Re: [ccp4bb] refined vs 'others'

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Subject: Re: refined vs 'others'
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2007-11-07

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Subject: Re: refined vs 'others'
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2007-11-07

Subject: Re: refined vs 'others'
From: Pavel Afonine pafonine {- at -} LBL {- dot -} GOV
Date: 2007-11-07

Hi,

> I reran that (same refmac version) but I cannot reproduce the output.
>

Of course, you cannot reproduce the output. This is most likely because
the H atoms were used internally in all calculations but they were not
deposited in PDB (like in most of cases). So, to reproduce the numbers
reported in PDB file header you need to re-do exactly same refinement as
the authors of that structure did.

This is why it's not too bad idea to not remove H atoms from the PDB
file if these hydrogens were used in calculations. In phenix.refine we
keep hydrogens for exactly this reason. This costs nothing but results
in easier reproducible results.

Cheers,
Pavel.

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CCP4bb <-- 2007 <-- November 2007 <-- 07 November 2007

Previous message:
Subject: Re: refined vs 'others'
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2007-11-07

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Subject: Re: refined vs 'others'
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2007-11-07