Dear CCP4ers,
also in my experience, processing the same raw images with different
programs results in unit cell constants that typically deviate at least
already in the first digit after the dot (if not before the dot), with
our usual unit cell lengths between, say, 50-350 A. This leads to a
rather low personal estimate of the accuracy (not precision) of unit
cell parameters.
Best regards,
Dirk.
Am 23.07.2014 09:49, schrieb Bernhard Rupp:
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
--
*******************************************************
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW: www.genzentrum.lmu.de
*******************************************************
