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

Subject: Re: torsion restraints and phi/psi
From: Jim Naismith naismith {- at -} ST-ANDREWS {- dot -} AC {- dot -} UK
Date: 2007-11-07

If memory serves correctly Ramachandran based his plot on VDW.
Therefore all programs which use VDW will tend to put residues in the right
place.
Certainly in phenix.refine adding H's to one of my problematic structures
(twinning) not only improved the clash score but pushed a further 4% into
the right phi psi.

I dont critise (I needed that few % for publication) but only add there is a
lot of hidden assumptions in restraints

James H. Naismith FRSE
Research mailto:naismith@st-and.ac.uk
Professor of Chemical Biology
Teaching mailto:jhn@st-and.ac.uk
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Fax : 1334-467229
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Lab : 1334-467245
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In UK add 0 to start of number
Fife Scotland, U.K., KY16 9ST
http://www.st-and.ac.uk/~strucbio

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Bernhard Rupp
Sent: 07 November, 2007 16:40
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] torsion restraints and phi/psi

Dear All,

I wonder about the exact use of torsion restrains and the effect
on phi/psi/w validation.

I think in refmac, omega is restrained with a 1-4 dihedral or
planarity, cis when the proper LINK statement is invoked - no
questions there.

In literature I find remarks like 'usually not restrained' as far
as phi/psi goes. This is not irrelevant because the phi-psi
angles are crossvalidation for the otherwise restrained
geometry. So questions arise.

a) does refmac restrain phipsi at all (except vdw repulsion
which does not bias them otherwise)?

b) do other programs restrain or not phipsi?

c) In particular, what does torsion angle refinement do to
the validity of phipsi crossvalidation?

I vaguely recall statements such as 'robust even against strong
empirical potentials' in the context of SA/TA/EREF refinement...
but don't find the ref anymore im my piles.

Best regards, br
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: elusive DNA density
From: price {- at -} UCHICAGO {- dot -} EDU price {- at -} UCHICAGO {- dot -} EDU
Date: 2007-11-07

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