On Wed, 2021-06-02 at 15:56 +0100, Paul Emsley wrote: > On Tue, 2021-06-01 at 20:45 +0100, David M Dranow wrote: > > Does anyone have a decent set of refinement parameters for Coot 0.9.5 in > > linux? My colleagues and I find that using > > the "r" shortcut causes most waters to fly off and center on carbons, > > sometimes as far away as 45 Å! I've tried to > > change the overall weight and Lennard-Jones epsilon, and Geman-McClure > > alpha and I find no combination that keeps > > all > > waters within the density that they already are in. I'd be happy to > > provide a model and map to demonstrate this > > phenomenon. Our current work-around is to use R, but this is not ideal. > > If anyone has any idea how to fix this, we > > would greatly appreciate any advice. > > > > This reminds me of the exchange about the new refinement on CCP4BB some time > ago. Briefly, people reported problems > that > I wasn't seeing. > > So I'd like to see what you see. Either make a screencast of your session or > conjure up a coordinates file and a list > of coot operations that makes the issue apparent. Until then, I am in the > dark. > >
Thanks to files provided by Philip Kiser I now see the problem. First, one had to create an unorthodox model - one that included a bad non-bonded contact distance to a water (this is not something I do) Second, one had to refine just the water, and not the residues to which it was hydrogen-bonded or other atoms in the environment (this is not something I do either) By its nature, refinement of this sort will give a considerable kick to a bad water. I have therefore introduced an optional "Soft Mode" for non-bonded-contact restraints. set_refinement_use_soft_mode_nbc_restraints(flag) This is available now in the repo and will be in the next release. But for me, the lessons are: Don't create models with poorly placed waters in the first place. But if you do, don't do isolated refinement of the waters one by one. 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/
