Compute positional RMSD to a reference structure.
Usage: targetRMSD [options] <target structure file> <structure files to compare>
Options are zero or more of:
-selection <selection> - Atoms used in comparison. An atom selection
enclosed in quotes. Default:
'(not hydro and not resname ANI)'.
-fitSelection <selection> - Atoms used to best-fit structures. An atom
selection enclosed in quotes.
Default: selection.
-selection2 <selection> - Atoms used in comparison for structure 2...
An atom selection enclosed in quotes.
Default: selection.
-fitSelection2 <selection> - Atoms used to best-fit structures 2...
An atom selection enclosed in quotes.
Default: fitSelection.
-psf <psf filename(s)> - One or more PSF filenames. If more than one
filename is specified, they must be either
space-separated and enclosed in quotes, or
colon-separated.
If this option is the value none, or omitted,
the PSF information is auto-generated.
-psf2 <psf filename(s)> - One or more PSF filenames for structure 2...
If more than one filename is specified, they
must be either space-separated and enclosed in
quotes, or colon-separated.
If this option is the value none or omitted,
the PSF information is auto-generated from
the first input structure file. The presence
of this option implies -diffSeq.
-diffSeq - Target and comparison structures have
different sequences - generate them
separately. All comparison structure files
must have the same sequence, though.
-removeMissing - Remove from a selection atoms not present in
the other, for cases where the selections
(selection, selection2), (fitSel, fitSel2) do
not have the same number of atoms.
-noFit - Omit the fitting procedure. If not specified,
the structures are best-fitted before pairwise
RMSD calculation.
-showRigid - Print full translation+rotation info for each
rigid body fit.
-write - For each comparison structure file, write the
corresponding fitted coordinates to a file
of the same name, appended with the suffix
".fit" (or the value specified by -fitSuffix).
-fitSuffix <string> - Specify custom suffix (e.g., <string> =
'.myfitsuffix') for the written fit
structures. As side effect, structures will
be written whether the -write option is
specified or not.
-model <model number> - Model number to use for the comparison
structure file[s]. The default behavior is
to compare to all models.
-useBIOMT - use the PDB's BIOMT field to generate the
full biological unit. Generated subunits will
have segids consisting of the ChainID followed
by the BIOMT number, starting with 2. [e.g.
the first might be A2.]
-perResidue - Report residue-by-residue RMSD values.
-perStructure - Report per-structure RMSD values.
Structures are first best-fit, and then the rmsd is calculated. This is done for each pair of structures. The average, deviation, min and max rmsd are printed.
If the -noFit is given, or if fitSelection != selection, the magnitudes of rotation and CM translation to fit selection onto selection2 is also printed.