[phenixbb] a question on completeness

fn1 at rice.edu fn1 at rice.edu
Sat Jul 7 13:55:15 PDT 2012


Thank you for your advices!
Fengyun

Quoting "Jeffrey, Philip D." <pjeffrey at princeton.edu>:

> Try looking at the differences in completeness when you run CCP4's  
> Truncate with TRUNCATE YES and TRUNCATE NO.  The former option  
> alters the intensity distribution such that most of the weak data  
> are set to small positive values.  Depending on phenix.refine's  
> current policies this may alter how many reflections are included in  
> refinement.
>
> Another way to see this is to look at the range of values for Imean  
> data in the MTZ file using something like Mtzdump - if the  
> completeness reported by Mtzdump is what you expect, but the range  
> of values includes negative intensities that might be the source of  
> your problem.  Negative intensities can be a significant proportion  
> of data for anisotropic diffraction.
>
> BTW: you're posting on Phenixbb for CCP4 programs.  Better to ask  
> this question in CCP4bb if the above doesn't answer it.
>
> Phil Jeffrey
> Princeton
>
>
> ________________________________________
> From: phenixbb-bounces at phenix-online.org  
> [phenixbb-bounces at phenix-online.org] on behalf of fn1 at rice.edu  
> [fn1 at rice.edu]
> Sent: Saturday, July 07, 2012 12:24 AM
> To: PHENIX user mailing list
> Subject: [phenixbb] a question on completeness
>
> 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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