---
name: "freesasa"
section: "1"
platform: "linux"
package: "freesasa"
version: "2.1.2-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/freesasa"
---

# freesasa(1)

calculate Solvent Accessible Surface Areas from PDB files

## 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.