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 <joel.tynd...@otago.ac.nz>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 <rrowl...@colgate.edu> > 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: 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**** > > **** > > **** > > **** > > ** ** >
