Dear Uma, The water pictured in W12-1.jpg: could this be a potential metal ion? If you flip the side chain on Asn at 3.08Angstrom, then this has 3 or 4 coordination with oxygen atoms. So, provided your crystallization condition or buffer contains metal ion(s), you could attempt to see if it fits better with a refinement cycle.
May be a similar situation with the water described in W11-1.jpg as well? Difficult to say from these figures. COOT within the "validate" wizard has an option to search for "hihgly-coordinated waters" like the one you have pictured. Hope this helps, Partha On Wed, Mar 7, 2012 at 4:21 PM, Uma Ratu <rosiso2...@gmail.com> wrote: > Dear Roger: > > Thank you very much for your comments. I use them as guideline and remove > many 'false waters". > > Still, I am not clear of some of these 'waters' are real or not. I have > the pic attached. > > In Pic-W11-1, the 'water' is connected to the adjust residues with 4 > contacts, which are 'N' or 'O' atoms. I would consider this 'water' is > false. My question is: if these 4 contacts include "C" from residues, will > it be a polar contact or not? > > In Pic-W12-1, the 'water' is connected to the adjust residues with 3 > contacts. The 4th is to another 'water'. > Will this 'water' is true or not? Similar case is seen in Pic-W190-1 > > In Pic-W109-1, some 'waters' are connected to adjust residues, some not. > Are these 'water' true or not? > > Further more, > > and the b-factors are not way out of line, > > I am not clear on how to define "out of line". > How to find b-factor of individual residue in Coot? I search the web, but > find no answer. > > Thank you for advice > > Uma > > On Wed, Mar 7, 2012 at 11:44 AM, Roger Rowlett <rrowl...@colgate.edu>wrote: > >> Uma, >> >> Remember that your structure, ultimately, is a model. A model is your >> best judgment of the true representation of the protein structure in your >> crystal. Your model should make chemical sense. Coot is pretty good at >> placing waters, but it cannot substitute entirely for the experimentalist. >> Coot will miss some waters, and mis-assign others into weak, unmodeled or >> alternate side- or main-chain density, or into density that might be >> attributable to cations and anions or other crystallization materials. Your >> waters should be subjected to inspection and verification. It is really >> helpful to turn on environment distances in Coot when you do this. Even in >> a large protein model, it is possible to inspect all waters for >> reasonableness pretty quickly. If you have no significant positive or >> negative difference density, and the b-factors are not way out of line, and >> hydrogen bonding partners are reasonable, then modeling a water is probably >> a good call. >> >> Waters should have hydrogen bonding partners with side chains or >> main-chain polar atoms, within reasonable distances, or be withing hydrogen >> bonding distance of other waters that are (chains of waters). If a "water" >> has strong electron density and more than 4 polar contacts, you might >> consider anion or cation occupancy. Most anions and cations will have >> higher electron density, and appropriately different types of polar >> contacts. (e.g. you might find sulfates near a cluster of basic residues). >> Low occupancy anions can often look a lot like water. PEGs can create ugly >> "snakes" of variable density that may be challenging to model. Modeling >> non-protein structural bits is endlessly entertaining for the protein >> crystallographer. ;) >> >> Cheers, >> >> _______________________________________ >> Roger S. Rowlett >> Gordon & Dorothy Kline Professor >> Department of Chemistry >> Colgate University >> 13 Oak Drive >> Hamilton, NY 13346 >> >> tel: (315)-228-7245 >> ofc: (315)-228-7395 >> fax: (315)-228-7935 >> email: rrowl...@colgate.edu >> >> >> On 3/7/2012 11:20 AM, Uma Ratu wrote: >> >> Dear All: >> >> I try to add water to my model. >> >> Here is how I did: >> Coot: Find Wates >> Map: FWT PHWT; 1.8 rmsd; Distances to protein atoms: >> 2.4 min/3.2 max >> >> Coot found 270 water molecules. >> >> I then examed these waters. Most of them had ball shape. Some had two or >> more balls together. Some had irregular shape (not glabol shape). >> >> I run Water Check. The program did not find any mis-matched water. >> >> Here is my question: how could I tell the waters are real? Or something >> else? >> >> Thank you for advice >> >> Ros >> >> >> >> >> >
