[phenixbb] a question on completeness
fn1 at rice.edu
fn1 at rice.edu
Sat Jul 7 13:53:11 PDT 2012
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
( having EITHER Iobs .LT. -3.7*SDobs OR Iobs .LT.
(SDobs)**2/MeanI - 4.0*SDobs )
this might be the reason completeness drops.
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?
> 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
>> Thanks in advance!
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>> phenixbb at phenix-online.org
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