Re: [ccp4bb] REFMAC5 residues with bad geometry

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

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Subject: Re: REFMAC5 residues with bad geometry
From: "Bernhard Rupp (Hofkristallrat a {- dot -} D {- dot -} )" hofkristallamt {- at -} GMAIL {- dot -} COM
Date: 2012-03-28

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Subject: Re: REFMAC5 residues with bad geometry
From: "Bernhard Rupp (Hofkristallrat a {- dot -} D {- dot -} )" hofkristallamt {- at -} GMAIL {- dot -} COM
Date: 2012-03-28

Subject: Re: REFMAC5 residues with bad geometry
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2012-03-28

On Tuesday, March 27, 2012 04:35:40 pm Bernhard Rupp (Hofkristallrat a.D.) wrote:
> >phenix.refine allows any number of alternate conformers.
>
> Hmm..... quoting our old friends from the validation circuit: Where freedom
> is given, liberties will be taken....

True, but...

[warning: back of the envelope calculation]

Consider, for example, an isoleucine sidechain.

It would require 12 positional parameters to refine the position of
each sidechain atom (XYZ * {CB CG1 CG2 CD1}) for a single conformation.

One the other hand there are only 7 rotamers in the library.
So if you limited the refinement to the relative occupancy of the
7 ideal rotamers, that is a more parsimonious model than refining
the individual atoms for one conformation.

Season to taste with arguments about geometry restraints, but still
I think the liberty being offered is not so dangerous.

Ethan

--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

CCP4bb navigation

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

Previous message:
Subject: Re: REFMAC5 residues with bad geometry
From: "Bernhard Rupp (Hofkristallrat a {- dot -} D {- dot -} )" hofkristallamt {- at -} GMAIL {- dot -} COM
Date: 2012-03-28

Next message:
Subject: Re: REFMAC5 residues with bad geometry
From: "Bernhard Rupp (Hofkristallrat a {- dot -} D {- dot -} )" hofkristallamt {- at -} GMAIL {- dot -} COM
Date: 2012-03-28