A technical remark in relation to the CC1/2, XDS issue: Refmac currently
reports Rfactors vs. resolution shells (i.e. Rw/Rf in each resolution shell).
That is useful for one aspect of the analysis, however, in the K & D paper,
it's the change in overall Rfactors vs. resolution that is reported. In the
cases analyzed in this paper this is the value which was used as criterion for
justifying adding higher resolution shells according to the CC1/2. Perhaps
reporting of the overall Rfactors vs. resolution can be added to Refmac (at
least as an option for interested users)?
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson
[eleanor.dod...@york.ac.uk]
Sent: Wednesday, August 08, 2012 12:10 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CC1/2, XDS and resolution cut off
Like Ian, I tend to use as much data as is reasonable - but it is useful to
look at the Rfactors plot again resolution in REFMAC output. If this shoots sky
high at the limit, the data is probably not very useful in refinement or map
calculation (and will automatically be down-weghted by the ML weighting) . So
all it does is make your Rfactors look worse!
Eleanor
On 6 Aug 2012, at 12:21, Marcus Fislage wrote:
> Dear all,
>
> We have in our lab a data set collected and are discussing where to cut
> the resolution for refinement. According to the work of Kai Diederichs
> and Andy Karplus one should use CC 1/2 of 12.5% (in case it is
> significant) to determine the highest resolution independent of the
> I/sigI and R factor rules used earlier. But I would like to know if this
> also counts for low completeness data?
> The problem is that we have in the highest resolution shell an I/sigI of
> 4, a good cc1/2 but only a completeness of 30%. Which I guess means we
> measured the high resolution data very accurate but not complete. Would
> you still use the low complete data in the highest resolution shell or
> should that be still a valid argument to cut your data towards lower
> resolution?
> My guess would be to use the data still even if the completeness drops,
> since the data we measured is good and according to CC1/2 significant.
> Are we right to do so or would you disagree?
>
> Thanks for any input
> Marcus
>
> --
> Marcus Fislage
> Structural Biology Brussels
> Vrije Universiteit Brussel
> Department of Structural Biology, VIB
> Oefenplein, Gebouw E
> Pleinlaan 2,
> 1050 Brussel
> Belgium
> Tel: +32-2-629 18 51
> Email : marcus.fisl...@vib-vub.be
> Url: http://www.verseeslab.structuralbiology.be
