Re: [ccp4bb]: ccp4bb- Warp-Arp

[Peter Zwart <Zwart@embl-hamburg.de>]

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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:

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>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:
>
>  
>
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>>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
>>
>>
>>
>>    
>>
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