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Hi The bonds and angle parameters were weighted relative to each other by assuming that the sample standard deviations of the fragment geometries correspond to a thermal distribution in a harmonic potential at a specific temperature. The bond and angle weights were thus weighted relative to each other, because they were derived from the same fragment sets. This was not rigorous in any sense, because of the implicit assumptions of orthogonality of bonds and angles, equal temperatures for fragment structures, etc. A more detailed analysis would not have been statistically significant at that time. The concept was thus that the restraints reflected a potential energy force field. -Rick --------------------------- Richard A. Engh Professor, Department of Chemistry The Norwegian Structural Biology Centre (Norstruct) Universitetet i Tromsø N-9037 Tromsø Roche Diagnostics GmbH Department of Medicinal Chemistry Nonnenwald 2 D-82377 Penzberg, Germany ------------------------------ -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Eleanor Dodson Sent: Wednesday, August 23, 2006 3:33 PM To: [EMAIL PROTECTED] Cc: CCP4 Bulletin Board; [EMAIL PROTECTED] Subject: Re: [ccp4bb]: Refmac vs Ramachandran (low resolution) According to Engh and Huber the geometric restraints are meant to have correct RELATIVE weights... I have forgotten how that was decided. Eleanor [EMAIL PROTECTED] wrote: > > I do not think I made myself clear... WEIGH AUTO does not work very > well (and Clemens's attempt to apply a similar method to weigh the > X-ray terms in autoBUSTER) because all the types of geometrical > restraints (DIST, ANGL, PLAN, CHIR, NONB, etc...) are scaled by the > same factor for all resolutions, with rmsd for 1-2 bonds being used as > an indicator of how well we balance the X-ray terms with the > geometrical ones (in the parameter matrix). > This indeed can lead to larger bond rmsd for high-resolution > structures (competition between DIST restraints with stronger X-ray > terms), and very small ones for low-resolution data (no competition, > DIST wins!). > I am suggesting applying different scale factors for different types > of geometrical restraints, depending on the resolution to have a more > realistic distribution of the deviations from "ideal" values for > different types of geometrical features. > > Tadeusz > > > > > > > > *"Roberto Steiner" <[EMAIL PROTECTED]>* > > 23-Aug-2006 12:05 > > > To > [EMAIL PROTECTED] > cc > "CCP4 Bulletin Board" <[email protected]>, [EMAIL PROTECTED] > Subject > Re: [ccp4bb]: Refmac vs Ramachandran (low resolution) > > > > > > > > > > Hi Tadeusz > > > Of course, one can adjust weights of individual types of restraints > (does anybody these days?), but It would be nice to have an automatic > weighing scheme in REFMAC, which would deal with the different needs > for restraints at different resolution ranges... > > You can try > > WEIG AUTO > > > The option is not yet available through the interface (I think). I > usually modify the CCP4i-generated refmac script with Run&View Com File. > Alternatively, you can just have a one-line file with the above > command and give the name of that file in the Developers option. > > Roberto. > > > Tadeusz > > > > *"P.R. Evans" <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>*>* > Sent by: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> > > 23-Aug-2006 10:17 > > > To > "CCP4 Bulletin Board" <[EMAIL PROTECTED] <mailto:[email protected]>> cc > > Subject > Re: [ccp4bb]: Refmac vs Ramachandran (low resolution) > > > > > > > > > > > > *** For details on how to be removed from this list visit the *** > *** CCP4 home page _http://www.ccp4.ac.uk_ > <http://www.ccp4.ac.uk/> *** > > > > > When I've done searches of the CCDC small molecule database for > molecular fragments, the rmsd of bond lengths has come out in the > range 0.02 - 0.03A. These deviations between different structures are > of course larger than the > estimate rmsd within a single structure, which I think are the number > around 0.014A quoted earlier in this thread, and probably give a > reasonable > estimate of the uncertainty. > > I usually try to adjust matrix weight to give rmsd bonds around 0.02A > > Phil > > > > > > > --- > Dr. Roberto Steiner > Randall Division of Cell and Molecular Biophysics > New Hunt's House > King's College London > Guy's Campus > London, SE1 1UL > Phone +44 (0)20-7848-8216 > Fax +44 (0)20-7848-6435 > e-mail [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> > > > >
