On Wed, 2021-06-02 at 10:44 +0100, Eleanor Dodson wrote: > I think it is a sphere refine problem. Just use the old real space refine.. > sphere refine hates clashes,
It's not "sphere refine" that hates clashes, it's that the non-bonded contact interactions have a new model. > so before you try to fix something you need to delete any feature which will > create one.. ... during real space refinement. Yes. Or add the entity that causes the bumps to the RSR molten zone/moving atoms. > I argue with Paul about the philosophy but he has the expertise! I am open to being wrong about how RSR works, but until I see a problem, I can't fix it. Paul > > 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 ######################################################################## 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/
