Re: [ccp4bb] Problems with phasing a protein (1300aa)

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

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Subject: Re: Problems with phasing a protein (1300aa)
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2009-03-23

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From: Daniel Jin jin_xiechen {- at -} YAHOO {- dot -} COM
Date: 2009-03-23

Subject: Re: Problems with phasing a protein (1300aa)
From: Jim Pflugrath jim {- dot -} pflugrath {- at -} RIGAKU {- dot -} COM
Date: 2009-03-23

On Mon, 23 Mar 2009, Phil Evans wrote:

> I'm happy to change the column titles if it makes it clearer. Actually the
> "I/sigma" column in the Scala output is not very useful:
> it is / RMSscatter, ie the mean intensity/mean error, for individual
> observations, not taking into account multiple measurements. Because it is
> ratio of means (rather than a mean of ratios), it can behave oddly depending
> on the distribution of intensities, for instance giving an overall value
> which is outside the range of values in resolution bins. It is the ratio of
> the previous two columns.
>
> On the other hand the column labelled "Mn(I)/sd" is the mean of ratios for
> each reflection, ie< /Ïƒ() > and does take into account the
> multiplicity of measurements, so is much more relevant as an indicator of
> data quality
>
> see
> http://www.ccp4wiki.org/~ccp4wiki/wiki/index.php?title=Scaling_experimental_intensities_with_Scala

FWIW, dtscaleaverage in the d*TREK has the same two columns of I/sigI and
labels them "I/sig unavg" and "I/sig avg"

Of course, going from one to the other takes into account the multiplicity
of the observations with the ASSUMPTION that the errors are random and
normally distributed. With all the systematic and erratic errors in
measurements, I'm not sure this assumption is always valid.

Note to students: I think this will be on the quiz I hand out next week!

Jim

> Scala also outputs a convenient "Table 1" summary
>...
CCP4bb navigation
CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Re: Problems with phasing a protein (1300aa)
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2009-03-23 Next message:
Subject: low insect cell expression
From: Daniel Jin jin_xiechen {- at -} YAHOO {- dot -} COM
Date: 2009-03-23