Re: [ccp4bb] unbiased electron density map

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CCP4bb <-- 2008 <-- January 2008 <-- 09 January 2008

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Subject: Re: Principal axes and moment of inertia matrix
From: James Stroud jstroud {- at -} MBI {- dot -} UCLA {- dot -} EDU
Date: 2008-01-09

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From: Alexander Aleshin aaleshin {- at -} BURNHAM {- dot -} ORG
Date: 2008-01-09

Subject: Re: unbiased electron density map
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2008-01-09

A 2Fo-Fc map is simply an Fc map with two times the Fo-Fc map added
to it. ( Fc + 2(Fo-Fc) = Fc + 2Fo - 2Fc = 2Fo - Fc ) The phase comes
from the Fc's. The basic formulation is biased toward the model used
to calculate the Fc's. You did, after all, start with a pure Fc map!

Various techniques are used to reduce bias in these maps. Usually
a technique that reduces bias in one kind of map reduces the bias in
the other, since they are so closely related. The procedures I know
of work by changing the calculation of Fc (and the weights on the
individual reflections, which aren't mentioned when using the simple
name Fo-Fc but are there none-the-less) and since the Fc is in both
maps both maps are "debiased".

These methods reduce bias. "Unbiased" is a stronger claim and if
you use that word you should state clearly how you know the bias is
gone.

Your quote bring up another matter. An "initial" map, i.e. before
refinement, is unbiased if it is an omit map. If you have done no
refinement and you leave the interesting part out of the calculation
of Fc there can not be any bias in either the Fo-Fc or the 2Fo-Fc map.
This is why an initial map is more reliable for proving binding of
a compound, for example, than a bias reduced map after refinement.

Dale Tronrud

michael nelson wrote:
> In my understanding, unbiased electron density map usually refers to the
> Fo-Fc map.But I have seen in some papers sentences like that "The
> initial, unbiased 2F_o -F_c map is contoured at".I was a bit confused
> since I was told by my instructor that the 2Fo-Fc was usually biased.
>
> Can anyone clear up this concept for me?
> Mike
>
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CCP4bb <-- 2008 <-- January 2008 <-- 09 January 2008

Previous message:
Subject: Re: Principal axes and moment of inertia matrix
From: James Stroud jstroud {- at -} MBI {- dot -} UCLA {- dot -} EDU
Date: 2008-01-09

Next message:
Subject: Crystal imaging system
From: Alexander Aleshin aaleshin {- at -} BURNHAM {- dot -} ORG
Date: 2008-01-09