Output & Analysis

Output Formats

JSON (default)

Pretty-printed JSON with 2-space indentation:

{
  "total_area": 18923.28,
  "atom_areas": [
    32.47,
    0.25,
    15.82
  ]
}

Use JSON for machine-readable output and long-term pipelines. Legacy text formats such as freesasa and rsa are best-effort compatibility outputs for tools or reports that expect FreeSASA/NACCESS-style text.

Compact JSON

Single-line JSON without whitespace:

{"total_area":18923.28,"atom_areas":[32.47,0.25,15.82]}

CSV

Basic CSV with atom index and area:

atom_index,area
0,32.470000
1,0.250000
2,15.820000
total,18923.280000

When input has structural info (mmCIF/PDB), rich CSV is generated:

chain,residue,resnum,atom_name,x,y,z,radius,area
A,ALA,1,N,1.000,3.000,5.000,1.500,32.470000
A,ALA,1,CA,2.000,4.000,6.000,1.700,0.250000
,,,,,,,,18923.280000

FreeSASA-Compatible Text (`calc --format=freesasa`)

The single-structure calc command can write a FreeSASA-style text summary:

## zsasa FreeSASA-compatible output ##

PARAMETERS
algorithm    : Shrake & Rupley
classifier   : naccess
probe-radius : 1.40
Test-points  : 100
input        : structure.pdb

RESULTS (A^2)
Total   :   18923.28

This format is intended for interoperability with workflows that expect a FreeSASA-like human-readable report.

RSA Text (`calc --format=rsa`)

The single-structure calc command can also write a FreeSASA/NACCESS-style RSA table:

REM  zsasa FreeSASA/NACCESS-compatible RSA
REM  Absolute and relative SASAs for structure.pdb
REM  Atomic radii and reference values for relative SASA: naccess
REM  Algorithm: Shrake & Rupley
REM  Probe-radius: 1.40
REM  Test-points: 100
REM RES _ NUM      All-atoms   Total-Side   Main-Chain    Non-polar    All polar
REM                ABS   REL    ABS   REL    ABS   REL    ABS   REL    ABS   REL
RES ALA   A 1      30.00  23.3  20.00   N/A  10.00   N/A  20.00   N/A  10.00   N/A
END  Absolute sums over single chains surface
CHAIN  1   A       30.0         20.0         10.0         20.0         10.0
END  Absolute sums over all chains
TOTAL              30.0         20.0         10.0         20.0         10.0

rsa requires residue metadata, so use PDB/mmCIF input or another input format that provides chain, residue name, residue number, and insertion code fields. Relative all-atom RSA values are reported for standard amino acids; unavailable relative values are printed as N/A, matching FreeSASA's convention.

The RSA text table follows legacy NACCESS-style fixed-width columns where possible. If residue labels, residue numbers, chain IDs, or SASA/RSA values are too wide for those columns, zsasa still writes the full values and prints a warning that columns may be misaligned. Use --format=json for robust machine-readable output.

The freesasa and rsa formats are available for single calc runs only. Batch output remains json, compact, csv, or jsonl.

Trajectory Output (CSV)

The traj subcommand outputs CSV with per-frame total SASA:

frame,step,time,total_sasa
0,1,1.000,1866.44
1,2,2.000,1977.96
2,3,3.000,1884.93
...

Analysis Features

Per-Residue Aggregation (`--per-residue`)

Groups atom SASA by residue (chain + residue number + insertion code):

Per-residue SASA:
Chain  Res    Num       SASA  Atoms
----- ---- ------ ---------- ------
    A  MET      1     198.52     19
    A  LYS      2     142.31     22
    A  ALA      3      45.67      5

RSA Calculation (`--rsa`)

Calculates Relative Solvent Accessibility (RSA = SASA / MaxSASA).

MaxSASA reference values from Tien et al. (2013):

Residue	MaxSASA (Å²)	Residue	MaxSASA (Å²)
ALA	129.0	LEU	201.0
ARG	274.0	LYS	236.0
ASN	195.0	MET	224.0
ASP	193.0	PHE	240.0
CYS	167.0	PRO	159.0
GLN	225.0	SER	155.0
GLU	223.0	THR	172.0
GLY	104.0	TRP	285.0
HIS	224.0	TYR	263.0
ILE	197.0	VAL	174.0

Output with RSA values (can exceed 1.0 for exposed terminal residues):

Per-residue SASA with RSA:
Chain  Res    Num       SASA    RSA  Atoms
----- ---- ------ ---------- ------ ------
    A  MET      1     198.52   0.89     19
    A  LYS      2     142.31   0.60     22
    A  ALA      3      45.67   0.35      5

Polar/Nonpolar Summary (`--polar`)

Classifies residues and shows SASA breakdown. Automatically enables --per-residue.

Polar: ARG, ASN, ASP, GLN, GLU, HIS, LYS, SER, THR, TYR
Nonpolar: ALA, CYS, PHE, GLY, ILE, LEU, MET, PRO, TRP, VAL
Unknown: Non-standard residues (ligands, modified residues, etc.)

Polar/Nonpolar SASA:
  Polar:       2345.67 Å² ( 45.2%) - 42 residues
  Nonpolar:    2845.23 Å² ( 54.8%) - 58 residues
  Unknown:        0.00 Å² (  0.0%) -  0 residues

Output Formats​

JSON (default)​

Compact JSON​

CSV​

FreeSASA-Compatible Text (calc --format=freesasa)​

RSA Text (calc --format=rsa)​

Trajectory Output (CSV)​

Analysis Features​

Per-Residue Aggregation (--per-residue)​

RSA Calculation (--rsa)​

Polar/Nonpolar Summary (--polar)​