[phenixbb] launching MR jobs from the command line.

Nathaniel Echols nechols at lbl.gov
Wed Jun 4 11:27:22 PDT 2014

On Wed, Jun 4, 2014 at 11:13 AM, Francis Reyes <Francis.Reyes at colorado.edu>

> For the moment (1.9-1692) phenix.automr still works from the command line
> but I received a note that it's a 'Deprecated program' .
> ************************************************************************
>                     WARNING - DEPRECATED PROGRAM
> Please note: the command-line AutoMR tool and associated GUI have been
> deprecated and will be removed in future releases.  We recommend that
> you use phenix.mrage or phenix.phaser, both of which are available in
> the GUI.
> The program will resume execution in 5 seconds.
> ************************************************************************
> phenix.mrage doesn't resolve to anything, and phenix.phaser runs the
> phaser binary.

What do you mean by "doesn't resolve to anything"?  Maybe it's an issue
with capitalization - the correct command is "phenix.MRage".  (Although on
Mac this probably won't matter, but I'll add "phenix.mrage" as a synonym
just in case.)

Is there a new way to launch MR jobs from the command line (which had all
> the PHIL friendly goodies that automr had?) ?

phenix.phaser only runs in CCP4-style mode if there are no command-line
arguments; otherwise it uses PHIL.  If you run this command:

phenix.phaser --show_defaults

it will print out the full parameters, and there is also some support for
simpler command-line arguments:

phenix.phaser model.pdb data.mtz sequence.fa model_rmsd=1.5 search_copies=2

However, unless you're trying to develop some kind of automation on top of
Phaser, this is pretty close to the bottom of our list of support
priorities, hence the lack of documentation.

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