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 170°  with  500  points
              anda peak width of 0.1°

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)