xenial (1) fox.1.gz

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)