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
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
