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Hello - The sigma issue a bit more complicated. What we call usually sigma is the root mean square deviation (rmsd) of the map. Lets first recall, that the variation within the protein region is quite large, while the solvent is rather flat. Now, lets take an 'extreme' example, of a protein with 80% solvent. The rmsd for that will be quite low, since most of the AU is flat. Thus, I would argue that you might want to consider waters in relatively 'low sigma'levels. Of course 80% solvent will also mean that most likely this protein will only diffract to low resolution, so you should maybe not be putting any waters. The inverse case argument also applies. Similar issues, maybe more severe, come up for atom removal. Admittedly, we had this discussion with Victor back at the EMBL- Hamburg library, back to what will soon be two decades ago, and I do not think we have good answers, although we try new things every couple of years. A. If anyone is interested thats the ARP/wARP code for removal atom sigma, I am not sure when we came up with that, but it did make some sense at the time. Cant even recall if its my or Victor or both putting that in ... basically it leaves waters in if they are above 1.0 rmsd (if resolution is better than 2.0 A), or above 0.6 rmsd if resolution is less than 2.8 A (I can hear the screams already ...), and uses a value in between for resolutions between 0.6-1.0 A. The rmsd for adding atoms is 3.4, since it does not really matter what to add, if you remove what should not be there ... (what a silly assumption ...? It looked logical at the time though) On Apr 19, 2010, at 16:38, Ed Pozharski wrote: > 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 / P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791