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:[EMAIL PROTECTED] Professor of Chemical Biology |Teaching mailto:[EMAIL PROTECTED] Centre for Biomolecular Sciences |Office: 1334-463792 The North Haugh |Fax : 1334-467229 The University |Lab : 1334-467245 St. Andrews |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:[EMAIL PROTECTED] 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 ----------------------------------------------------------------- Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.ruppweb.org/ ----------------------------------------------------------------- The hard part about playing chicken is to know when to flinch -----------------------------------------------------------------
