[phenixbb] AssertionError in twin refinement...

Pavel Afonine PAfonine at lbl.gov
Thu Mar 26 14:45:58 PDT 2009

Hi Francis,

the problem was in this line (and this is really our technical problem 
and not your fault):

primary_map_type = "m*Fobs-D*Fmodel"

which is in newer version looks like this:

primary_map_type = "mFobs-DFmodel"

It would not matter in refinement using non-twinned data (both will be 
recognized automatically), but in twin refinement phenix.refine uses 
some different internal routines that are less automated about this.

The take-home lesson: it is always the best to use newly generated 
parameter sets to make sure you are up-to-date with all eventual changes 
in parameters that might come along with a newer version.

> Command:
> phenix.refine *004.def --overwrite --unused_ok 
> refinement.input.xray_data.r_free_flags.generate=True

Just a couple of comments on the above line:

It is a bit dangerous to use "--unused_ok" because it will force 
phenix.refine to ignore the parameters that it did not recognize and so 
it will keep going, while you may still be thinking that those 
parameters are used. So, I wouldn't use this option unless you are very 

This "refinement.input.xray_data.r_free_flags.generate=True" should be 
used only once at the very beginning BEFORE any refinement is done, 
otherwise it will re-create the test set reflections every time you 
start the refinement therefore making the Rfree statistics invalid.


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