Although Zby's remarks re precision are beyond my original bewilderment about listed zepto-meter range digits (sans precision measure), I wonder whether the argument that we have so many data and thus a quite high precision (n.b. not accuracy) can be attained, is perhaps somewhat optimistic. What we measure or assign as a 'spot' is largely predetermined by various integration, profile, box selection, etc, parameters and whatever does not fit that spot model cannot be properly accounted for. I therefore argue that any precision estimate is probably biased towards optimism by the limitations of the particular reflection spot model. Most reflection 'spots' are dirty little creatures with tentacles, fuzz, bumps, etc....
In the listed mmCIF case the senseless printing of double precision format was actually the simple point to be made. Best, BR -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Zbyszek Otwinowski Sent: Dienstag, 22. Juli 2014 23:49 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Protein Crystallography challenges Standard Model precision 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 >>>>> >>>>> 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 >> > -- Zbyszek Otwinowski UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, TX 75390-8816 (214) 645 6385 (phone) (214) 645 6353 (fax) zbys...@work.swmed.edu
