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:[log in to unmask]
Professor of Chemical Biology |Teaching mailto:[log in to unmask]
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-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
Bernhard Rupp
Sent: 07 November, 2007 16:40
To: [log in to unmask]
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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