After more off-list correspondence, I further investigated the water refinement
issue. I now think that the problem
isn't what I thought it was.
A few months ago, I had noticed how frustratingly long it took for Coot to
start moving the atoms when RSRing a fragment
into a cryo-EM map. I
On Thu, 2021-06-03 at 09:02 -0700, Philip Kiser wrote:
> Thank you for spotting the problem and introducing the new restraint. I have
> to say that it was easy to get in the
> habit of creating poorly placed water molecules when filling difference map
> peaks as the prior refinement method for
>
Hi Paul,
Thank you for spotting the problem and introducing the new restraint. I
have to say that it was easy to get in the habit of creating poorly placed
water molecules when filling difference map peaks as the prior refinement
method for isolated waters would just move them into the nearby
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
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.
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
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
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
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
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,
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