Re: [ccp4bb] help with wwPDB validation warning

2024-06-14 Thread Edward Berry
This old message claims that / = "weighted" by s. If counting error is significant, s will be larger for stronger reflections, which are likely to have small I/s, so in general / > unweighted . As Werten points out. However this seems to be the opposite of the OP's situation, if both measur

Re: [ccp4bb] help with wwPDB validation warning

2024-06-11 Thread Kay Diederichs
Dear Gerard, I disagree in two points with what you write: On Mon, 10 Jun 2024 19:15:43 +0100, Gerard Bricogne wrote: ... > Much worse, in fact: that quantity (I_avg/sigI_avg) makes no sense >whatsoever in statistical terms. It must be a relic of a quantity that may >have seemed like a good

Re: [ccp4bb] help with wwPDB validation warning

2024-06-10 Thread Ezra Peisach
Ok - I have tracked down where it is coming from. The value being reported is sum(I)/sum(sigma_I).   This is not the same as Mean(I/sigmaI) - as I interpret the later as (Sum(I/sigma))/n. Where I comes from is the intensity_meas, intensity_meas_au, or intensity column - whichever is present (

Re: [ccp4bb] help with wwPDB validation warning

2024-06-10 Thread Gerard Bricogne
Dear Aline, This is an intriguing message: by what exact piece of software was it produced? The notation I_avg/sigI_avg does not appear in the definition of the closest item in the mmCIF dictionary, which would be _reflns_shell.meanI_over_sigI_obs that can be f

Re: [ccp4bb] help with wwPDB validation warning

2024-06-08 Thread Kay Diederichs
Hi Aline, I see nothing wrong with / being 0.83 Mean((I)/sd(I)) is , which is not the same as / so you cannot expect the numerical values to be the same (even in case the resolution shell definition is identical), although the two values usually do not differ much. Take for example two reflect

Re: [ccp4bb] help with wwPDB validation warning

2024-06-07 Thread Eleanor Dodson
Hmm - no idea but perhapd=s interesting that 0.83 ~ 1.7/2 Eleanor On Fri, 7 Jun 2024 at 15:13, Aline Dias da Purificação < d5ed37c6eb7b-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear all, > > I am currently validating a structure for deposition in the wwPDB and > encountered the following warnin

[ccp4bb] help with wwPDB validation warning

2024-06-07 Thread Aline Dias da Purificação
Dear all, I am currently validating a structure for deposition in the wwPDB and encountered the following warning in the validation system: Warning: Value of (I_avg/sigI_avg = 0.83) is out of range (check Io or SigIo in SF file). The Mean((I)/sd(I)) in the aimless log is 1.7 in the OuterShel