[phenixbb] questions related to Phenix refinement

[Kay Diederichs]

Dear Pavel,

Am 18.01.15 um 07:23 schrieb phenixbb-request at phenix-online.org:
> Date: Sat, 17 Jan 2015 20:36:30 -0800
> From: Pavel Afonine <pafonine at lbl.gov>
> To: Smith Lee <smith_lee123 at yahoo.com>,	"phenixbb at phenix-online.org"
> 	<phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] questions related to Phenix refinement
> Message-ID: <54BB384E.30602 at lbl.gov>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
> 
> Hello Smith,
> 
>> > In the X-ray statistics by resolution bin of the Phenix.refine result, 
>> > there is a column "%complete".  For my refinement data, I find the 
>> > better the resolution (from lower resolution to the higher 
>> > resolution), the lower the completeness (for example for 40-6 A, 
>> > %complete is 98, for 3.1-3.0 A, %complete is 60%, for 2.2-2.1 A, 
>> >  %complete is  6%).
>> >
>> > Will you please tell me what does this "%complete" mean? why it 
>> > decreases in the better diffraction bin?
> Completeness is how many reflections you have compared to theoretically 
> possible. So the higher completeness the better. Ideally (and it's not 
> that uncommon these days) you should have 100% complete data set in 
> d_min-inf resolution. Anything below say 80 in any resolution bin is 
> bad, and numbers you quote 6-60% mean something is wrong withe the dataset.
> 

Given your standing in the community, the last sentence will lead many
unexperienced people to believe that they should cut their data at the
resolution where the completeness falls below "say 80"%.

But that would be wrong. There is no reason to consider a completeness
as "too low in a high-resolution shell" as long as the data in that
shell are good. Particularly in refinement any reflection helps to
improve the model, and to reduce overfitting.

Of course, more complete is better! Nowadays there should be no reason
_not_ to get >95% (>99% in high-symmetry spacegroups) completeness in
the low resolution shells, unless people stick to the "collect minimum
rotation range" paradigm, and get the starting angle (or the point
group!) wrong.

best,

Kay




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