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Re: [ccp4bb] Water

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CCP4bb <-- 2012 <-- March 2012 <-- 07 March 2012
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From: mark Mayer mayerm {- at -} MAIL {- dot -} NIH {- dot -} GOV
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Subject: Re: Water
From: Joel Tyndall joel {- dot -} tyndall {- at -} OTAGO {- dot -} AC {- dot -} NZ
Date: 2012-03-07

Subject: Re: Water
From: Uma Ratu rosiso2011 {- at -} GMAIL {- dot -} COM
Date: 2012-03-07

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


On Wed, Mar 7, 2012 at 11:44 AM, Roger Rowlett 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: 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 water.
> Here is my question: how could I tell the waters are real? Or something
> else?
> Thank you for advice
> Ros

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