I second Tim's opinion. In the days of CNS/O, there was a popular rule to place waters in 3 sigma peaks that make chemical sense, then re-refine and keep those waters that produce more than 1 sigma in 2fo-fc map. (With Coot the default cutoff is 5).
There could be a bizarre probabilistic argument for a particular choice of sigma cutoff - with 3 sigmas you have ~0.3% chance of a particular peak to be simply a random spike. Which means that if the map is on, say, 0.5A grid, there is a decent chance to have one such peak per 3.5x3.5x3.5A volume. With 5 sigmas the size of the cube goes up to ~60x60x60A, so 5 sigma peaks are almost guaranteed not to be flukes. On Sat, 2010-04-17 at 22:46 +0200, Tim Gruene wrote: > Hello Sudhir Kumar, > > most of all the waters in your structure should make chemical sense. When the > density around the water is weak it may just mean that the water is not fully > occupied. > > Tim > > On Sat, Apr 17, 2010 at 09:47:35PM +0900, Sudhir Kumar wrote: > > hi all > > sorry for such a basic query, i'ld like to know what is the acceptable sigma > > cut off for waters to be kept in a model if data is of about 1.6 A. > > thanks in advance > > Sudhir Kumar > > Research Scholar > > Structural Biology Laboratory > > SLS, JNU, > > New Delhi-110067 > -- 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 /
