I keep seeing people having trouble refining their structures in
Couple of comments: phenix.refine just because they were using "-->unused-ok" option. Well, with every powerful tool come caveats. The unused_ok option is a expert option and if people who have difficulties understanding what they are doing use it and encounter problems then it begs the question why expert users need to suffer the consequences of their inabilities. I use this option often and it is warranted in the current environment in which phenix goes through a lot of revisions, which break compatibility with previous versions, but provide new/better functionality I'd like to use. And yes, if you are doing a couple of structures a day, reediting the parameter file(s) is a serious drag.
Finally, I don't understand what the trouble is to run this command: phenix.refine --diff-params your_old_parameters.def > your_new_parameters.def
It is NOT usable in a automation environment. Since phenix goes through so many releases, which change the parameter file and bails by default if the parameter file does not match the current version, automation is difficult to achieve. Correct me if I am wrong, but I believe it would almost be impossible to pick up a previous refinement done with a old phenix version again via an automated approach if the parameter file has changed and phenix bails. Granted I could freeze the phenix version used for automation and could maintain a couple of different versions for different purposes, but that quickly becomes impractical. So in essence, for the "high-throughput-bleeding-edge-junky-users" the --unsed_ok option is essential and I hope that it remains. Cheers. Carsten