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.

2.1.2                                                 2017                                           freesasa(1)