Re: [ccp4bb] Depositing coordinates with riding hydrogens

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

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Subject: Re: Depositing coordinates with riding hydrogens
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-12-17

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Date: 2008-12-17

Subject: Re: Depositing coordinates with riding hydrogens
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2008-12-17

Hi Jon,

- obviously, the model should not be manipulated once the final
statistics is obtained, or if it is manipulated, then the final
statistics must be re-calculated;

- I can't imagine someone thinking that hydrogens were refined
individually in a X-ray structure say at 2A resolution.

- also, it's much easier to remove H atoms later on, rather than add
them back the *exact same *way you did. I don't see any logic of making
the depositing information artificially less complete by removing hydrogens.

Cheers,
Pavel.

On 12/17/2008 3:53 PM, Jonathan Winger wrote:
> Hi all-
>
> Just wondering what the consensus is - should a structure refined with
> riding hydrogens be deposited with the coordinates for the hydrogens
> included? One could argue that, since they were used in the
> refinement to obtain the model and statistics reported, they should be
> included in the deposited pdb file. On the other hand, the presence
> of hydrogens in the pdb file might lead some to think the hydrogens
> were refined against density when they really weren't. Thoughts?
>
> Thanks,
> Jon

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

Previous message:
Subject: Re: Depositing coordinates with riding hydrogens
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-12-17

Next message:
Subject: CCP4 6.1.0 release and CCP4MG
From: Victor Alves vdalves {- at -} FMV {- dot -} UTL {- dot -} PT
Date: 2008-12-17