There is also a standalone findwaters executable from Coot if you prefer a
command line tool to using the library:
> findwaters
Usage: findwaters --pdbin pdb-in-filename --hklin mtz-filename --f
f_col_label --phi phi_col_label --pdbout waters-filename --cifout
waters-filename --sigma sigma-level --min-dist min-dist-to-protein
--max-dist max-dist-to-protein --flood --flood-atom-radius --chop
--mapin ccp4-map-name can be used instead of --hklin --f --phi
where pdbin is the protein (typically)
and pdbout is file for the waters.
The default sigma level is 2.0
Use --chop to remove waters below given sigma-level
In this case, pdbout is the modified input coordinates
Use --flood to fill everything with waters (not just water peaks)
and --flood-atom-radius to adjust contact distance
(default 1.4A).
On Tue, 25 Nov 2025 at 17:19, Martin Noble <
[email protected]> wrote:
> Coot and the gui free library versions thereof can provide a very long
> list of candidate water positions !
>
> Sent from Outlook for iOS <https://aka.ms/o0ukef>
> ------------------------------
> *From:* CCP4 bulletin board <[email protected]> on behalf of Wild,
> Conor (DLSLtd,RAL,LSCI) <[email protected]>
> *Sent:* Monday, November 24, 2025 12:15:26 PM
> *To:* [email protected] <[email protected]>
> *Subject:* [ccp4bb] Experience with Automated Water Completion Software
>
>
> ⚠ External sender. Take care when opening links or attachments. Do not
> provide your login details.
> Hey folks, I was just wondering what people's experience with automated
> water completion methods was.
>
> I'm hoping to experiment with blind water placement into PanDDA event maps
> in the near future, which is obviously not a use case any of these methods
> were designed for.
>
> I've got a fairly reliable method for evaluating waters in these maps
> given candidate positions, but I was hoping to avoid reimplementing the
> generation of the candidate water model by hooking into an existing
> framework. As I'm fairly happy with the evaluation I'm actually not very
> concerned about false positive errors, and so a method that can avoid false
> negatives at the cost of many false positives is actually fairly ideal.
>
> PanDDA event maps are obviously real space maps that are highly
> non-crystallographic in the sense that large parts of the unit cell are
> masked to zero, which means that software that is real space native would
> probably be preferable, but reciprocal space is only an FFT away so I doubt
> it matters. Structural models are still related to the map unit cell by
> symmetry rather than offsets so cryo-em software might take some hacking
> but that also seems fine!
>
> Thanks!
> Conor
>
> Diamond Light Source Ltd
>
> Diamond House
>
> Harwell Science & Innovation Campus
>
> Didcot Oxfordshire OX11 0DE
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