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*To*: Bart Hazes <bhazes@ualberta.ca>*Subject*: Re: [ccp4bb]: ccp4bb- Warp-Arp*From*: Peter Zwart <Zwart@embl-hamburg.de>*Date*: Tue, 04 Feb 2003 20:42:29 +0100*CC*: Bernhard Rupp <br@llnl.gov>, "'Anastassis Perrakis'" <perrakis@nki.nl>, "'syed ibrahim'" <b_syed_ibrahim@yahoo.com>, "'ccp4'" <ccp4bb@dl.ac.uk>*References*: <Pine.A41.4.33.0302041130470.37956-100000@gpu1.srv.ualberta.ca>*Sender*: owner-ccp4bb@dl.ac.uk*User-Agent*: Mozilla/5.0 (Macintosh; U; PPC Mac OS X; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0

*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** According to the Refmac paper (Acta D53 240) a resolution depended function describing sigmaA in refmac is estimated by a 'bulk solvent correction' like formula for each partial structure . They quote that in total 6 parameters need to be fitted when 2 partial structures (dummy atoms + solvent model) are present and that about 200 reflections was enough in our of their test cases to get reasonable estimates. P Bart Hazes wrote: >*** For details on how to be removed from this list visit the *** >*** CCP4 home page http://www.ccp4.ac.uk *** > > >For ARP/wARP the relevant quantity is not so much Rfree, but the ability to >derive meaningful SIGMAA coefficients for the maximum likelihood target. Will >the 1/sqrt(n) relation apply to that as well. If so we need to know what >accuracy we need (can get away with). If 5% is tolerable then just 400 >reflections would do the job. Perhaps the fact that Sigmaa has to be estimated >as function of resolution increases the number of rfree reflections. Randy, >Raj, Garib ...??? > >Bart > >On Tue, 4 Feb 2003, Bernhard Rupp wrote: > > > >>*** For details on how to be removed from this list visit the *** >>*** CCP4 home page http://www.ccp4.ac.uk *** >> >>Tassos wrote: >> >> >> >>>A small note: I always use 1000-1500 reflections for Rfree instead >>>of the more 'standard' 10%. Saving on a few reflections sometimes >>>for me simply does the trick. >>> >>> >>This 10% indeed is the same unreflected number like 10mg/ml conc >>for crystallization. Meth enz 277 B pp 382 essentially states >>in more cryptic words that 'as many reflections as necessary to make >>free R statistically meaningful' i.e., the error in Rfree reasonable. >>That std error (p384) appears to be Rfree/sqrt(n), with n the number of >>test >>reflections, and not a percentage. >> >>Handy ref in case one needs to respond to a review comment. >> >>BR >> >> >> >> >> > >=============================================================================== > >Assistant Professor >Dept. of Medical Microbiology & Immunology >University of Alberta >1-15 Medical Sciences Building >Edmonton, Alberta, T6G 2H7, Canada >phone: 1-780-492-0042 >fax: 1-780-492-7521 > >=============================================================================== > > > > >

**References**:**RE: [ccp4bb]: ccp4bb- Warp-Arp***From:*Bart Hazes <bhazes@ualberta.ca>

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