freesasa1

Calculate solvent accessible surface areas from pdb files

Usage

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)}

Overview

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 ⟨⟩

Options

Parameters

-S, --shrake-rupley: Use Shrake & Rupley algorithm

-L, --lee-richards: Use Lee & Richards algorithm [default]

-p, --probe-radius NUMBER: Set probe radius in Angstroms [default: 1.40 Å]

-n, --resolution INTEGER: Set resolution for calculation.
S&R: number of test points/atom [default: 100],
L&R: slices/atom [default: 20].

-t, --n-threads INTEGER: Number of threads to use [default: 2]

Atom radii and classes (maximum one of the following)

-O, --radius-from-occupancy: Read atomic radii from Occupancy in PDB input

-c, --config-file FILE: Clasifier to determine radii and classes. Example files in 'share/'

--radii protor|naccess: Use either ProtOr or NACCESS radii and classes [defatul: protor]

Input options

--cif: Input is in mmCIF format

-H, --hetatm: Include HETATM entries from input

-Y, --hydrogen: Include hydrogen atoms, suppress warnings with -w

-m, --join-models: Join all MODELs in input into one structure

-C, --separate-chains: Calculate SASA for each chain separately

-M, --separate-models: Calculate SASA for each MODEL separately

--unknown guess|skip|halt: When unknown atom is encountered, either guess its radius/class, skip it, or halt. [default: guess]

-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

-o, --output FILE: Output file

-e, --error-file FILE: Redirect errors and warnings to file

-f, --format log|res|seq|pdb|rsa|cif|xml|json: Output format, can be repeated. [default: log]

-d, --depth structure|chain|residue|atom: Depth of 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

--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 other format selected. Option has no effect.

Releases

Unchanged in 2 releases since Debian 12 (Bookworm).

12–13