[3dem] Placing waters

[radu at mrc-lmb.cam.ac.uk]

Hi Dmitry,

There is no substitute to looking at the map I would say, and there would a
lot to miss of course, because high resolution maps are so beautiful! Stephen
is a most experienced crystallographer, so would certainly use the Coot
functions for finding and validating waters. ARP/wARP is also very powerful at
making sense of solvent (although I have't tried the EM version yet, it is on
ccp4).

Regarding the more general question, the chemistry must simply make sense.
Water-protein interactions are well established from high-resolution
crystallography, there is a lot of literature on this. PMID: 15306376  is a
good starting point for those interested.

Best wishes,

Radu


> 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
> 10010 North Torrey Pines Road, La Jolla, CA 92037
> T: 858-453-4100 x1155
> 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
> --
> ********************************************************************** Dr.
Stephen Cusack, FRS
> Head of EMBL Grenoble
> Group leader in the structural biology of protein-RNA complexes and viral
proteins
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> Radu Aricescu
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-- 
Radu Aricescu
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44-(0)1223-267049
fax: +44-(0)1223-268305
www: http://www2.mrc-lmb.cam.ac.uk/group-leaders/a-to-g/radu-aricescu