[phenixbb] changing test set flag

Michael Hothorn michael at hothorn.de
Fri Dec 10 18:30:38 PST 2010

Thank you Nat. Refmac is not the problem (you can change the free R flag 
in the GUI as well) but some loop modeling server that apparently uses 
refmac but expects  the flag to be 0.


Nathaniel Echols wrote:
> 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
> matter).
> 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:
> FREE 1
> (although that won't help you in CCP4i.)
> -Nat
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