Thanks to Markus Rudolph for the solution/workaround. The python command `coot.move_waters_to_around_protein(0)` where the number is the molecule number (0 in this case), does the trick. After running this command, there is console output indicating what was done.
Perhaps the menu item is not wired up correctly since nothing happens in the console output. -Chip [cid:logo_c70edd4a-e7f0-4d54-be6f-d03f53f0c961.png] Charles Lesburg Senior Vice President, Structural Biology odysseytx.com<https://protect.checkpoint.com/v2/___https:/odysseytx.com/___.YzJ1Om9keXNzZXl0aGVyYXBldXRpY3M6YzpvOmJkOGFjYWVhZjlkYWRhMThlM2ZkMDQ2YTQ0ZWZjN2Q5OjY6NDI5MTo4Y2M4ZjgyYWU5OGQ2MjBkZjNhODFmZWQwZjBjMzBiYTA5ZThiMzUxNjdiMDZlMzFkMGJmMzkxYTlkOWQxYWNhOnA6RjpO> This message is for the named person's use only. It may contain confidential, proprietary or legally privileged information. If you receive this message in error, please immediately delete it and all copies of it from your system, destroy any hard copies of it and notify the sender. ODYSSEY THERAPEUTICS, INC. ("ODYSSEY THERAPEUTICS") reserves the right to monitor all e-mail communications through its networks. ODYSSEY THERAPEUTICS cannot be committed by this e-mail or warrant the accuracy or validity of any information presented. Any views expressed in this message are those of the individual sender. From: Chip Lesburg <[email protected]> Date: Thursday, May 21, 2026 at 12:31 PM To: Mailing list for users of COOT Crystallographic Software <[email protected]> Subject: Coot 1.x: Arrange waters around protein? For a structure with multiple protomers in the asymmetric unit (chains A and B), I want to pick a different arrangement of chains A and B in the asymmetric unit using crystallographic symmetry. In The Old Days, I would use the “Arrange Waters Around Protein” menu item to move the lonely waters to be close to their protein mates, but in Coot 1.3.1 I don’t think that this menu item does anything. No waters change position and I don’t see anything in the console to indicate that anything happened. Any ideas? Chip ######################################################################## 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/
