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 <[log in to unmask]> 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

CAMERA: http://camera.lbl.gov/

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