freesasa(1)

💖 NAME 💖

FreeSASA — calculate Solvent Accessible Surface Areas from PDB files ✨

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🌸 SYNOPSIS 🌸

freesasa PDB-FILE ... [ --shrake-rupley | --lee-richards
    --probe-radius=NUMBER
    --resolution=INTEGER --n-threads=INTEGER
    --radius-from-occupancy | --config-file=FILE |
--radii=protor|naccess
    --separate-models | --join-models
    --hetatm --hydrogen
    --separate-chains | --chain-groups=STRING ...
    --unknown=guess|skip|halt
    --cif
    --output=FILE --error-file=FILE --no-warnings
    --select=STRING ...
    --format=log|res|seq|pdb|rsa|xml|json ...
    --depth=structure|chain|residue|atom ]

freesasa [options] < PDB-FILE

freesasa (--help | --version | --deprecated)

so basically bestie, there's three whole ways to call this thing 👑

1. Hand it one or more PDB-FILE arguments plus whatever options you're feeling, and it goes off 💅
2. Feed the PDB in on stdin with < PDB-FILE and pass your [options] 🫶
3. Just vibe-check it with --help, --version, or the nostalgic --deprecated ✨

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🦋 DESCRIPTION 🦋

Calculate the Solvent Accessible Surface Area (SASA) of biomolecules from PDB files, using either Lee & Richards' algorithm or Shrake & Rupley's algorithm. Pick your fighter, no cap 💀

Report bugs to: https://github.com/mittinatten/freesasa/issues

Home page: http://freesasa.github.io

fr fr if something's broken, tell the maintainers, don't just suffer in silence 🥺

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👑 OPTIONS 👑

🎀 Parameters

• -S, --shrake-rupley — Use the Shrake & Rupley algorithm.
• -L, --lee-richards — Use the Lee & Richards algorithm. [default] — this one's the main character unless you say otherwise 👑
• -p, --probe-radius NUMBER — Set the probe radius, in Angstroms. [default: 1.40 Å]
• -n, --resolution INTEGER — Set the resolution for the calculation. It's giving depends who you ask:
  • S&R: number of test points per atom [default: 100]
  • L&R: slices per atom [default: 20]
• -t, --n-threads INTEGER — Number of threads to use. [default: 2] — multitasking queen 🧚

🍓 Atom radii and classes (maximum one of the following)

listen. maximum one. not two, not three. pick a lane bestie 🫶

• -O, --radius-from-occupancy — Read the atomic radii from the Occupancy column in the PDB input.
• -c, --config-file FILE — Classifier to determine radii and classes. Example files live in 'share/' 📁
• --radii protor|naccess — Use either ProtOr or NACCESS radii and classes. [default: protor]

💜 Input options

• --cif — Input is in mmCIF format.
• -H, --hetatm — Include HETATM entries from the input.
• -Y, --hydrogen — Include hydrogen atoms. Suppress the warnings with -w (because it will be noisy, iykyk 🙈).
• -m, --join-models — Join all MODELs in the input into one single structure.
• -C, --separate-chains — Calculate SASA for each chain separately.
• -M, --separate-models — Calculate SASA for each MODEL separately.
• --unknown guess|skip|halt — When an unknown atom shows up, either guess its radius/class, skip it, or halt. [default: guess] — choose your adventure ✨
• -g, --chain-groups LIST — Each group will be treated separately.

Examples:

'-g A', '-g A+B', '-g A -g B', '-g AB+CD'

🌈 Output options

• -w, --no-warnings — Skip most warnings. living your peace era 🕊️
• -o, --output FILE — Output file.
• -e, --error-file FILE — Redirect errors and warnings to a file.
• -f, --format log|res|seq|pdb|rsa|cif|xml|json — Output format. Can be repeated. [default: log] — yes you can stack them, greedy little icon 💅
• -d, --depth structure|chain|residue|atom — Depth of the JSON and XML output. [default: chain]
• --select COMMAND — Select atoms using Pymol select syntax. Can be repeated.

Examples:

--select "AR, resn ala+arg", --select "chain_A, chain A"

💀 Deprecated

These options have been replaced and will disappear in later versions. Use them while you can, but don't get attached 😭

• --rsa — Equivalent to --format=rsa.
• -B, --print-as-B-values — Equivalent to --format=pdb.
• -r, --foreach-residue-type — Equivalent to --format=res.
• -R, --foreach-residue — Equivalent to --format=seq.
• -l, --no-log — Log suppressed if another format is selected. This option has no effect. literally nothing. a ghost. 🫠

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and that's the whole page bestie, go calculate some surfaces 🦋✨

freesasa(1) — version 2.1.2, dated 2017, from the FreeSASA man page. mwah, take care of her 💖🎀