On 3/5/2020 11:00 AM, Jessica Besaw wrote:
> Hello Matthias,
>
> Excellent point. Most of the the ordered water are easily visible at 2
> rmsd. The central disordered (or partially occupied) water becomes
> visible only at 1.3 - 1.4 rmsd, and it is very visible at 1 rmsd (which
> I have displayed all of the maps). In your opinion, do you think this
> would be noise?
"Noise" is a word that I hate. Usually it is just a label we put on
something that we want an excuse to ignore. If you decide to ignore
something you should be honest and have a specific reason.
Personally, I think it is sufficient reason to not place an atom when
you are unsure if an atom should be placed. With the density you have
shown, it is hard to imagine a consistent model that contains a
partially occupied water molecule in this little peak. That "water
molecule" would be inconsistent with full occupancy of the atom to the
left, but that atom already has the lowest B factor when refined at full
occupancy. These two atoms are too close together to both be present in
the same unit cell.
Without a reasonable atomic model in mind, you can't build a
reasonable model. Building a model is not simply the task of placing
atoms in peaks. The resulting structure has to make physical sense.
What hydrogen bonding network are you proposing to exist when this rare
conformation is present?
If you don't have confidence in a model, don't build it. You will be
left with this little difference map peak, and you will take a tiny hit
on your R values. Them's the breaks! Putting in an atom you don't
believe would give you those slightly smaller R values, but is that
honest? It seems to me that building a model that doesn't make
chemical sense just to lower R values borders on deception.
Whether that makes this peak "noise" is irrelevant. Maybe in five or
ten years someone will come up with a new tool for building overlapping,
partially occupied, water networks and this peak will be explained.
Would that change if this peak is "noise" or not? All we have now is a
peak that we don't have a good way to interpret.
Dale Tronrud
>
> Jessica
>
> On Wed, 4 Mar 2020 at 12:45, Barone, Matthias <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> hey Jessica
>
> a tip that might come up later on anyway: once you put every
> reasonable bit into the desity, what I like to to when facing such
> blobbs: I take a well defined water out to create a diff density at
> a position where I know it is real. Having a feeling of how much you
> have to contour the diff density at that point can give you a good
> feeling how much of noise is actually in your density right in
> between the waters..?
>
> best, matthias
>
>
> Dr. Matthias Barone
>
> AG Kuehne, Rational Drug Design
>
> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> Robert-Rössle-Strasse 10
> 13125 Berlin
>
> Germany
> Phone: +49 (0)30 94793-284
>
> ------------------------------------------------------------------------
> *From:* CCP4 bulletin board <[log in to unmask]
> <mailto:[log in to unmask]>> on behalf of Jessica Besaw
> <[log in to unmask] <mailto:[log in to unmask]>>
> *Sent:* Wednesday, March 4, 2020 6:42:34 PM
> *To:* [log in to unmask] <mailto:[log in to unmask]>
> *Subject:* Re: [ccp4bb] A question of density
>
> Hey Nukri,
>
> Here are the details: Rwork/Rfree = 0.21 / 0.23 for a 2 Angstrom
> structure
>
> I absolutely agree with you on the refinement. I did previously do
> that, and I attached the picture.
>
> What is the BB?
>
> Cheers!
>
> Jessica
>
>
>
>
>
>
> On Wed, 4 Mar 2020 at 12:20, Nukri Sanishvili <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Hi Jessica,
> You do not say how well is the rest of the structure refined.
> First, you should refine the structure best you can, without
> placing anything in the unclear blob of your interest so to
> obtain the best possible phases and hopefully improve the blob
> density as well.
> Then you should let the BB see what that density looks like.
> Looking at only the list of possibilities has very little value
> without seeing the density itself.
> Best wishes,
> Nukri
>
> On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw
> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>
> Hello friends,
>
> I have a "blob" of density in an active site of my protein.
>
> I am struggling to determine if I should place a water in
> this spot, if I should model it as a disordered water, if
> the density may be a ligand that I have not considered, or
> if it should be left as unaccounted for density. I would
> like to publish this structure without compromising the science.
>
> I have attached several possibilities that I have considered
> below.
>
> Any suggestions would be appreciated.
>
> Cheers!
>
> Jessica Besaw
>
>
>
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