The integration programs report a negative intensity simply because that is the observation. 

Because of noise in the Xray background, in a large sample of intensity estimates for reflections whose true intensity is very very small one will inevitably get some measurements that are negative. These must not be rejected because this will lead to bias (because some of these intensities for symmetry mates will be estimated too large rather than too small). It is not unusual for the intensity to remain negative even after averaging symmetry mates.

Andrew


On 20 Jun 2013, at 11:49, Douglas Theobald <[log in to unmask]> wrote:

> Seems to me that the negative Is should be dealt with early on, in the integration step.  Why exactly do integration programs report negative Is to begin with?
> 
> 
> On Jun 20, 2013, at 12:45 PM, Dom Bellini <[log in to unmask]> wrote:
> 
>> Wouldnt be possible to take advantage of negative Is to extrapolate/estimate the decay of scattering background (kind of Wilson plot of background scattering) to flat out the background and push all the Is to positive values?
>> 
>> More of a question rather than a suggestion ...
>> 
>> D
>> 
>> 
>> 
>> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Ian Tickle
>> Sent: 20 June 2013 17:34
>> To: ccp4bb
>> Subject: Re: [ccp4bb] ctruncate bug?
>> 
>> Yes higher R factors is the usual reason people don't like I-based refinement!
>> 
>> Anyway, refining against Is doesn't solve the problem, it only postpones it: you still need the Fs for maps! (though errors in Fs may be less critical then).
>> -- Ian
>> 
>> On 20 June 2013 17:20, Dale Tronrud <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>>  If you are refining against F's you have to find some way to avoid
>> calculating the square root of a negative number.  That is why people
>> have historically rejected negative I's and why Truncate and cTruncate
>> were invented.
>> 
>>  When refining against I, the calculation of (Iobs - Icalc)^2 couldn't
>> care less if Iobs happens to be negative.
>> 
>>  As for why people still refine against F...  When I was distributing
>> a refinement package it could refine against I but no one wanted to do
>> that.  The "R values" ended up higher, but they were looking at R
>> values calculated from F's.  Of course the F based R values are lower
>> when you refine against F's, that means nothing.
>> 
>>  If we could get the PDB to report both the F and I based R values
>> for all models maybe we could get a start toward moving to intensity
>> refinement.
>> 
>> Dale Tronrud
>> 
>> 
>> On 06/20/2013 09:06 AM, Douglas Theobald wrote:
>> Just trying to understand the basic issues here.  How could refining directly against intensities solve the fundamental problem of negative intensity values?
>> 
>> 
>> On Jun 20, 2013, at 11:34 AM, Bernhard Rupp <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>> As a maybe better alternative, we should (once again) consider to refine against intensities (and I guess George Sheldrick would agree here).
>> 
>> I have a simple question - what exactly, short of some sort of historic inertia (or memory lapse), is the reason NOT to refine against intensities?
>> 
>> Best, BR
>> 
>> 
>> 
>> 
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