[phenixbb] Phenix.refine Questions

Mary Fitzgerald mary.x.fitzgerald at gmail.com
Thu Feb 21 11:23:24 PST 2008

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.


Mary X. Fitzgerald
Postdoctoral Associate
Arnold Lab
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