On Wed, 2021-06-02 at 09:03 -0700, Philip Kiser wrote: > I also have observed the unusual behavior with waters not staying in the > density after using the "r" key binding.
Do you have an example? The "R" key (I mean not "Shift-R") should not move waters if the centred residue is not a water. > In many cases, there aren't any egregious clashes that could be forcing the > water out of the density. I wonder what "egregious" means here. Does Validate → Atom Overlaps (Coot) give you anything other than green (or nothing)? > I tried changing the Lennard-Jones setting in the refine/regularize panel but > it didn't help. Changing epsilon will change the refinement, but may well not make it behave as you want it to behave if indeed the interaction is egregious. > The issue frequently happens while placing waters into peaks identified by > difference map peak searching. Often, for > weakly bound waters, the center of the Fo-Fc peak does not overlap with the > 2Fo-Fc peak (at 1 RMSD) indeed... > and if one uses the "place water" key binding followed directly by the "r" > key binding, the water often ends up in > some distant 2Fo-Fc peak. That doesn't sound familiar. It sounds like it's getting kicked by some non-bonding interaction. > Switching to the Fo-Fc map for RSR fixed the problem but it is a little > inconvenient to be switching back and forth > between the maps. I imagine that you can create a custom toggle button in a few lines of python to do this switching. Paul. > On Wed, Jun 2, 2021 at 8:03 AM Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > > 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/ > > > > > > 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/
