FOX(1)

💖 FOX(1) — like, the manual page, bestie 💖

okay so welcome to the General Commands Manual entry for fox, and babes, we are going to get you so comfy with this. sit down, grab a strawberry 🍓, and let's go.

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✨ NAME ✨

fox — ab-initio structure determination from diffraction data

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🦋 SYNOPSIS 🦋

fox [options] [file.xml]

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👑 DESCRIPTION 👑

The fox program — short for Free Objects for Crystallography, iconic name, no notes — was made for the ab initio crystal structure solution from diffraction data. and like, the features it brings to the table for ab initio structure determination are genuinely giving main character energy:

• 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 🌈

periodt. that's the whole vibe.

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🎀 OPTIONS 🎀

so this program my be executed with or without command line options or input file (file.xml) — and ngl, 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 at http://objcryst.sourceforge.net/Fox/Manual 🫶

• --help — Show summary of options. the classic. the icon.
• --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. and heads up bestie, --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°

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🌸 EXAMPLES 🌸

here's where it gets fun. live footage of fox in the wild:

• Fox silicon.xml Load file silicon.xml and launch GUI. easy. effortless. slay. 💅

Fox silicon.xml

• 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 1000000 -o 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. ten runs?? she's working hard, we love a hustle queen 👑

Fox Cimetidine-powder.xml --nogui --randomize -n 10000000 --nbrun 10 -o 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. silent AND powerful, it's giving mysterious 🕶️

Fox Cimetidine-powder.xml --nogui --silent --randomize -n 10000000 --nbrun 10 --finalcost 200000 -o best.xml

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💜 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). 💖

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and that's the whole page bestie, we ate, no crumbs left. this little love letter to the docs comes to you from July 24, 2008, straight out of the Debian project — iykyk. bye babe, go solve some crystal structures 🦋💅✨