Re: [COOT] Wild refinement of waters
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 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=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=1 > To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=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/
Re: [COOT] Wild refinement of waters
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=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=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/
Re: [COOT] Wild refinement of waters
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. Regards, Paul. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=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/
Re: [COOT] Wild refinement of waters
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 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=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=1 > > > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=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/
Re: [COOT] Wild refinement of waters
Hi Everyone, I also have observed the unusual behavior with waters not staying in the density after using the "r" key binding. In many cases, there aren't any egregious clashes that could be forcing the water out of the density. I tried changing the Lennard-Jones setting in the refine/regularize panel but it didn't help. 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) 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. 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. Regards, Philip On Wed, Jun 2, 2021 at 8:03 AM Paul Emsley 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 > 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=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=1 > > > > > > > To unsubscribe from the COOT list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 > > > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=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=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/
Re: [COOT] Wild refinement of waters
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 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 > > > 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=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=1 > > > > > > > > > > > > > > > > To unsubscribe from the COOT list, click the following link: > > > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 > > > > > > > > > > > > > > > > To unsubscribe from the COOT list, click the following link: > > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 > > > > > > > > This message was issued to members
