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

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 component_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.

-Nat