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Re: [ccp4bb] Adding H in refinement
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Adding H in refinement
From: Sara_Züger szueger {- at -} BIOC {- dot -} UZH {- dot -} CH
Date: 2010-01-12		Next message:
Subject: Re: Adding H in refinement
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2010-01-12


Subject: Re: Adding H in refinement
From: Vellieux Frederic Frederic {- dot -} Vellieux {- at -} IBS {- dot -} FR
Date: 2010-01-12

Hi Sara,

I don't know what "a good average B" is (or what "a bad average B" is).
I know that the for the refined structure should fall in the
same ball-park range than the temperature factor of the data computed
from the Wilson plot. I am not saying that they should match exactly
though. If they really differ wildly (e.g. 10 A**2 vs 140**2) then you
double check things. Like the resolution range used to compute the
Wilson B. And at 1.9-2.0 A resolution you should be able to compute a
proper Wilson B.

Fred

Sara Züger wrote:
> Dear CCP4bb,
>
> since the discussion about H-atoms is on, I wanted to ask about what I saw during my refinements:
>
> I did refinement with phenix of my 1.9-2.0 Angstroem structures and included the hydrogens (riding). However, when I checked on the statistics (refinement close to the end), the average B-factor was extremely high (in phenix.polygon it was higher than with any other structure in similar resolution range). It makes sense though that this happens, if you have a residue which has a high B-factor and carries a lot of hydrogens the average B-factor will raise quite a lot (since the B-factor of hydrogens is calculated 1-1.5x of B-factor from the atom it sits on), right?
> (When I removed the hydrogens again, the average B-factor was fine...)
>
> My question is now did I do something wrong in my refinement (-> do I have to change something that this does not happen), or is this something everybody sees?
>
> If this is common, what would happen (during evaluation) if you want to publish a structure and the statistics show such a high average B-factor? Is it better to have hydrogens on, but a bad average B, or no hydrogens on and a good average B... Obviously, I never published a structure ;)
>
> Thanks for sharing your opinion!
>
>
> Sara
>



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