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 This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom. ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
