[phenixbb] rfree set

r n ramme29 at yahoo.com
Mon Apr 5 09:54:26 PDT 2010

Thanks, I will send you the mtz file, paper is under progress , so will send you asap.

I like to know  !

1. If I use mtz as default, which contains following labels,  F, SIGF, IMEAN, ISIGMA, RFRee flags.
Why  phenix picks up IMEAN instead of Fs. 

The number of reflections used for refinements are different after IMEAN is converted to Fobs by phenix..

With IMEAN , the number of reflection is 8770
output from phenix .log  Number of F-obs in resolution range:                   9120
                                           Number of F-obs <= 0:                                  377

I used mtz after phenix  run that convert Imean to Fobs, numberof reflections :              9121

same number of Rfree various by 15 reflections in both case.

I run both phenix with default
 phenix.refine model.pdb x.mtz

any suggestions.

From: Ralf W. Grosse-Kunstleve <rwgk at cci.lbl.gov>
To: phenixbb at phenix-online.org
Sent: Fri, April 2, 2010 2:16:10 PM
Subject: Re: [phenixbb] rfree set

> I converted mtz to xplor file and did the refinement . Also trying to use mtz file as it self, phenix
> complaining about MDchecksum Rfree.  
> I do have F, SIGF, I, IMEAN , Rfree-flags in the mtz file, converted to xplor format, phenix did not give me any
> warning about MDchecksum,

That's odd. I'd expect phenix.refine to work with either reflection
file and to pickup the correct value for the test set flag
automatically. If you send me the files (off-list) I'll take a look.

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