FOX(1)							      General Commands Manual							    FOX(1)

NAME

       fox - ab-initio structure determination from diffraction data

SYNOPSIS

       fox [options] [file.xml]

DESCRIPTION

       The  fox  (Free Objects for Crystallography) program was made for the ab initio crystal structure solution from diffraction data.  Its most
       interesting features for ab initio structure determination are:

       * versatile description of the crystal contents;

       * automatic correction for special positions and shared atoms between polyhedra;

       * the ability to use simultaneously multiple powder patterns;

       * smart global optimization algorithms;

       * a graphical interface with a 3D crystal structure view and live updates during the optimization process.

OPTIONS

       This program my be executed with or without command line options or input file (file.xml).  It follows the usual GNU command  line  syntax,
       with  long  options  starting with two dashes (`-').  A summary of options is included below.  For a complete description, see the fox wiki
       http://objcryst.sourceforge.net/Fox/Manual

       --help Show summary of options.

       --loadfouriergrd map.grd
	      Load and display 'map.grd' fourier map with (first) crystal structure

       --loadfourierdsn6 map.DN6
	      Load and display a DSN6 fourier map with (first) crystal structure

       --nogui
	      Run without GUI, automatically launches optimization --nogui may be accompanied by the following options:

       -n 10000
	      Run for 10000 trials at most (default: 1000000)

       --nbrun 5
	      Do 5 runs, randomizing before each run (default: 1), use -1 to run indefinitely

       -o out.xml
	      Output in 'out.xml'

       --randomize
	      Randomize initial configuration

       --silent
	      Produce (almost) no text output

       --finalcost 0.15
	      Run optimization until cost < 0.15

       --cif2pattern 1.5406 170 5000 .1
	      Simulate pattern for input crystal, wavelength=1.5406 up to 170o with 500 points anda peak width of 0.1o

EXAMPLES

       Fox silicon.xml
	      Load file 'silicon.xml' and launch GUI.

       Fox Cimetidine-powder.xml --nogui --randomize -n 1000000 -o best.xml
	      Load file 'ktartrate.xml', randomize, then make 1 optimization of 1 million trials, and save the best structure in 'best.xml'.

       Fox Cimetidine-powder.xml --nogui --randomize -n 10000000 --nbrun 10 -o best.xml
	      Load file 'Cimetidine-powder.xml', then make 10 runs (starting from a random structure) of 10 million trials (each run saves one xml
	      file), and save the best structure in 'best.xml'.

       Fox Cimetidine-powder.xml --nogui --silent --randomize -n 10000000 --nbrun 10 --finalcost 200000 -o best.xml
	      Load  file  'Cimetidine-powder.xml',  then make 10 silent runs of 10 million trials (each run saves one xml file), and save the best
	      structure in 'best.xml'.	For each run, the optimization stops if the cost goes below 200000.

AUTHOR

       fox was written by Vincent Favre-Nicolin <Vincent.Favre-Nicolin@cea.fr>.

       This manual page was written by Carlo Segre <segre@debian.org>, for the Debian project (but may be used by others).

								   July 24, 2008							    FOX(1)