If you want even more confusion on the labeling -- take a look at
the PDB to mmCIF correspondence mappings for conversion between
PDB and mmCIF format.
In the PDB file format under REMARK 200
http://www.wwpdb.org/documentation/format32/remarks1.html#REMARK%20200
there is a line written as
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET :
and
REMARK 200 <I/SIGMA(I)> FOR SHELL :
<I/SIGMA(I)> is not defined, but I always read it as
the mean of [I/sigma(I)] and not the mean of I / mean of sigma(I).
However, using the pdb to mmCIF correspondence guide.
http://mmcif.pdb.org/dictionaries/pdb-correspondence/pdb2mmcif.html#REMARK200
This <I/SIGMA(I)> FOR THE DATA SET is linked to the pdb mmCIF dictionary token
_reflns.pdbx_netI_over_av_sigmaI
http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/Items/_reflns.pdbx_netI_over_av_sigmaI.html
this is defined as "The ratio of the average intensity to the average uncertainty, /."
which sounds like <I>/<sigma(I)> and not <I/sigma(I)>.
Likewise, the
REMARK 200 <I/SIGMA(I)> FOR SHELL :
shell value is linked to the mmCIF token _reflns_shell.meanI_over_sigI_obs
using the PDB exchange dictionary give the definition
"The ratio of the mean of the intensities of the reflections
classified as 'observed' (see _reflns.observed_criterion) in
this shell to the mean of the standard uncertainties of the
intensities of the 'observed' reflections in this shell."
There is a separate pdb mmCIF dictionary token _reflns.pdbx_netI_over_sigmaI
http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/Items/_reflns.pdbx_netI_over_av_sigmaI.html
Which is defined as "The mean of the ratio of the intensities to their standard uncertainties,"
or < I/SIGMA(I) >
So I have never understood why the PDB to mmCIF correspondence maps
<I/SIGMA(I)> FOR THE DATA SET to _reflns.pdbx_netI_over_av_sigmaI and not
to _reflns.pdbx_netI_over_sigmaI. Or if the PDB file format is supposed to
have the mean of <I> / mean <sigI> then why is it written as <I/SIGMA(I)>
in the header and not as <I>/<SIGMA(I)>? I never got a satisfactory answer
when I asked the deposition staff. I haven't checked the latest version of
pdb_extract, but in one of the previous versions, depending on which
scaling program you used it would extract either mean (I) / mean (sigmaI) or
mean (I/sigmaI) and assign it to the same _reflns.pdbx_netI_over_av_sigmaI
token.
Regards,
Mitch
(P.S. There are other strange mappings in the conversion between PDB and
mmCIF formats but that is for another day...)
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Anastassis Perrakis
Sent: Monday, March 30, 2009 11:40 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] I/sigma continued
On 30 Mar 2009, at 20:30, James Holton wrote:
> Frank von Delft wrote:
>>> So, what statistic do we want to look at? That depends on what you
>>> are trying to do with the data. There is no way for Phil to know
>>> this, so it is good that he prints out lots of different
>>> statistics. That said, when talking about the data quality
>>> requirements for structure solution by MAD/SAD, I suggest looking at
>>> I/sigma(I) where:
>>> I - merged intensity (proportional to photons) assigned to a
>>> reciprocal lattice point (hkl index)
>> Does ANY program print this out...?
> SCALA calls this "Mn(I/sd)". Sounds like d*TREK calls it "I/sig avg".
That is my understanding as well.
>
> With HKL you compute it "by hand" from the average I and average
> "error".
hmmm ... from "error" or from "stat."? Should chi^2 be 1 first?
> Not sure about XDS...
Confusingly, XDS calls that I/SIGMA from what I understand (which as I
said before is NOT what SCALA calls I/sigma)
Since we only use XDS and (mostly) SCALA in the lab, that is very
confusing.
I am pretty sure btw that I have myself -wrongly- quoted I/sigma as
being <I/sigma(I)> in at least 3-4 papers.
And I can bet I am not the only one that did so.
<I>/sigma<I> and <I/sigma(I)> are in my view more deterministic labels
and will get safer on their way to "Table 1".
Tassos
>
>
> -James Holton
> MAD Scientist
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