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.