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Manual

freesasa

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
Parameters
Atom radii and classes (maximum one of the following)
Input options
Output options
Deprecated

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NAME

FreeSASA - calculate Solvent Accessible Surface Areas from PDB files

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 )

DESCRIPTION

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.

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