Synopsis

Superpose [-hrvVw] [--dRMSD] [--ih] [--ps] [--save] [--aa=<selection>] [--bb=-1] [--ia=<selection>] [--ss=<secondaryStructure>] files…​

Description

Superpose frames one or two trajectory files to calculate RMSD.

Options

--bb, --backboneSelection=-1

Restrict selection to backbone atoms [0 == C_ALPHA or 1 == BACKBONE]. Note C_ALPHA uses N1 or N9 for NA.

--dRMSD

Calculate dRMSD in addition to RMSD.

-h, --help

Print command help and exit.

--ih, --includeHydrogen

Include hydrogen atoms.

--ps, --printSymOp

Print optimal SymOp to align input structures.

-r, --restart

Attempt to restart from a previously written RMSD matrix.

--save, --saveSnapshots

Save superposed snapshots (only for single process jobs).

--ss, --secondaryStructure=<secondaryStructure>

Restrict selection using a secondary structure string.

-v, --verbose

Write out RMSD information.

-V, --version

Print the Force Field X version and exit.

-w, --write

Write out the RMSD matrix.

Atom Selection Options

--aa, --active=<selection>

Ranges of active atoms [NONE, ALL, Range(s): 1-3,6-N].

--ia, --inactive=<selection>

Ranges of inactive atoms [NONE, ALL, Range(s): 1-3,6-N].

Arguments

files…​

Atomic coordinate file(s) to compare in PDB or XYZ format.