Re: [ccp4bb] Fwd: calculate the real space R factor using OVERLAPMAP

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

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Subject: [Fwd: Is it possible for the Tris buffer to strip the Zn ions from the Zinc Finger motif of a protein?]
From: Maia Cherney chern {- at -} UALBERTA {- dot -} CA
Date: 2010-05-23

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From: Paul Lindblom lindblom {- dot -} paul {- at -} GOOGLEMAIL {- dot -} COM
Date: 2010-05-23

Subject: Re: Fwd: calculate the real space R factor using OVERLAPMAP
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2010-05-23

Hi Ian,

On 5/23/10 5:01 AM, Ian Tickle wrote:
>>> Thanks a lot! Actually my map has very weak density at only certain
>>> region, and I want to numerically say that this region is "weakly"
>>> correlated to the atomic map at this region. But according to the CC
>>> formula, if investigating by residue, CC only depends on the relative
>>> "shape" of the density, NOT the relative "density".
>>>
>> This is exactly why I suggested to look at the triplet of values {map CC,
>> 2mFo-DFc, mFo-DFc}. The map CC will tell you similary of shapes, indeed, and
>> the two maps (2mFo-DFc, mFo-DFc) will tel you how to qualify this
>> similarity.
>>
>>
>>> Instead, I think real-space R will reflect the weak density.
>>>
>
> I have long been advocating the use of the RMS density deviation
> Z-score statistic for this purpose, i.e.
> sqrt(sum(delta_rho^2)/Npoints)/sigma(rho), where delta_rho is a
> grid-point value in a 2(mFo-DFc) map, the sum is over the region of
> interest (atom, residue, side-chain etc), Npoints is the number of
> grid points in the region, and sigma(rho) is the uncertainty in the
> density (which must be estimated for the asymmetric unit of the map,
> NOT just the region). Note that it's equivalent to the negative
> log-likelihood, which IMO is the appropriate statistic for this
> situation, if it's assumed that the errors in the density have a
> normal distribution.
>

very interesting... Could you please explain some more, namely:

- where this formula come from and what are the grounds for this?
- how to make sense of the numbers. Say I used this formula and I got a
number X; how can I tell if it is good or not good?
- do you think it is better than looking at three values {map CC,
2mFo-DFc, mFo-DFc} and why?

Plus some technical questions:

- why 2(mFo-DFc)?
- how the "region of interest is defined"?
- how you compute sigma(rho)?

By suggesting to use {map CC, 2mFo-DFc, mFo-DFc} I was assuming that:
- map CC will tell you about similarities of shapes and it will not tell
you about how strong the density is, indeed. So, using map CC alone is
clearly insufficient. Also, we more or less have feeling about the
values, which is helpful.
- 2mFo-DFc will tell you about the strength of the density. I mean, if
you get 2.5sigma at the center of atom A - it's good (provided that map
CC is good), and if it is 0.3sigma you should get puzzled.
- Having excess of +/- mFo-DFc density will tell you something too.

Thanks!
Pavel.

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

Next message:
Subject: Finding best model for molecular replacement
From: Paul Lindblom lindblom {- dot -} paul {- at -} GOOGLEMAIL {- dot -} COM
Date: 2010-05-23