Re: [ccp4bb] torsion restraints and phi/psi

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

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Subject: Re: elusive DNA density
From: Jacob Corn jcorn {- at -} BERKELEY {- dot -} EDU
Date: 2007-11-07

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Subject: Re: torsion restraints and phi/psi
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-11-07

Subject: Re: torsion restraints and phi/psi
From: Edward A Berry eaberry {- at -} LBL {- dot -} GOV
Date: 2007-11-07

Bernhard Rupp wrote:
> Dear All,
>
> I wonder about the exact use of torsion restrains and the effect
> on phi/psi/w validation.
>
----
>
> a) does refmac restrain phipsi at all (except vdw repulsion
> which does not bias them otherwise)?
>

Isn't it the case that vdw interactions are turned off
between atoms in a residue, and perhaps with the residues
before and after?
Otherwise positional refinement would in fact tend to drive
the residues into the rama-allowed region?

Might it be a good idea to use torsion restraints, or
intra-residue vdw repulsion, in the last stage of refinement
after calculating an unbiased ramachandran plot;
especially in low-resolution problems where we need all the
restraints we can get?

Ed

CCP4bb navigation

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

Previous message:
Subject: Re: elusive DNA density
From: Jacob Corn jcorn {- at -} BERKELEY {- dot -} EDU
Date: 2007-11-07

Next message:
Subject: Re: torsion restraints and phi/psi
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-11-07