On Fri, Mar 25, 2011 at 1:14 AM, Keitaro Yamashita
I'm using phenix-1.7-650 (current latest).
I noticed that r_free_flags.export_for_ccp4 option of iotbx.reflection_file_editor, which convert flag convention to ccp4 style, does always assign 1..19 to working set at random.
In CCP4 style, I think working set flag numbers should be 1 .. (1 / fraction - 1). Otherwise, I'm afraid it might have a bad influence on further processing e.g. flag value completion using ccp4 program.
Good point - this does not appear to be difficult to change, so I will do this now. In all honesty, that option is a huge hack - I wasn't happy about adding it, but we've been unable to convince anyone else to make their programs more automatic in identifying the correct flag. I suspect (I hope) that the flag value completion in CCP4 will only look at the %free, not the counts of all values, but I haven't looked at their code to confirm this. That said, we recommend using Phenix to extend existing flags anyway, because Phenix will take lattice symmetry into account by default, preventing twinning-related bias problems. (You can still make it output the flags in CCP4 format when doing this.) The one warning I have about this option is that the propagation of other (non-test) values is not guaranteed, i.e. the test set '0' will always be preserved, but what is '7' in the input may not be '7' in the output. The 'preserve_input_values' option will propagate unmodified R-free flags, but extending the flags will break this. (I'm not sure why - that's what I have written in the code - but I'll see if it's fixable too.) -Nat