[phenixbb] Completeness issue by phenix

Pavel Afonine pafonine at lbl.gov
Tue Dec 16 08:56:45 PST 2008

Hi Young-Jin,

> Another small wondering is about differently automatic(?) resolution pick up: my refmac assigned resolution range between 1.48 and 54.23 whereas my phenix.refine set it between 1.363 and 31.041 by default. 

phenix.refine does not remove your Fobs by default (would be weird if it 
did so) (a few Fobs outliers, is any, is an exception): it uses all data 
that you give it in your reflection file (all Fobs > 0). I do not know 
why Refmac removes data between 1.363 and 1.48.

You can tell phenix.refine to cut your data at resolution you want: use 
"xray_data.high_res=1.48" for this. Same for low resolution.

> Also while the refmac provides both entire and high resolution bin completeness, the phenix only gives a whole completeness. 

phenix.refine reports completeness in resolution bins too. Look .log 
file or PDB file header after refinement.


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