Kay,
Thank you for your explanation. The radiation damage was not the factor,
but there was something strange about this crystal (actually two
crystals had the same strange behavior). I could not process them in
HKL2000, but it showed the problem (see pictures in the attachment). The
processing in XDS was done at the CLS (Canadian Light Source). I know
they always have the latest version of XDS.
Maia
Kay Diederichs wrote:
> Maia,
>
> provided radiation damage is not a major detrimental factor, your data
> are just fine, and useful also in the high resolution shell (which
> still has <I/sigma> of 2.84 so you could probably process a bit beyond
> 2.25A).
>
> There is nothing wrong with R_meas of 147.1% since, as others have
> said, R_meas is not limited to 59% (or similar) as a refinement
> R-factor is. Rather, R_meas is computed from a formula that has a
> denominator which in the asymptotic limit (noise) approaches zero -
> because there will be (almost) as many negative observations as
> positive ones! (The numerator however does not go to zero)
>
> Concerning radiation damage: First, take a look at your frames - but
> make sure you have the same crystal orientation, as anisotropy may
> mask radiation damage! Then, you can check (using CCP4's loggraph) the
> R_d plot provided by XDSSTAT (for a single dataset; works best for
> high-symmetry spacegroups), and you should also check ISa (printed in
> CORRECT.LP and XSCALE.LP).
>
> HTH,
>
> Kay
>
> P.S. I see one potential problem: "XSCALE (VERSION December 6, 2007)"
> when the calculation was done 28-Aug-2009. There were quite a number
> of improvements in XDS/XSCALE since that version. The reason may be
> that a licensed, non-expiring version was used - make sure you always
> rather use the latest version available!
>
>
> > -------- Original Message --------
> > Subject: [Fwd: Re: [ccp4bb] I/sigmaI of >3.0 rule]
> > Date: Thu, 3 Mar 2011 10:45:03 -0700
> > From: Maia Cherney <[log in to unmask]>
> >
> >
> >
> > -------- Original Message --------
> > Subject: Re: [ccp4bb] I/sigmaI of >3.0 rule
> > Date: Thu, 03 Mar 2011 10:43:23 -0700
> > From: Maia Cherney <[log in to unmask]>
> > To: Oganesyan, Vaheh <[log in to unmask]>
> > References: <[log in to unmask]>
> > <[log in to unmask]>
> > <[log in to unmask]>
> > <[log in to unmask]> <[log in to unmask]>
> > <[log in to unmask]>
> >
> >
> >
> > Vaheh,
> >
> > The problem was with Rmerg. As you can see at I/sigma=2.84, the Rmerge
> > (R-factor) was 143%. I am asking this question because B. Rupp wrote
> > "However, there is a simple relation between <I/sigI> and R-merge
> > (provided no other indecency has been done to the data). It simply is
> > (BMC) Rm=0.8/<I/sigI>."
> > Maybe my data are indecent? This is the whole LP file.
> >
> > Maia
> >
> > MMC741_scale-2.25.LP
> >
> >
> >******************************************************************************
>
> > XSCALE (VERSION December 6, 2007) 28-Aug-2009
> >******************************************************************************
>
> >
> > Author: Wolfgang Kabsch
> > Copy licensed until (unlimited) to
> > Canadian Light Source, Saskatoon, Canada.
> > No redistribution.
> >
>
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