[phenixbb] changing test set flag

Nathaniel Echols nechols at lbl.gov
Fri Dec 10 18:26:01 PST 2010

On Fri, Dec 10, 2010 at 6:08 PM, Michael Hothorn <michael at hothorn.de> wrote:
> I used phenix.refine to generate the test set flag for my dataset which it
> did with a value of 1.  I now use a program that expects the test set flag
> in the mtz file to be 0. Is there a simple way to change the flag from 1 to
> 0 keeping the flagged reflections identical?

In theory the reflection file editor in the GUI can do this, as follows:

- add your file to the top list, and copy all arrays to the output list
- click the button "R-free flags generation"
- change the "User level" menu to "Advanced"
- check the box labeled "Convert R-free flags to CCP4 convention"

and it should output a file with the test set numbered 0 and
everything else numbered randomly from 1 to 19 (assuming 5% free,
otherwise the upper limit will be different, but this shouldn't

That said, if you're using REFMAC (which is usually where people start
to run into Phenix compatibility issues), you could also just add this
to the input:


(although that won't help you in CCP4i.)


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