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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
