Dear Zbyszek,
when you optimise a set of parameters against a set of data, I guess you
can also provide their errors. If I understand correctly, this comes
with least-squares-routines. I only pointed out that cell errors are
listed in the XDS output (provided you refine them, of course). I am
sure those errors are well defined.
Best wishes,
Tim
On 07/22/2014 06:53 PM, Zbyszek Otwinowski wrote:
> Error estimates for the unit cell dimensions in macromolecular
> crystallography belong to atypical category of uncertainty estimates.
>
> Random error contribution in most cases is below 0.001A, so it can be
> neglected. Wavelength calibration error can be also made very small;
> however, I do not know how big it is in practice. Goniostat wobble error
> is taken into account in Scalepack refinement. Crystal-to-detector
> distance is not used in postrefinement/global refinement.
>
> Due to the measurement error being very small, even small variations in
> unit cell parameters can be detected within cryocooled crystals. These
> variations almost always are _orders_of_magnitude_larger_ than measurement
> uncertainty. Current practise is not to investigate the magnitude of the
> changes in the unit cell parameters, but when beam smaller than crystal is
> used, observing variations as large as 1A is not unusual.
>
> The main question is: what the unit cell uncertainty means? For most
> samples I could defend to use values: 0.001A, 0.01A, 0.1A and 1A as
> reasonable, depending on particular point of view.
>
> Without defining what the unit cell uncertainty means, publishing its
> values is pointless.
>
>
> Zbyszek Otwinowski
>
>
>
> Hi Bernhard,
>
> A look at the methods section might give you a clue. Neither XDS nor
> XSCALE create mmCIF - files (you are talking about mmCIF, not CIF -
> subtle, but annoying difference), so that the choice is limited. I
> guess some programmer (rather than a scientist ;-) )used a simple
> printf commmand for a double precision number so the junk is left over
> from the memory region or other noise common to conversions.
>
> XDS actually prints error estimates for the cell dimensions in
> CORRECT.LP which could be added to the mmCIF file - a cif (sic!) file,
> I believe, requires those, by the way and checkCIF would complain
> about their absence.
>
> Cheers,
> Tim
>
> On 07/22/2014 01:01 PM, Bernhard Rupp wrote:
>>>> I am just morbidly curious what program(s) deliver/mutilate/divine
>>>> these cell constants in recent cif files:
>>>>
>>>>
>>>>
>>>> data_r4c69sf
>>>>
>>>> #
>>>>
>>>> _audit.revision_id 1_0
>>>>
>>>> _audit.creation_date ?
>>>>
>>>> _audit.update_record 'Initial release'
>>>>
>>>> #
>>>>
>>>> _cell.entry_id 4c69
>>>>
>>>> _cell.length_a 100.152000427
>>>>
>>>> _cell.length_b 58.3689994812
>>>>
>>>> _cell.length_c 66.5449981689
>>>>
>>>> _cell.angle_alpha 90.0
>>>>
>>>> _cell.angle_beta 99.2519989014
>>>>
>>>> _cell.angle_gamma 90.0
>>>>
>>>> #
>>>>
>>>>
>>>>
>>>> Maybe a little plausibility check during cif generation might be
>>>> ok
>>>>
>>>>
>>>>
>>>> Best, BR
>>>>
>>>>
>>>>
>>>> PS: btw, 10^-20 meters (10^5 time smaller than a proton) in fact
>>>> seriously challenges the Standard Model limits..
>>>>
>>>> ----------------------------------------------------------------------------
>>>>
>>>>
> ------------
>>>>
>>>> Bernhard Rupp
>>>>
>>>> k.-k. Hofkristallamt
>>>>
>>>> Crystallographiae Vindicis Militum Ordo
>>>>
>>>> [log in to unmask]
>>>>
>>>> [log in to unmask]
>>>>
>>>> http://www.ruppweb.org/
>>>>
>>>> -----------------------------------------------------------------------
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>
>>
>
>
> Zbyszek Otwinowski
> UT Southwestern Medical Center at Dallas
> 5323 Harry Hines Blvd.
> Dallas, TX 75390-8816
> Tel. 214-645-6385
> Fax. 214-645-6353
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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