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Re: [ccp4bb]: contour ?
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On Thu, 6 Sep 2001, Gerard "DVD" Kleywegt wrote:
> i seriously disagree with your seriously disagreeing.
I'd love to continue that thread, but..
> assume that the sigma level at the end of a refinement
> is 0.0001 e/A3. then a 10-sigma feature is noise. my point
> is that the "number of sigmas" of a feature in an fo-fc
> map is meaningless - the absolute sigma level is not, of
> course (but this assumes that you calculate your maps on
> an absolute scale to begin with !).
There's nothing mystical about an Fo-Fc map and it obeys some sort of
statistics not completely removed from reality. Ergo a 5 sigma peak is
potentially significant and should be considered carefully even if you are
a slob like me and normalise all your maps. (I can hear the purists
recoiling in horror even as I write this ;).
Although I would hate to have to retreat to wearing sack-cloth and
speaking Latin, it's not unreasonable to contour Fo-Fc maps at plus and
minus 3 sigma for the purpose of finding things to look at. One will want
to consider things like geometry, environment, and yea even electrons per
cubic Angstrom in assessing the peak, but dogma is no substitute for care
and experience in interepreting such features. It might work quite well
for buying beer, however.
IMHO.
Regards,
Phil
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| Phil Jeffrey | |
| Crystallography Facility Manager | If you lie to the compiler, |
| Memorial Sloan-Kettering Cancer Center, NYC | it will get its revenge |
| phil@xray2.mskcc.org | - Henry Spencer |
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