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<div class="moz-cite-prefix">Okay, so could one build them and
restrain their positions and occupancies to those of the high res
structure?<br>
<br>
The point is: if you've seen a 1st shell water in conserved 20
structures, the chances of it not being there are in fact rather
slim - which is the identical assumption we make to justify NCS.<br>
<br>
<br>
On 25/11/2014 07:11, Pavel Afonine wrote:<br>
</div>
<blockquote cite="mid:54742BAE.9080204@lbl.gov" type="cite">
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No, this is different. Note: you restrain to high-res structure,
not add it to the model.<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 11/24/14 10:54 PM, Frank von Delft
wrote:<br>
</div>
<blockquote cite="mid:547427B0.5040002@sgc.ox.ac.uk" type="cite">
<div class="moz-cite-prefix">Well, we happily restrain (these
days) low resolution structures to high resolution
structures. I see no philosophical difference. <br>
<br>
<br>
On 25/11/2014 05:58, Pavel Afonine wrote:<br>
</div>
<blockquote cite="mid:54741A8A.4000208@lbl.gov" type="cite"> Hi
Guenter,<br>
<br>
while I clearly understand your motivations, I don't feel very
comfortable with placing explicit atoms that are not supported
by the data. <br>
<br>
The fact that those atoms are present in high-resolution
structure does not mean that they are also present in
low-resolution structure. You can argue that adding these
waters improves Rfree and you may think of it as an
improvement. However, as a counterargument one can say that
R-factor is a global metric that is unlikely to be sensitive
to adding/removing just one single molecule. Therefore, while
adding bulk of "structured" waters may be an improvement in
general this still does not mean that all the waters you add
are true and good ones. Say what if 70% of them are good and
30% are rubbish? In this case still Rfree may improve because
you add more good water than bad, but adding bad ones is
counterproductive anyway and introduces model bias and thus
must be avoided.<br>
<br>
All the best,<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 11/17/14 1:33 AM, Guenter
Fritz wrote:<br>
</div>
<blockquote cite="mid:5469C0DE.5040802@uni-konstanz.de"
type="cite">
<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">
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>
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