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Re: [ccp4bb] Water

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
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Subject: Re: Water
From: Joel Tyndall joel {- dot -} tyndall {- at -} OTAGO {- dot -} AC {- dot -} NZ
Date: 2012-03-07
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Date: 2012-03-08


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

Hi, Joel:

Thank you for your comments.

Some of these waters have 4 contacts all with "O" from adjacent residues.
As "O" can be doner as well as acceptor, I would consider them as 'real'
water. Some of these 'water' have more than 4 contacts, I
would consider them as 'false'.

I lower the H-bond seeting to 2 - 3.2. This helps to reduce the noise.

>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



I found the B-factor using both ways.



Thank you very much!



Uma

On Wed, Mar 7, 2012 at 5:39 PM, Joel Tyndall wrote:

> 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
> http://www.researcherid.com/rid/C-2803-2008****
>
> Pukeka Matua
> Te Kura Taiwhanga Putaiao
> Te Whare Wananga o Otago
> Pouaka Poutapeta 56 Otepoti 9054
> Aotearoa
>
> Ph / Waea +64 3 4797293
> Fax / Waeawhakaahua +64 3 4797034****
>
> ** **
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Uma
> Ratu
> *Sent:* Thursday, 8 March 2012 10:22 a.m.
>
> *To:* CCP4BB@JISCMAIL.AC.UK
> *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****
>
> ****
>
> Uma****
>
> 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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