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Re: [ccp4bb] Water

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
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Subject: Water
From: Uma Ratu rosiso2011 {- at -} GMAIL {- dot -} COM
Date: 2012-03-07
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Subject: Re: Water
From: Roger Rowlett rrowlett {- at -} COLGATE {- dot -} EDU
Date: 2012-03-07



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. ;)



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: rrowlett@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


Here is my question: how could I tell the waters are real? Or
something else?


Thank you for advice






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