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freesasa(1) FreeSASA man page freesasa(1)

FreeSASA - calculate Solvent Accessible Surface Areas from PDB files

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)

Calculate the Solvent Accessible Surface Area (SASA) of biomolecules from PDB files using either Lee & Richards' or Shrake & Rupley's algorithms.

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

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

Use Shrake & Rupley algorithm
Use Lee & Richards algorithm [default]
Set probe radius in Angstroms [default: 1.40 Å]
Set resolution for calculation.
S&R: number of test points/atom [default: 100],
L&R: slices/atom [default: 20].
Number of threads to use [default: 2]

Read atomic radii from Occupancy in PDB input
Clasifier to determine radii and classes. Example files in 'share/'
Use either ProtOr or NACCESS radii and classes [defatul: protor]

Input is in mmCIF format
Include HETATM entries from input
Include hydrogen atoms, suppress warnings with -w
Join all MODELs in input into one structure
Calculate SASA for each chain separately
Calculate SASA for each MODEL separately
When unknown atom is encountered, either guess its radius/class, skip it, or halt. [default: guess]
Each group will be treated separately.
Examples:
'-g A', '-g A+B', '-g A -g B', '-g AB+CD'

Skip most warnings
Output file
Redirect errors and warnings to file
Output format, can be repeated. [default: log]
Depth of JSON and XML output [default: chain]
Select atoms using Pymol select syntax, can be repeated.
Examples:
--select "AR, resn ala+arg", --select "chain_A, chain A"

These options have been replaced and will disappear in later versions

Equivalent to --format=rsa
Equivalent to --format=pdb
Equivalent to --format=res
Equivalent to --format=seq
Log suppressed if other format selected. Option has no effect.
2017 2.1.2