---
name: "fox"
section: "1"
platform: "linux"
package: "objcryst-fox"
version: "2022.1-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fox"
---

# fox(1)

ab-initio structure determination from diffraction data

## 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).