Dear All: I appreciate for your comments and inputs.
Thank you Uma On Thu, Mar 8, 2012 at 12:16 AM, Shekhar Mande <shekhar.ma...@gmail.com>wrote: > Well....just to add, it has been our contention that many of the metal > ions have been modelled as waters in several structures- due perhaps to the > lack of sufficiently high resolution data. We published some of the > potential metal binding sites in many structures a few years ago: > > Proteins. 2008 Mar;70(4):1206-18. > > Shekhar > > > On Thu, Mar 8, 2012 at 9:42 AM, Parthasarathy Sampathkumar < > spart...@gmail.com> wrote: > >> Dear Uma, >> >> The water pictured in W12-1.jpg: could this be a potential metal ion? If >> you flip the side chain on Asn at 3.08Angstrom, then this has 3 or 4 >> coordination with oxygen atoms. So, provided your crystallization condition >> or buffer contains metal ion(s), you could attempt to see if it fits better >> with a refinement cycle. >> >> May be a similar situation with the water described in W11-1.jpg as well? >> Difficult to say from these figures. >> >> COOT within the "validate" wizard has an option to search for >> "hihgly-coordinated waters" like the one you have pictured. >> >> Hope this helps, >> Partha >> >> On Wed, Mar 7, 2012 at 4:21 PM, Uma Ratu <rosiso2...@gmail.com> wrote: >> >>> 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 >>>> >>>> >>>> >>>> >>>> >>> >> > > > -- > Shekhar C. Mande (शेखर चिं मांडे) > Director, National Centre for Cell Science > Ganeshkhind, Pune 411 007 > Email: shek...@nccs.res.in, direc...@nccs.res.in > Phone: +91-20-25708120 > Fax:+91-20-25692259 > >
