[phenixbb] a question on completeness

fn1 at rice.edu fn1 at rice.edu
Sat Jul 7 13:53:11 PDT 2012


Hi Pavel,

Sorry that i didn't state clearly. When I say 97 to 99%, they are the  
numbers for different resolution shells.

I read from the truncate output file that many reflections are  
rejected because,

   ( having EITHER  Iobs .LT. -3.7*SDobs  OR  Iobs .LT.  
(SDobs)**2/MeanI - 4.0*SDobs )

this might be the reason completeness drops.
Thanks!
Fengyun

Quoting Pavel Afonine <pafonine at lbl.gov>:

> 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?
>
> Pavel
>
> 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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>
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