Dear Nat,
Good point - this does not appear to be difficult to change, so I will do this now.
I'm very happy to hear it. Thank you for your consideration. As Pavel said, converting flag convention is dirty work, but I think it's sometimes useful. (For some programs which assume ccp4 freeR-flag convention) So I hope this function will be maintained.
I suspect (I hope) that the flag value completion in CCP4 will only look at the %free, not the counts of all values,
Reading the manual of freerflag (ccp4 program), I found this description: "The fraction of data per bin is taken from the highest value of the freeR flag" when completing existing freeR flags. http://www.ccp4.ac.uk/html/freerflag.html
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.
Yes, this is very helpful! Cheers, Keitaro