Superpose frames one or two trajectory files to calculate RMSD.
Superpose(1) Manual Page
Name
Superpose - Superpose frames one or two trajectory files to calculate RMSD.
Synopsis
Superpose [-hrvVw] [--dRMSD] [--ih] [--ps] [--save] [--aa=<selection>] [--aa=<selection>] [--bb=-1] [--ia=<selection>] [--ia=<selection>] [--ss=<secondaryStructure>] files…
Description
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.