMsd command will calculate the rmsd between any sets of atoms without doing a superimposition. (note: if you want to compare all atoms instead of only CA atoms, use the ATom_types command first)
see the manual: - NOmenc http://xray.bmc.uu.se/usf/lsqman_man.html#S32 - FIx_at http://xray.bmc.uu.se/usf/lsqman_man.html#S33 - RMsd http://xray.bmc.uu.se/usf/lsqman_man.html#S59 - ATom_t http://xray.bmc.uu.se/usf/lsqman_man.html#S39 --dvd (live from poor little denmark) ****************************************************************** 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. ******************************************************************
