After more off-list correspondence, I further investigated the water refinement issue. I now think that the problem isn't what I thought it was.
A few months ago, I had noticed how frustratingly long it took for Coot to start moving the atoms when RSRing a fragment into a cryo-EM map. I increased the initial step size and the RSR was noticeably quicker. Good. I tested that the new step size made sense for refinement of protein in an x-ray map - and it was. Good. However, what I didn't check was the most minimal case, i.e. what we have been discussing here: the refinement of just one (water) atom. And hence the problems you've been seeing (and I haven't). So today I changed the initial step size back to how it was calculated last year and the water refinement stabilized - and that is without needing soft harmonic-approximation NBC restraints. As of now, the initial step size depends on the number of atoms, so, I think, we can satisfy both scenarios. I have pushed a commit to the repo (7b7a7e2db0c6760c4467c6de0c8d2ac5364624c9) and the fix will be in the next release. Paul. ######################################################################## 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/
