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) Regards, Daniel From: Paul Emsley <[email protected]> Date: Monday, 8 September 2025 at 09:03 To: Daniel Larsson <[email protected]>, <[email protected]> Subject: Re: check water map level behaves unexpectedly On 07/09/2025 15:32, Daniel Larsson wrote: - I want to report a strange behavior of the “check waters” tool in Coot 0.9 (I use version 0.9.8.95). If I set “with map r.m.s.d. level less than” 3 electrons/A3 and use the “Any Chriterion” switch, it will give me all weak waters below 3. But if I use the “All Criteria”, it will give me the strong waters above 3. I wrote that code more than 20 years ago. This is the first time I've seen a bug report for it. I will fix it (both will be "lower/weak") for the next release. Thanks, Paul. VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
