[phenixbb] Phenix.refine Questions

Peter Zwart PHZwart at lbl.gov
Thu Feb 21 14:05:43 PST 2008

The & should work actually. What makes you think it doesn't?

Regarding twinning, detwinned maps are used. There was a bug somewhere
that was fixed recently. I suggest you download the latest cci_apps
and try it with that version.



2008/2/21, Mary Fitzgerald <mary.x.fitzgerald at gmail.com>:
> 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.  It would be nice to start a job and go home without
> leaving myself logged into the computer.  I didn't see anything in the
> documentation which makes me think I'm being dull.
> Second, a technical question.  When phenix.refine does ordered solvent, does
> it use detwinned maps if you've put in the appropriate twin operator and
> indicated it was twinned?  When I've tried running phenix.refine with my
> perfect twin, it doesn't seem to find waters like I can using the CNS
> twinned water picking script.
> 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.
> Thanks,
> Mary X. Fitzgerald
>  Postdoctoral Associate
> Arnold Lab
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