Ok - I have tracked down where it is coming from.
The value being reported is sum(I)/sum(sigma_I). This is not the same
as Mean(I/sigmaI) - as I interpret the later as (Sum(I/sigma))/n.
Where I comes from is the intensity_meas, intensity_meas_au, or
intensity column - whichever is present (priority left to right).
No averages here.
It is a simple diagnostic >80 or < 2 - report a warning.
This is from the old sf_convert program (written > 15 years ago) and the
various warnings were carried over to a re-implementation in python.
At the time the program was implemented, the PDB had only started trying
to make sense of the experimental data provided by the authors.
Remember, experimental X-ray data were not required by the PDB until
2008. Prior to that the data were optional, and some are a mess. Use of
experimental data in validation came afterwards. MTZ files might have
been accepted back then (I cannot remember) - so ensuring that the
conversion did not result in incorrect translation was important.
The person doing the work at the time was a structural biologist, but
may have come up with his own analyses to find conversion issues. There
will likely not be a reference. Certainly the sources do not reference
a methodology here.
So - what can we do moving forward? Using community standards for
identification of such errors should be incorporated. Changing the code
is relatively easy. Choosing the correct formulas would be the most
meaningful. And if sf_convert reports different data from AIMLESS - we
should strive to understand why.
Ezra
On 6/10/24 2:15 PM, Gerard Bricogne wrote:
Dear Aline,
This is an intriguing message: by what exact piece of software was it
produced?
The notation I_avg/sigI_avg does not appear in the definition of the
closest item in the mmCIF dictionary, which would be
_reflns_shell.meanI_over_sigI_obs
that can be found at
https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns_shell.meanI_over_sigI_obs.html
As Kay explained, the quantity for which you are getting a warning is a
ratio of averages, which is not at all the same as the usual average of
(signal-to-noise) ratios, denoted Mean((I)/sd(I)) in AIMLESS.
Much worse, in fact: that quantity (I_avg/sigI_avg) makes no sense
whatsoever in statistical terms. It must be a relic of a quantity that may
have seemed like a good idea to someone at some stage, and has since been
dutifully carried along forever after, and "gold-plated" so as to still be
present in the latest revision of the mmCIF dictionary.
Perhaps you could request a reference to the publication in which this
quantity was proposed as a validation criterion and its acceptable limits
were derived :-) .
This being said, if it is indeed the case that the average value of
your intensities is smaller than the average of their standard deviations,
there is definitely something wrong somewhere. Perhaps a confusion between
columns containing values pertaining to intensities vs. amplitudes?
To sober me up from all this speculation, Clemens Vonrhein tells me
that it is very likely that it is not the I_avg/sigI_avg quantity that is
actually being calculated, and that it is simply a "normal" quantity (e.g.
Mean((I)/sd(I)) that is being mis-described in the warning message.
With best wishes,
Gerard.
--
On Fri, Jun 07, 2024 at 03:03:30PM +0100, Aline Dias da Purificação wrote:
Dear all,
I am currently validating a structure for deposition in the wwPDB and
encountered the following warning in the validation system:
Warning: Value of (I_avg/sigI_avg = 0.83) is out of range (check Io or SigIo in
SF file).
The Mean((I)/sd(I)) in the aimless log is 1.7 in the OuterShell, so I didn't
understand the warning.
Has anyone experienced this before and could assist me?
Thank you.
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