Re: [ccp4bb] Water

[Roger Rowlett]

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