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.
>
> ########################################################################
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at
> https://www.jiscmail.ac.uk/policyandsecurity/
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
