On 9/8/25 13:45, Daniel Larsson wrote:
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With modest-size structures, I guess there is less need for this tool.
But for large complexes at high resolution where you already have a
solvated reference structure or have used phenix.douse, this tool is
very useful.
I have some suggestions for improvements. Perhaps some of them could
get into the next version:
* Make a new object with deleted atoms
* Show how many waters were selected with the “checking” option
* Button to “delete all” after “checking”
* Ability to interactively sort the list for arbitrary property
* Toggle between V, RMSD or e/Å^3
* Histograms (thresholds indicated with a line), perhaps with
interactive/live update thresholds
* All properties should have higher/lower/between
* Break out distance to macromolecule, ion and other water
* Calculate sphericity of density (if it not too slow)
* Value of reference map, such as local resolution map in cryo-EM
* Renumber waters afterwards
* Enter custom residue name (for ions etc)
These are good suggestions and I will add (some of) them to the gui for
Coot 1.1.
I am no longer making changes to the gui for the 0.9.x series.
Paul.
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