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: Re: Can CCP4 print the sigma level of the electron density at each residue or atom center?
From: "Edward A {- dot -} Berry" BerryE {- at -} UPSTATE {- dot -} EDU
Date: 2010-05-25

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From: John R Helliwell jrhelliwell {- at -} GMAIL {- dot -} COM
Date: 2010-05-25

Subject: Re: Fwd: calculate the real space R factor using OVERLAPMAP
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2010-05-25

Hi Ian,

thanks for very detailed reply!

>> - do you think it is better than looking at three values {map CC, 2mFo-DFc,
>> mFo-DFc} and why?
>>
>
> Yes, because all the information you need is encapsulated in 1 number
> per region of interest!

I agree it's a good reason.

> But I don't understand what you mean by
> 2mFo-DFc & mFo-DFc being counted each as 1 number.

Given the map and model, you can get the map value at (x,y,z) position,
for example, at the center of atom. This is what phenix.model_vs_data
reports. For each atom you get three numbers: map CC, and the values of
2mFo-DFc and mFo-DFc maps at the atomic position.

>> 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.
>>
>
> The problem is how is all this information quantified in an objective
> and statistically justifiable way in order to arrive at a firm
> conclusion?
>

We can more or less relate these values to the map appearance and
model-to-map fit quality. Looking at these numbers one can approximately
tell whether it's good, so so, or bad. It's like crystallographic
reciprocal space R-factor. If I see R=35% for a structure at 2A
resolution - it's not good, and R=17% is much better.

Anyway I will code that formula and play with it.

Thanks again!
Pavel.

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

Next message:
Subject: Re: Charge flipping.
From: John R Helliwell jrhelliwell {- at -} GMAIL {- dot -} COM
Date: 2010-05-25