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Re: [ccp4bb] Water

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CCP4bb <-- 2012 <-- March 2012 <-- 07 March 2012
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Subject: Re: Water
From: Uma Ratu rosiso2011 {- at -} GMAIL {- dot -} COM
Date: 2012-03-07
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Subject: Re: Water
From: Uma Ratu rosiso2011 {- at -} GMAIL {- dot -} COM
Date: 2012-03-07

Subject: Re: Water
From: Joel Tyndall joel {- dot -} tyndall {- at -} OTAGO {- dot -} AC {- dot -} NZ
Date: 2012-03-07

Hi Uma,

Water has the capability of making 4 h-bonds, 2 from the two non-bonding pairs of electrons (h-bond acceptors - expect an N-H from an amide for example) as well as the two hydrogens (h-bond donors). I would refine all those waters and assume they are waters. If the distance to the other atoms is between 2.5-3.2 then you can assume the water to be correct. In many cases waters will h-bond (only) to other water molecules.

The B-factor is displayed in Coot along the bottom (left) when you middle click on an atom. You can also see the B-factor when you read the pdb file as text

Hope this helps.

Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
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From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Uma Ratu
Sent: Thursday, 8 March 2012 10:22 a.m.
Subject: Re: [ccp4bb] Water

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:

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 water.

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

Thank you for advice


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