Shouldn't the cell dimensions be identical in the coordinate
file and in the structure factor file? In this case they
are not.
Frances
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On Tue, 22 Jul 2014, Zbyszek Otwinowski wrote:
> The least-square procedure for unit cell parameter refinement provides very
> precise estimates of uncertainty. Why they are so precise? Because we use
> many thousands of unmerged reflections to determine the precision 1 to 6
> parameters (unit cell parameters). However, although error propagation
> through the least squares provides precision of about 0.001 A, or better in
> some cases, this is only precision not accuracy, and the precision is
> calculated typically with respect to the unit cell parameters averaged across
> the exposed volume of a crystal.
>
> In practice, the range of unit cell parameters within a crystal can be quite
> broad, and when we consider accuracy it is not clear, which unit cell
> parameters should be a reference point. Typically, the distribution of unit
> cell parameters in a crystal will not follow Gaussian distribution.
> Therefore, the accuracy of unit cell parameters determination is not well
> defined, even when we know the experimental conditions very well and
> propagate experimental uncertainties correctly.
>
> Variability of unit cell parameters can be quite high for data sets from
> different samples. However, description of this variability is typically not
> related to the very high precision of determination of unit cell parameters
> for an individual sample.
>
> Zbyszek
>
>
> On 07/22/2014 12:33 PM, Tim Gruene wrote:
>> 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
>>>
>>
>
>
> --
> Zbyszek Otwinowski
> UT Southwestern Medical Center
> 5323 Harry Hines Blvd., Dallas, TX 75390-8816
> (214) 645 6385 (phone) (214) 645 6353 (fax)
> [log in to unmask]
>
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