[phenixbb] Transfer FreeR and FreeR test set flag value

Pavel Afonine pafonine at lbl.gov
Sun Sep 6 20:40:27 PDT 2015

Hi Matt,

If asked to generate new flags, phenix.refine will use 1 for test and 0 
for work. However, it uses a smart flags interpretation machinery that 
can guess the right choice, if possible (for example, if 1 and 0 are 
flipped, it will take 0 as test just going by the fraction). If you have 
flags from 0 to 19 it will figure it is ccp4 format and use 0 as test by 
default. On top of that the user always can tell what flags to use as 
test flag. Also, the log file will always tell what was chosen as test 
and work flags.

Bottom line is: for phenix.refine does not care what value is used for 
free/work flag as long as phenix.refine can guess it automatically or 
the user explicitly specifies it.

Reflection file editor from Phenix GUI can transfer the flags.

I suggest you just try to do what you want and let us know should you 
encounter any problem.


On 9/4/15 13:24, Matthew Chu wrote:
> Dear All,
> I am trying to refine my model against a higher resolution dataset. My 
> colleage's old-low resolution dataset was processed in HKL/scalepack 
> and the FreeR was assigned by Phenix.reflection file editor, which I 
> assume the test set was marked as "1". Now I got a new-higher 
> resolution dataset, and plan to process it in XDS/Aimless. I want to 
> transfer the FreeR set from his old mtz and also use his low res model 
> for the new refinement. My question is, when I transfer the FreeR set 
> from his old mtz with flag value as "1" in Aimless, is the flag value 
> now "1" or "0" in the new mtz output by Aimless? Can Aimless recognize 
> the FreeR flag from the old mtz which are marked as "1"?
> I also read an old post from Nat Echols in 2011: "For Phenix, 1 is 
> test, 0 is work, but you could reverse this and it will still figure 
> out what to do automatically", so does it mean it doesn't matter if 
> the FreeR is "1" or "0" in the mtz from Aimless, if I use 
> phenix.refine for my new dataset, Phenix can figure out which is the 
> correct FreeR value?
> It's a mix of CCP4 and Phenix question, so I have crossed posted it in 
> the CCP4bb as well.
> Many thanks,
> Matt
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