Thanks all - also for jogging my memory.
Peter, I think Garib ended up doing something statistically
sophisticated, but I couldn't track down the slides or documentation I
remember seeing somewhere. But I didn't dig very hard, and if it's been
there since 2012, then that explains why I failed.
Thank god your supervisor and his/her ilk haven't had sole discretion
over the research funding that's been supporting the algorithm and
method developers all these decades; if they had, we'd still in the
year 2020 be wasting millions per project just to get those 200um
crystals that yield the signal needed for the ancient algorithms to
recognise the presence of a diffraction spot.
The other quiet revolution in structural biology: algorithms.
Frank
On 29/04/2020 21:53, Petrus Zwart wrote:
I am not quite sure how it is done in Refmac, but in phenix it works
as follows
- difference maps are gradient maps for a least squares target and
they do not contain any amplitude contamination from twinning.
- Fo type maps are computed either via classic detwinning (solving the
linear equations) or this is done using some proportionality rule like
James and Eleanor allude to.
An alternative way would be use something like this relation
Map coefficients we want: 2Fo-Fc
Realize that 2Fo - Fc = Fc + 2(Fo-Fc)
and compute
Fcalc + 2*difference map*magic scale factor
It is a bit of a hack, no FOM's etc and I worry about bias. It would
be far better to get map coefficients from the joint distribution of
the structure factors that take into account twinning. In this way,
you can handle experimental error as well in a proper fashion. I
wouldn't be surprised if this happens in Refmac, it doesn't in Phenix
(yet).
My PhD supervisor's advice always holds btw: "Grow better crystals"
Regards
Peter
On Wed, Apr 29, 2020 at 12:40 PM James Holton <jmhol...@lbl.gov
<mailto:jmhol...@lbl.gov>> wrote:
Yes, they are "de-twinned". There is really no other way to do it.
Without de-twinning you'd be looking at a map of two overlapping
structures. How do you turn a single observation of the sum of
intensities from two different hkls into two different Iobs
values? You
need to know the ratio. The twin fraction is one way, but once it
gets
close to 0.5 the "de-twinning" gets very noisy. I believe what the
refinement programs do is use the ratio of the two Fcalc^2 values in
order to "split" the Iobs value. Doesn't that introduce "bias"?
Yes, of
course it does. That's one of the many reasons why twinning sucks.
Now, of course, there are probably fancy weighting schemes that make
things a bit better, but rather than speculate I'd ask the program
authors themselves. The best thing, of course, is to refine until
Icalc
becomes more accurate than Iobs, which is the typical result of
small-molecule refinements. I expect that is why they are not
nearly as
afraid of twinning as we are.
-James Holton
MAD Scientist
On 4/28/2020 2:19 PM, Frank von Delft wrote:
> Hi all - feel free to point me to the docs if it's already clear
> somewhere:
>
> When refmac generates 2mFo-DFc maps after twinned refinement,
are they
> the "untwinned" view of the electron density? I.e. with the
twinnig
> convoluted out by his statistical magic?
>
> I remember Garib mentioning the ambition a few years ago; but I've
> not been paying enough attention to remember if it's actually
> implemented, or still in progress (because it's hard).
>
>
> Thanks
> Frank
>
>
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--
------------------------------------------------------------------------
P.H. Zwart
Staff Scientist
Molecular Biophysics and Integrated Bioimaging &
Center for Advanced Mathematics for Energy Research Applications
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
PHENIX: http://www.phenix-online.org <http://www.phenix-online.org/>
CAMERA: http://camera.lbl.gov/
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