Running PHENIX Wizards from the command-line

Any of the PHENIX Wizards can be run from the command line. A sample command-line run of each Wizard is:

phenix.autosol w1.sca seq.dat 2 Se f_prime=-8 f_double_prime=4.5
phenix.autobuild data=datafile model=model.pdb seq_file=seq.dat
phenix.automr native.sca search.pdb RMS=0.8 mass=23000 copies=1
phenix.ligandfit data=datafile model=partial_model.pdb ligand=ligand.pdb

You can get complete help on any of the command-line versions by typing the name of the wizard and --help or --help and the name of a keyword:

phenix.autosol --help
phenix.autobuild --help seq_file
phenix.automr --help
phenix.ligandfit --help

You may find that the command-line versions are much quicker and easier to usethan the GUI or script versions for routine cases. The command-line versions can do almost anything the GUI or script versions can do, with the exception that the AutoSol Wizard command-line version cannot run MIR or multiple datasets.

Running PHENIX Wizards from a Script

Any of the PHENIX Wizards can be run from a script. A sample script is:

#!/bin/csh
source /usr/local/phenix-1.24.1b/phenix_env # this is your standard phenix_env
phenix.runWizard AutoSol                    # run AutoSol

The Wizard will read inputs from Facts.list if this file is present. A sample Facts.list file (full lists are available in the Information icons for each wizard and in the Help tab on the main GUI under Wizard Help):

!  Sample Facts.list file for AutoSol
sg c2
cell_params 76.08 27.97 42.36 90.0 103.2 90.0
datafile_list test_wvb.sca

If you run a wizard (either from a GUI or a script) and stop it in the middle, it will remember where it is. If you restart, it will continue on from there. If you want to start all over and forget everything done with this wizard when running from a script, add the word restart to the runWizard command:

% phenix.runWizard AutoBuild restart      # run AutoBuild and start all over

Running a Wizard from a GUI or from a Script

You can mix running a Wizard from a GUI with a script. They will each read the same database and continue from the same place. When running the Wizard from a GUI after running from a script, you may need to hit RUN and then PAUSE once to reset the GUI.

Copying a directory containing a PDS (Project Data Storage) and Wizard databases from one machine to another.

You can copy an entire directory where you have run a Wizard from one machine to another. You can then run the same wizard (from script or GUI) on the new machine. This can be useful for handing all the results from a run to someone else for viewing or analysis.

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