The Bruker integration program SAINT determines the cell at regular
intervals during the processing and uses the variations to estimate
standard uncertainties in the cell dimensions. This seems to give
sensible values, especially since it is normally applied to a set of
scans about different axes relative to the crystal.
George
On 27.07.2016 13:25, Phil Evans wrote:
> There are many issues here
>
> 1. Yes of course we should estimate the cell dimension errors and propagate them downstream from the data integration program, which should generate robust estimates of variances and importantly covariances. These will be larger at low resolution, in low symmetry (6 parameters in P1), and with narrow wedges of data. I suspect that covariances between cell lengths and angles may be quite high in some cases.
>
> 2. The current MTZ file format, both unmerged and merged, has no slot for these error estimates, and despite some moans from me and others over the years, nobody really wants to change the format as it might break lots of things. However, DIALS has a pretty complete (and extensible) model of the diffraction experiment and results, including time-dependent cell dimensions if required, and there is at least preliminary work in representing this model in a Nexus/HDF5 file as a replacement for the unmerged MTZ file, and I think this should be adopted for downstream use of unmerged data. Use of unmerged data in refinement would allow proper allowance for time(dose)-dependent structural changes, partly overlapped multiple lattices and twin fractions which vary with crystal rotation.
>
> 3. Uses for cell error estimates:
> (a) in determining the “true” point- and space-group, e.g. in Pointless, it would be useful to have some estimate of the likelihood of a slightly different unit cell produced by imposing lattice constraints (e.g. a=b, angle = 90deg, etc)
> (b) when merging data from different crystals, it would be useful to estimate whether observed differences are likely to be due to true crystal differences (non-isomorphism) rather than just errors in cell estimation. This is particularly a problem when merging data from narrow wedges of data from radiation-sensitive crystals (or in the extreme case of XFEL data). Error estimates would help in providing the “best” estimates of an average cell to go with merged data.
>
> 4. In the past when the wavelength of some synchrotron beamlines was less reliably known than it is now, I did try refining a multiplier on the cell lengths as a proxy for wavelength, in a script, and observed a very flat minimum in Rfree, trading X-ray fit for geometric fit. This suggested to me that with care it might be possible to refine at least one cell parameter, but that refining 6 parameters of a triclinic cell is likely to be dangerous, except possibly at very high resolution. However at very high resolution the cell dimensions from data processing are likely to be more accurate anyway.
>
> Just some thoughts
> Phil
>
>
>> On 27 Jul 2016, at 09:08, Dirk Kostrewa <[log in to unmask]> wrote:
>>
>> Dear CCP4ers,
>>
>> this paper nicely reflects my experience whenever I processed the same raw data with different data processing programs (HKL2000, MOSFLM, XDS): the refined unit cell constants with typical cell axes lengths around 100 A deviated already in the first digit after the dot. The reported standard deviations from the data processing programs, which are usually two orders or magnitude smaller, apparently reflect the internal precision that can be reached within each program.
>>
>> Best regards,
>>
>> Dirk Kostrewa.
>>
>>
>> On 26.07.2016 18:18, Jeffrey B Bonanno wrote:
>>> ZB published on this topic recently:
>>>
>>> Acta Crystallogr D Biol Crystallogr. 2015 Nov;71(Pt 11):2217-26. doi: 10.1107/S1399004715015503. Epub 2015 Oct 31.
>>> On the accuracy of unit-cell parameters in protein crystallography.
>>> Dauter Z1, Wlodawer A2.
>>> Author information
>>> Abstract
>>> The availability in the Protein Data Bank (PDB) of a number of structures that are presented in space group P1 but in reality possess higher symmetry allowed the accuracy and precision of the unit-cell parameters of the crystals of macromolecules to be evaluated. In addition, diffraction images from crystals of several proteins, previously collected as part of in-house projects, were processed independently with three popular software packages. An analysis of the results, augmented by published serial crystallography data, suggests that the apparent precision of the presentation of unit-cell parameters in the PDB to three decimal points is not justified, since these parameters are subject to errors of not less than 0.2%. It was also noticed that processing data including full crystallographic symmetry does not lead to deterioration of the refinement parameters; thus, it is not beneficial to treat the crystals as belonging to space group P1 when higher symmetry can be seen.
>>>
>>> Jeffrey B. Bonanno, Ph.D.
>>> Department of Biochemistry
>>> Albert Einstein College of Medicine
>>> 1300 Morris Park Avenue
>>> Bronx, NY 10461
>>> off. 718-430-2452 fax. 718-430-8565
>>> email [log in to unmask]
>>>
>>> -----Original Message-----
>>> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Andrew Leslie
>>> Sent: Tuesday, July 26, 2016 12:09 PM
>>> To: [log in to unmask]
>>> Subject: Re: [ccp4bb] Why don't we quote errors on unit cell constants in MX
>>>
>>> I think Phil Evans has been trying to get this implemented for many years. As already mentioned, errors in cell dimensions are not part of the data model for MTZ files (although I think there probably is space in the header where they could be stored). Mosflm does give error estimates for the cell parameters if the "Refine cell" option is used (but not for the cell determined by indexing), but these are not currently saved to the MTZ file.
>>>
>>> For my own part, this is simply because there has not been any real pressure from users to include this information, and there are always many other things to be done!
>>>
>>> Cheers,
>>>
>>> Andrew
>>>
>>>
>>> On 26 Jul 2016, at 16:07, Graeme Winter <[log in to unmask]> wrote:
>>>
>>>> Dear CCP4BB
>>>>
>>>> Does anyone know why we don't quote standard uncertainties on unit cell constants in the way that the small molecule community do? It would seem in the new world of multi-crystal data sets and serial crystallography some idea of the measure of ignorance would be particularly valuable.
>>>>
>>>> I'm not worried about whether they are "right" or "true" just interested in why we don't quote them...
>>>>
>>>> An example for thaumatin may look like this, for example:
>>>>
>>>> Unit cell (with estimated std devs):
>>>> 57.7841(1) 57.7841(1) 149.9963(3)
>>>> 90.0000(0) 90.0000(0) 90.0000(0)
>>>>
>>>> (in other news, there is no place to store this information in an MTZ file...)
>>>>
>>>> Thanks & best wishes Graeme
>>>>
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>>
>> *******************************************************
>> Dirk Kostrewa
>> Gene Center Munich, A5.07
>> Department of Biochemistry
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>> Germany
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--
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