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 >>>> >>>> b...@ruppweb.org >>>> >>>> b...@hofkristallamt.org >>>> >>>> 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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