Dear all,
On Sat, May 30, 2020 at 03:40:53PM +0100, Eleanor Dodson wrote:
> My pennysworth. If you find your maps look better after the
> anisotroy correction use it, but it may be helpful to those wo want to mine
> your data if you deposit the whole sphere..
Agree (which is what e.g. we provide when using STARANISO via autoPROC
[1]).
And in the same vein: those depositing isotropically truncated data
should consider also providing data to a higher diffraction limit to
give a potentially more accurate picture (if there is even a slight
indication of anisotropy - which there often is).
I find it very helpful even looking at an idealised (and therefore
simplified) picture of anisotropy as in
http://staraniso.globalphasing.org/anisotropy_about.html
We can consider
(1) for refinement:
(1a) green+red, i.e. spherical (i.e. isotropically) truncated
data
(1b) green+blue, i.e. anisotropycally truncated data
(2) for deposition:
(2a) green+red => full sphere, but dropping real observations
(blue)
(2b) green+blue => all observations, but not providing
insignificant/weak data (red) in all directions
(2c) a sphere to the "tip" of blue (i.e. anisotropic diffraction
limit) => all observations and all insignificant/weak data
Cheers
Clemens
[1] https://www.globalphasing.com/autoproc/ - which gives a mmCIF file
with (2a), (2b) and (2c) ready for deposition.
> eleanor
>
> On Sat, 30 May 2020 at 09:36, Robbie Joosten <[log in to unmask]>
> wrote:
>
> > Hi Everyone,
> >
> > I've been looking at some recent PDB entries that have much lower
> > spherical) completeness than reported in the coordinate file. One reason
> > for this is that the data were anisotropicly truncated, another reason is
> > some mess-up with the deposition of the reflection data. There is a lot of
> > discussion about the former practice and I don't want to go in to that, but
> > the second one is obviously an error. Now how do I distinguish these cases?
> >
> > Sometimes, you can look at the reported number of reflections and compare
> > that to the deposited reflection file and you will find that something has
> > clearly gone wrong. However, the reported number of reflections is not
> > entirely reliable because of other issues so I'd rather not use it. If you
> > use PDBpeep (e.g. for 6rjy) you can see something is wrong, but that is
> > completely visual. Is there a tool in CCP4 that reports both spherical and
> > ellipsoidal completeness (on merged reflection data)? That would make it
> > easy to distinguish such cases.
> >
> > Cheers,
> > Robbie
> >
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--
*--------------------------------------------------------------
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park
* Cambridge CB3 0AX, UK www.globalphasing.com
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