Hi Marcin,
- probe and reduce are called in mmtbx through phenix wrappers (phenix.probe and phenix.reduce). We prefer to call them directly, but I guess it's not to be changed in cctbx. But after changing the name I also had to remove error checking in mmtbx/validation/clashscore.py that checks return code from phenix.reduce. Reduce itself quite often returns non-zero, it's just that the phenix.reduce wrapper ignores it and always returns 0 (probably not intentionally).
what you mean by "call them directly"? Yes, there are multiple instances of calling these programs in mmtbx like this trim = "phenix.reduce -quiet -trim -" result = easy_run.fully_buffered(trim) which is super-ugly! Ideally those C (or C++?) programs should be wrapped using boost.python and thus made available in Python. Pavel