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Re: [ccp4bb] refined vs 'others'
 

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CCP4bb <-- 2007 <-- November 2007 <-- 07 November 2007
Previous message:
Subject: Re: refined vs 'others'
From: Pavel Afonine pafonine {- at -} LBL {- dot -} GOV
Date: 2007-11-07 		Next message:
Subject: staff scientist Keck Center for Molecular Structure
From: "Kantardjieff, Katherine" kkantardjieff {- at -} EXCHANGE {- dot -} FULLERTON {- dot -} EDU
Date: 2007-11-07


Subject: Re: refined vs 'others'
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2007-11-07
> Of course, you cannot reproduce the output.

The question was actually different. Minor differences
in numbers are not the problem. The absence of 'others' in the
restraint table is inconsistent with the statement
at the end of the table that riding hydrogens were used.

BR



-----Original Message-----
From: Pavel Afonine [mailto:pafonine@lbl.gov]
Sent: Wednesday, November 07, 2007 3:44 PM
To: bernhardrupp@sbcglobal.net
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] refined vs 'others'

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.

CCP4bb navigation

CCP4bb <-- 2007 <-- November 2007 <-- 07 November 2007
Previous message:
Subject: Re: refined vs 'others'
From: Pavel Afonine pafonine {- at -} LBL {- dot -} GOV
Date: 2007-11-07 		Next message:
Subject: staff scientist Keck Center for Molecular Structure
From: "Kantardjieff, Katherine" kkantardjieff {- at -} EXCHANGE {- dot -} FULLERTON {- dot -} EDU
Date: 2007-11-07


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