Re: [ccp4bb] I/sigma continued

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: I/sigma continued
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-03-30

Next message:
Subject: Re: I/sigma continued
From: Kay Diederichs kay {- dot -} diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2009-03-30

Subject: Re: I/sigma continued
From: "Miller, Mitchell D {- dot -} " mmiller {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2009-03-30

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 FOR THE DATA SET :
and
REMARK 200 FOR SHELL :

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 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 / and not .

Likewise, the
REMARK 200 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
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 / mean then why is it written as
in the header and not as /? 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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Anastassis Perrakis
Sent: Monday, March 30, 2009 11:40 AM
To: CCP4BB@JISCMAIL.AC.UK
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 in at least 3-4 papers.
And I can bet I am not the only one that did so.

/sigma and 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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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Re: I/sigma continued
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-03-30 Next message:
Subject: Re: I/sigma continued
From: Kay Diederichs kay {- dot -} diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2009-03-30