I think it is a sphere refine problem. Just use the old real space refine.. sphere refine hates clashes , so before you try to fix something you need to delete any feature which will create one..\ I argue with Paul about the philosophy but he has the expertise! Eleanor
On Wed, 2 Jun 2021 at 09:43, F.Xavier Gomis-Rüth <xgr...@ibmb.csic.es> wrote: > I have experienced the same issue with 0.9.5 for Mac. > Most strikingly, this seems to occur randomly: some waters are refined > as usual but other are shifted dozens of Å to stick to a carbon of the > model. > A similar effect is observed when refining solvents with the "x" key. > > > On 1/6/21 21:45, David M Dranow wrote: > > Hi All, > > 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. > > Thank you! > -David > > ######################################################################## > > 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/ > > > -- > > ------------------------------ > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > ######################################################################## 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/
