[phenixbb] Phenix.refine Questions - specifically running Phenix in the background

Edward Snell esnell at hwi.buffalo.edu
Thu Feb 21 13:11:23 PST 2008

Message: 8
Date: Thu, 21 Feb 2008 14:23:24 -0500
From: "Mary Fitzgerald" <mary.x.fitzgerald at gmail.com>
Subject: [phenixbb] Phenix.refine Questions
To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
	<2fc50e280802211123h192c095x9c65f5bd6f1d4a55 at mail.gmail.com>
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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.

Apologies if someone has already answered this but you can set up a
little command file e.g. 'refine.com', something along the lines of:

phenix.refine model_from_coot.pdb data.mtz ligand.cif
my_favourite.params --quiet

With all your parameters in 'my_favourite.params' and run it with

> nohup ./refine.com &

You can then log off and check it later and it will still be running.
The key seems to be the nohup and the '--quiet' switch.

Works for me, hope it works for you.



Edward Snell Ph.D.
Assistant Prof. Department of Structural Biology, SUNY Buffalo,
Hauptman-Woodward Medical Research Institute
700 Ellicott Street, Buffalo, NY 14203-1102
Phone:     (716) 898 8631         Fax: (716) 898 8660
Email: esnell at hwi.buffalo.edu  Telepathy: 42.2 GHz
Heisenberg was probably here!

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