[phenixbb] Phenix.refine Questions

Mary Fitzgerald mary.x.fitzgerald at gmail.com
Fri Feb 22 04:44:08 PST 2008

Thanks for answering.

I must have been half asleep when I tried using & before in linux.  I
remember it not working but I probably misskeyed something as it was the
first couple of time I ran phenix.  It's working now.

I was using a cci application from January so I'll try the newest version
for the ordered solvent.

Thanks again,

On 2/21/08, Ralf W. Grosse-Kunstleve <rwgk at cci.lbl.gov> wrote:
> 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
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