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Hi Phil, On Wed, Aug 23, 2006 at 10:17:18AM +0100, Phil Evans wrote: > 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 Is that independent of resolution? Wouldn't that mean that this approach then says: my structure relies on external restraints to the same extent, no matter what the resolution? Or maybe all your structures are in the same resolution range ;-) I've once done a quick check through the whole PDB (about 2-3 years ago I tyhink): the RMS(bond) in nearly all resolution ranges is on average 0.011. I'm sure there is some bias towards refinement practice in there. I was interested in this to do exactly what Tadeusz was suggesting: automating at least the Xray weighting (as part of [auto]BUSTER). I was quite disaponited not to see the trend I was expecting: small rms(bond) at low resolution and larger rms(bond) at high resolution. But then, analysing the content of the PDB might tell us more about the quirks of refinement programs than to give us some sound statistics ;-) Cheers Clemens -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************
