[phenixbb] how to extend R-free set

Nathaniel Echols nechols at lbl.gov
Wed May 19 09:36:03 PDT 2010

On Wed, May 19, 2010 at 9:13 AM, Pavel Afonine <PAfonine at lbl.gov> wrote:

> you can use "Reflection file editor" for this. It is available from PHENIX
> GUI. I'm not sure if the corresponding command line option exists, Nat knows
> this better.

In a hurry right now, but to summarize: iotbx.reflection_file_editor will do
this on the command line, but it's intended as a tool for automation and
testing, and is currently undocumented.  Something like this should do it:

iotbx.reflection_file_editor data.mtz r_free_flags.extend=True

but I'd really recommend trying the GUI first.  FYI, it assumes that R-free
flags were initially generated randomly, not by thin resolution shells (i.e.

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