Does the diffraction pattern change if you shoot the crystal from phi
= n or n+180 deg (a la inverse-beam geometry)? I was thinking it was
identical, but I am not sure now--is it a mirror image? Maybe
different space groups are different?

JPK

On Fri, Feb 11, 2011 at 10:35 AM, James Holton <[log in to unmask]> wrote:
>
> The indexing ambiguities do not include anomalous pair confusion because
> there is no way to rotate the lattice to make every h,k,l overlap with
> -h,-k,-l.  I.E. you can't rotate your left hand to superimpose it on your
> right.  The only way to mix those up is to change the sign of some detector
> geometry parameter (I.E. looking in a mirror).
>
> That said, anomalous differences tend to be very weak and noisy in all but
> the most exotic cases of macromolecular diffraction.  Twinning makes this
> worse because you are (to a first order approximation) averaging DANO(h,k,l)
> with DANO(k,h,-l) and the result will tend to be closer to zero than either
> one taken individually.  However, the biggest source of error in LCLS
> datasets at the moment is partiality.  Basically, you only get one shot per
> crystal, you can't rotate it appreciably in the 70 fs exposure time, the
> beam is a laser so there is essentially no divergence or dispersion, and the
> crystals are so small as to be one mosaic domain each, so there is no
> "mosaic spread".  The "3D profile" of the spots is therefore dominated by
> the finite size of the crystal itself (Sherrer broadening).  We were
> actually worried for a while that we wouldn't see any spots at all at LCLS!
>
> So, everything is a partial, and we currently don't have postrefinement
> software that can model the shape of each crystal and give us a partiality.
>  At least, not in a reasonable amount of time.  If we spent 30 s on each of
> the 3 million images, we would still be processing them for a few more
> years.  So, for the first run, it was decided to jut average out the
> partiality errors.  For example, unknown partiality means that each spot is
> measured with 100% error (at best), but if you have 700 of them, then the
> expected error of the average is ~3%.  John Spence called this a "Monte
> Carlo integration", and it turned out to be a really good idea.  We measured
> the error of the average by splitting the images into two heaps and
> comparing the merged datasets that resulted from each heap.  I proposed
> calling this "R-internal" for internal agreement, since a traditional Rmerge
> does not really apply.  However, I admit that for the PDB deposition I
> entered R-internal as "Rmerge".  Technically, R-internal is exactly what an
> Rmerge used to be: the R-factor between data from different crystals.
>
> Personally, I think "the way" to crack this "twin problem" is to scale all
> the data and look at the partial intensity histograms for each spot.  In
> situations where the "true" values of h,k,l and k,h,-l have radically
> different intensities, there will be a bimodal distribution, and that will
> allow us to re-index the ~700 images that contained a spot from one of those
> two hkls.  Which group to flip (the bright ones or the dim ones) is an
> interesting question, but probably the dim ones, since they are the least
> consistent with the average intensity.  Might need to try both.  After
> re-mergeing and re-scaling, there will be another hkl with the strongest
> bimodal distribution, and then you iterate.  That's the idea anyway.
>
> -James Holton
> MAD Scientist
>
> On 2/10/2011 6:32 AM, Jacob Keller wrote:
>>
>> Would it be true that the anomalous differences could not be measured
>> in these types of datasets, because one would not know which
>> Friedel/Bivoet reflection one is measuring in a given frame? Perhaps,
>> given anomalous signal, there would be a way to tease out which
>> orientation one was looking at from the correlations of the
>> signs/magnitudes of anomalous-scattering-induced deviations from the
>> mean intensities (derived from the whole dataset) for all of the
>> relections observed in each frame? I guess this might also detwin the
>> data?
>>
>> JPK
>>
>> On Thu, Feb 10, 2011 at 7:17 AM, Anastassis Perrakis<[log in to unmask]>
>>  wrote:
>>>>
>>>> Anyway, I thought that was a cool idea, but like so many other cool
>>>> things, it had to be cut from the Nature paper.  Admittedly, the problem
>>>> has
>>>> not actually been solved yet.  This is why we used REFMAC in TWIN mode.
>>>
>>> Is that a hint on the:
>>>
>>> a. wisdom of the editor
>>> b. wisdom of 'the third referee'
>>> c. wisdom of the dogma 'five years of eight eight lifes in 2000 words'
>>> d. All of the above
>>>
>>> ;-)
>>>
>>> A.
>>>
>>
>>
>
>



-- 
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: [log in to unmask]
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