[phenixbb] all reflections are equal, but some more than others

esko.oksanen at helsinki.fi esko.oksanen at helsinki.fi
Wed May 19 00:44:05 PDT 2010


   Having had a case of such hectic pseudosymmetry, it turns out that  
the problem originates already from the scaling that assumes a  
unimodal intensity distribution. The weak reflections then have their  
sigmas heavily overestimated and the strong ones overestimated. I had  
to scale the weak and strong reflections separately and ridig-body  
refine against the weak ones... Of course this type of problem has  
little to do with issue of treating negative intensities.


Quoting "Frank von Delft" <frank.vondelft at sgc.ox.ac.uk>:

> The philosophical arguments are fine, but is Pavel not justified in  
> asking for real cases where it matters?  It's not like he hasn't  
> spent time thinking about it, and it's not like the whole phenix  
> community isn't sitting in his ear about their own favourite missing  
> fix.
> I suppose what comes to mind is a case with hectic pseudotranslation  
> causing half the reflections to be systematically almost but not  
> quite zero.  But then again, I understand that even if you don't  
> toss the weak ones out, current algorithms don't deal with this well  
> anyway, so it needs special treatment (for now: refine in smaller  
> cell, then rigid-body refine in super-cell).
> phx.
> On 18/05/2010 18:33, Ed Pozharski wrote:
>> On Mon, 2010-05-17 at 16:20 -0700, Peter Zwart wrote:
>>> You make it sound like it is a bad thing. The effect of restraint
>>> weights (ADP, geometry) has most likely a much bigger impact on the
>>> final structure then a small fraction of smallish intensities (*)
>> Peter,
>> I think discarding data has to be justified.  Two points:
>> 1.  The fraction of negative intensities is not necessarily small.  It
>> depends on resolution cutoff (and you make an excellent point about
>> PTS), but looking at scalepack log-files I can tell that in my hands the
>> fraction is often 10% or more (DISCLAIMER: I belong to I/sigma=1
>> resolution cutoff cult).
>> 2.  Just because these reflections are weak does not mean that they are
>> insignificant.  Their contribution to the maps may be small (now I fear
>> another round of "fill-in missing Fobs with Fc for map calculation"
>> discussion), but keeping Fc close to zero for these reflections during
>> refinement seems to be just as important as to keep Fc close to whatever
>> values the strong reflections have.
>> The weak reflections are not fundamentally worse than strong(er)
>> reflections in the same resolution range.  They are measured with
>> roughly the same precision.  Moreover, the practice of setting negative
>> intensities to zero and then ignoring them in refinement discards those
>> that are barely negative and leaves in those that were (quite randomly)
>> barely positive.
>> You are absolutely right that other factors will have impact on the
>> model.  But that does not mean that discarding weak data is justified.
>> Crystallographic refinement is a Rube Goldberg machine, and all the
>> components should be as good as we can make them.  Perhaps there could
>> be something better than French&Wilson, but discarding negative
>> intensity reflections is hardly the solution.
>> Cheers,
>> Ed.
>> PS.  Personally I have no stake in this, since I always use truncate.
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