Hi Mary,
First, I have a hopefully easy question. I can't seem to figure it out although feel like I should be able to. Is there a way to run a phenix.refine job in the background? I tried using the & like I usually do and it didn't work.
In this respect, phenix.refine is like any other Unix command. It will work if you direct both "stdout" and "stderr" to a file, e.g. in tcsh: phenix.refine model.pdb data.mtz >& logfile & I think newer bash versions also support the simple ">&" syntax. It is a good habit to redirect the output of all background jobs in this way. The --quiet option pointed out by others is a good idea, too. But to be sure a background command doesn't hang always use the redirection to a file.
Third, is it possible to run phenix.refine in parallel at all. My structure is annoying large and the parallelization of FFT in CNS seems to help speed things up abit.
No, sorry. We will address this at some point in the future. Ralf