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<div class="moz-cite-prefix">Dear Pavel,<br>
<br>
yes, such an exact prediction of ordered water molecules might be
very helpful. I was sure that somebody else had this idea already.
<br>
I was playing around with a few datasets truncated a low
resolution (3.5 - 4.0 A) and then compared Rwork/Rfree using an
input model with and without water molecules. Clearly the water
molecules had a large contribution in the refinement of� these
artificially truncated datasets. Sascha pointed me to an example
in your paper from 2002:<br>
<br>
Lunin, V.Y., Afonine, P. & Urzhumtsev, A.G. (2002)
"Likelihood-based refinement. 1. Irremovable model errors.". Acta
Cryst., A58, 270-282.
<br>
<br>
I had a look into the� literature to get an idea and found several
programs evaluating the inner shell water molecules and some
programs predicting water positions. I had a try only on a few
programs. I found that a nice summary is given in the publication
on an approach called WaterDock:<br>
<br>
Ross GA, Morris GM, Biggin PC (2012) "Rapid and accurate
prediction and scoring of water molecules in protein binding
sites." PLoS One 7(3):e32036. <br>
<br>
But before analyzing many structures and see whether it might work
in general,� my aim is much simpler. I have high resolution
structures of with water molecules and try to implement the
ordered water molecules into the refinement of a protein complex
at low resolution. My approach was maybe a bit of naive so far but
I am sure there is good way to do that. <br>
<br>
Best wishes, Guenter<br>
<br>
</div>
<blockquote cite="mid:546928AF.5090206@lbl.gov" type="cite">
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Hello,<br>
<br>
I tried this idea back in 2004. In a nutshell: using all (or
categorized subset of) structures in PDB we can learn about
distribution of structured water and given this knowledge we can
build an a priori contribution of scattering arising from such
water to the scattering of any given new structure or a structure
at low resolution (where the water is not visible in maps).<br>
<br>
Either I did not spend enough time on this or the idea wasn't
viable, but one way or another this did not work in my hands. I
think it may be worth revisiting this 10 years later! Perhaps I
would do it better now than back then!<br>
<br>
All the best,<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 11/16/14 2:19 PM, Nathaniel Echols
wrote:<br>
</div>
<blockquote
cite="mid:CALeAa1M3mUeYcWEYNEBjtCt21UcSExt+o-j8P-mnDXOsUtN+YQ@mail.gmail.com"
type="cite">
<div dir="ltr">I will leave it to others to debate the wisdom of
this strategy, but to answer the purely technical question:
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sun, Nov 16, 2014 at 2:06 PM,
Guenter Fritz <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guenter.fritz@uni-konstanz.de"
target="_blank">guenter.fritz@uni-konstanz.de</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Is it
possible to use protein and water atoms from the
reference models to generate restraints for the low
resolution refinement?<br>
</blockquote>
<div><br>
</div>
<div>I don't think so.� You'll probably find it easier to
refine the atoms separately, i.e. one run with reference
model and the individual sites selection set to "not
resname HOH", followed by a run with harmonic restraints
on waters and selection "resname HOH".� Alternately, you
could try applying harmonic restraints to the entire
model, although I suspect that the waters and protein
require different weights (or sigmas).</div>
<div><br>
</div>
<div>-Nat<br>
</div>
</div>
</div>
</div>
</blockquote>
<br>
<br>
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