I'm moderately in favor of the "just let B go through the roof" option. Here's why: Most "user friendly" programs like pymol have an option to color the atoms by B but not by occupancy. Most end-users I interact with know enough to see if coloring by B makes a side chain flaming red, but they'd never think (or know how) to check occupancy. (So if you do set occ to zero, please set B to the max!) And truncating side chains screws up simple electrostatics calculations, which matters if you deal with nucleic acid-binding proteins. Phoebe ===================================== Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alpha... http://www.rsc.org/shop/books/2008/9780854042722.asp