Clearly, using a single weight for X-ray and geometry terms, with the rmsd of bond lengths as a monitor is not satisfactory. As several people pointed out earlier, at low(ish) resolution the bond-length restraints do not compete with the X-ray terms and can be easily satisfied while the larger structural features can be completely wrong.
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...
Tadeusz
| "P.R. Evans"
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Sent by: [EMAIL PROTECTED] 23-Aug-2006 10:17 |
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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
