[phenixbb] Phenix.refine Questions

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Thu Feb 21 15:58:30 PST 2008

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.


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