*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk ***
Possibly, but there may be problems if the phase errors are correlated, also there would be noise due to series termination / incompleteness errors which would be difficult to take account of. I don't know how well it would work in practice, I've never heard of it being done. -- Ian > -----Original Message----- > From: James Holton [mailto:[EMAIL PROTECTED] > Sent: 12 August 2005 16:26 > To: Ian Tickle > Subject: Re: [ccp4bb]: Quantifying density peaks in MAPMAN > > > Couldn't you just propagate SIGF and (somehow) FOM through > the Fourier > sum and get SIGrho that way? > > -James > > > Ian Tickle wrote: > > >All - > > > >The statistical standard uncertainty SU (previously known as > "estimated > >standard deviation" or "standard error") is NOT the same thing as the > >"RMS deviation from the mean", and cannot be computed from > the Fourier > >components. The RMSD (and the Fourier components) include > contributions > >from all grid points in the map, including the ones in the atomic > >densities, which can hardly be described as "error". To get the true > >uncertainty you have to exclude all these points, which can obviously > >only be done in real space. Hence the SU will always be smaller than > >the RMSD, and there will indeed be significant features in > the map < 1 > >sigma, if sigma is incorrectly equated to the RMSD instead of the SU. > > > >The extends program makes an attempt at estimating the true > SU, though > >probably not a very rigorous one. The correct procedure would be to > >estimate the SU from a normal probability plot. This > involves ordering > >the deviations by their (signed) magnitudes, then comparing them with > >the theoretical values assuming a normal distribution of errors. The > >outliers due to the signal will then appear at the extremes > of the plot, > >which can excluded from consideration, and the true SU due > to the random > >errors can be estimated from the gradient of the central > part. This is > >something I've been meaning to do in extends for a while > (but then how > >many people other than me are using extends anyway?). > > > >The difference between SU and RMSD is most obvious in a > 2mFo-DFc map (or > >indeed any type of Fobs map), because a large fraction of the map is > >then signal and it's impossible to estimate a sensible SU. As others > >have pointed out before, the RMSD of such a map depends > largely on the > >solvent content of the crystal, not the true error! > > > >This is not the first time RMSD and SU have been confused, > there was a > >recent discussion concerning the RMSD of bond lengths from the > >dictionary values after refinement. In this case the RMSD > will always > >be less than the rms SU of the bond lengths (which is known from the > >small molecule data) because of the reduction in the degrees > of freedom > >by the number of refined parameters (indeed there's nothing > to stop the > >RMSD being zero if the NDF is zero!). > > > >-- Ian > > > > > > > ********************************************************************** CONFIDENTIALITY NOTICE This email contains confidential information and may be otherwise protected by law. Its content should not be disclosed and it should not be given or copied to anyone other than the person(s) named or referenced above. If you have received this email in error, please contact [EMAIL PROTECTED] **********************************************************************
