[phenixbb] a question on completeness

Pavel Afonine pafonine at lbl.gov
Fri Jul 6 22:21:17 PDT 2012

Hi Fengyun,

I have trouble understanding the statement "The output from SCALA give 
the completeness of about 97 to 99%". Overall completeness is just one 
number. Completeness in bins is a bunch of numbers, which are 
completeness per resolution bin. Completeness may be in range (eg. from 
d_min to d_max) or from d_min to inf. Sometimes they may be very 
different numbers.

Anyway, when it comes to refinement, phenix.refine log file reports 
initial reflection statistics somewhere at the very beginning of log 
file: this is what actually in your input reflection file. Later on 
phenix.refine may (or may not) remove a few reflections as outliers, 
which is also reported in the log file. I guess same information is 
obvious in the GUI as well.

So what exactly is your question?


On 7/6/12 9:24 PM, fn1 at rice.edu wrote:
> Hi all,
> I have one question on completeness. The output from SCALA give the 
> completeness of about 97 to 99%, but after TRUNCATE, the completeness 
> becomes only 90%. I tried to refine my model against intensity or 
> amplitude. They show different completeness too. I guess some 
> reflections are deleted during the truncation, but i could not see the 
> corresponding information in the log file. Does anybody have any 
> experience on what cause the difference in completeness?
> Thanks in advance!
> Fengyun
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> phenixbb at phenix-online.org
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