[3dem] Placing waters

[Dmitry Lyumkis]

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.

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 (https://www.biorxiv.org/content/10.1101/722991v2). Coot also has a validation tool, which considers the B-factor the placed water, the closest contacts, etc.

My question to the list is: does anyone have good suggestions for validating water molecules, especially at borderline resolutions? Is there a set standard?

Dmitry

Dmitry Lyumkis
Assistant Professor
The Salk Institute for Biological Studies
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E: dlyumkis at salk.edu<mailto:dlyumkis at salk.edu>
https://lyumkis.salk.edu






On Dec 11, 2019, at 10:22 AM, radu at mrc-lmb.cam.ac.uk<mailto:radu at mrc-lmb.cam.ac.uk> wrote:

Hi Stephen,

We use Coot+Phenix and they work beautifully, just like in the X-ray world :-)

Best wishes,
Radu

Dear All,

What programs do people use to place and refine waters in high
resolution cryoEM maps ?

thanks

Stephen

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Radu Aricescu
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