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There is also a function in Coot to place waters into bumps of density (Other Modeling Tools —> Find Waters). But you still have to go through the map/model and delete ones that are not appropriate.
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<div class="">On that note, I have a broader question for the list of how one would validate the water placements? We have the advantage that we’re working with multiple high-resolution maps that are otherwise (nearly) identical, with the exception of bound
ligand. Therefore it is actually straightforward (albeit tedious) to cross-validate the waters using independently refined maps, even at borderline resolutions. However, this is not the case when you only have a single map with which to work. In such a case,
you have to look at the surrounding chemistry, consider the size of the bump of the density, perhaps use tools to quantify the resolvability of the bump. One example of the latter was recently posted on bioRxiv (<a href="https://www.biorxiv.org/content/10.1101/722991v2" class="">https://www.biorxiv.org/content/10.1101/722991v2</a>).
Coot also has a validation tool, which considers the B-factor the placed water, the closest contacts, etc. </div>
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<div class="">My question to the list is: does anyone have good suggestions for validating water molecules, especially at borderline resolutions? Is there a set standard? </div>
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<div class="">Dmitry </div>
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<div class="">On Dec 11, 2019, at 10:22 AM, <a href="mailto:radu@mrc-lmb.cam.ac.uk" class="">
radu@mrc-lmb.cam.ac.uk</a> wrote:</div>
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<div class="">Hi Stephen,<br class="">
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We use Coot+Phenix and they work beautifully, just like in the X-ray world :-)<br class="">
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Best wishes,<br class="">
Radu<br class="">
<br class="">
<blockquote type="cite" class="">Dear All,<br class="">
<br class="">
What programs do people use to place and refine waters in high<br class="">
resolution cryoEM maps ?<br class="">
<br class="">
thanks<br class="">
<br class="">
Stephen<br class="">
<br class="">
--<br class="">
<br class="">
**********************************************************************<br class="">
Dr. Stephen Cusack, FRS<br class="">
Head of EMBL Grenoble<br class="">
Group leader in the structural biology of protein-RNA complexes and viral<br class="">
proteins<br class="">
**********************************************************************<br class="">
<br class="">
Email:<span class="Apple-tab-span" style="white-space:pre"> </span><a href="mailto:cusack@embl.fr" class="">cusack@embl.fr</a>,
<a href="mailto:stephen.cusack@embl.org" class="">stephen.cusack@embl.org</a><br class="">
Website: <a href="http://www.embl.fr" class="">http://www.embl.fr</a><br class="">
Tel:<span class="Apple-tab-span" style="white-space:pre"> </span>(33) 4 76 20 7238 Secretary (33) 4 76 20 7123<br class="">
Fax: (33) 4 76 20 7199<br class="">
Postal address: EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181,<br class="">
38042 Grenoble Cedex 9, France<br class="">
Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue<br class="">
des Martyrs, 38000 Grenoble, France<br class="">
**********************************************************************<br class="">
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-- <br class="">
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MRC Laboratory of Molecular Biology<br class="">
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