On Tue, 2008-12-09 at 09:31 +0100, Tim Gruene wrote: > ...you must set the occupancy of those residues to > zero...
I think this approach (which Tim is not supporting) makes no sense. When I place an ATOM record into a pdb-file, what I am really saying is "based on the data, this atom's position is best described statistically by normal distribution with this (x,y,z) and this temperature factor". Occupancy is normally 1.0, and when it is not, it means "this atom occupies two (or more) distinct positions and here are the normal distribution parameters for one of them". Now substitute zero occupancy. It says "here are some parameters for an atomic position, but my atom is not there". What is really happening with weak density is that you don't know where the atom is (and neither you know where it is not). So placing any ATOM record is misleading. It's all semantics, of course. -- 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 /
