[COOT] Coot v1 rotation smoothness (or lack thereof)

2022-05-19 Thread Phil Jeffrey
After (finally) getting Coot to work install via Homebrew I find that 
the rotation smoothness is much, much worse compared to v0.9.8.1, when 
the window is enlarged via the buttons at the lower right of the menu 
from 1800x1500 -ish to 2900x2300 -ish which is a more useful size.
This seems almost independent of map radius (within reason) or if I have 
just a simple difference map with relatively few lines drawn.


I tried playing with shader settings but Basic and Plain do not increase 
draw speed and they shrink the drawn area into 1/4 of the area of Fancy. 
 And they don't draw any faster in that smaller viewport.



Coot 1.0.06-pre

iMac Retina 5K, late 2015, High Sierra

Any suggestions for tweaking ?

Phil Jeffrey
Princeton



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Re: [COOT] absolute map levels

2022-05-02 Thread Phil Jeffrey
Later in refinement the missing water molecule will also have a higher 
peak because the phases will be better (e.g. your R-free is 20% lower). 
 The fact that it was placed later in refinement both reflects the RMSD 
effect but also reflects the fact that it's more obviously a legitimate 
water late in refinement.


This isn't a phenomenon restricted to macromolecular refinements.

The peak heights are not the same during refinement, and I scroll around 
the levels all the time to look for things that I might have missed, 
including in one case an entire monomer that *was* lurking in the noise 
level in the map since it was being clobbered by solvent flattening.  It 
was also partial occupancy.


While e/Å^3 is probably a better measure than RMSD, it's not a panacea 
and there is no universal ideal contour level - it must be chosen on its 
merits every single time.  The contour level you want to use while 
looking at the partially-occupied monomer is unquestionably lower than 
the one you'd use while looking at the best-ordered monomer in the map - 
and there's always better and worse parts of the asymmetric unit and 
better and worse parts of any monomer.  Changing the units has no effect 
on that.


Phil Jeffrey
Princeton



On 5/2/22 3:19 PM, Dale Tronrud wrote:
    If you view the value of the density as the number of electrons per 
cubic Angstrom relative to the local average it is both accurate and 
precise.  This framing avoids the most serious problems with a measure 
based on the rms, such as the problem that the "rms" depends on the 
particular volume of space calculated (how much of the bulk solvent 
region is included) and what stage of refinement is the project (late in 
refinement the difference map will have a much smaller rmsd and the same 
missing water molecule will have a much taller peak.).


    When a map is viewed at a particular contour based on e/A^3 a 
missing atom will tend to have the same difference map peak height in 
all stages, while the height will vary all over the place when the 
contour is based rmsd.  When I watch people model building I see many 
scrolling the contour level up and down without regard for the numeric 
value of the level, apparently just choosing a value that makes the 
peaks appear the way they prefer the peaks to appear.  This way of 
choosing a contour level seems dangerous to me as it seems to bias the 
appearance of the map towards the modeler's expectation.


Dale Tronrud

On 5/2/2022 11:51 AM, Tim Gruene wrote:

Hi Ian,

thanks - this makes it clear(er) to me. The unit [e/A^3] suggested an
accuracy to me that isn't really there, while rmsd felt more what it
really is (maybe only due to habit and training).

Cheers,
Tim

On Mon, 2 May 2022 15:27:13 +0100
Ian Tickle  wrote:


Hi Tim

I would say that it's not the displayed map density value in whatever
units that's arbitrary: it's completely defined as the true density
on an absolute scale minus the F000 contribution ('b' below) and
optionally divided by the RMS.  It's just that we don't have a good
estimate of F000 and as I said it's your choice of contour level
that's arbitrary.

The Buster map is scaled to the model so is on an absolute scale.  We
can write the linear transformation:

rho[map] = a.(rho[true] - b)

where the scale factor a = 1 so that rho[map] is on the same absolute
scale as rho[true] (i.e. differences in rho[true] are equal to
differences in rho[map]), and b is the F000 contribution.

Cheers

-- Ian


On Mon, 2 May 2022 at 15:04, Tim Gruene 
wrote:


Hi Paul,

I'd rather you comment on the unit "e/A^3" displayed at the top of
my Coot canvas when I change the contour level of a map. Is this
arbitrary?

I noticed that the Buster Wiki states that their FWT is on an
absolute scale. Would there be a paper or url to advance my rusty
habits?

Cheers,
Tim


On Mon, 2 May 2022 13:52:05 +0100 Paul Emsley
 wrote:

On 02/05/2022 12:44, John R Helliwell wrote:

I was intrigued by Paul’s 5sigma Fo-Fc default cut off, rather
than 3.



It's 5.6 now :-)

 



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