With the RMS (Root Mean Square) command sentence it is possible to compare (calculate a RMS deviation) between two different data sets (atomic COORDINATES, CHARGES, RADII, INTERNAL COORDINATES or POINTS) and also optimize the rotational matrix and translational vector for superposition atomic COORDINATES of two given SELECTIONS or a PAIR list, so that the RMS of compared coordinates gives a minimum.
RMS SELECT ... END SELECT ... END
PAIR
COORDINATES ()
ALL / BOTH
TRANSLATE
ROTATE
POLAR
FLAGS 6 or 3 inte
INIT / GUESS 6 * real
EIGEN
CHARGE
RADII
INTERNAL DISTANCE
ANGLES
DIHEDRALS
(ALL)
POINTS SURFACE
POTENTIAL
MAPS 2*inte
... SELECT ... END
... PAIRS ...
Two SELECTIONS define an implicit pair list, while the PAIR keyword accesses PAIRS as they appear in the PAIR list.
Points can not be PAIRED by the PAIR command word - 2 SELECTIONS should be specified.
... COORDINATES
ALL / BOTH
TRANSLATE
ROTATE
POLAR
FLAGS 6 or 3 inte
INIT / GUESS 6 * real
EIGEN
Coordinates of atoms can be also matched by a fitting procedure, when one of the command words (ALL, BOTH, ROTATE or TRANSLATE) follows the COORDINATE command. The coordinates of atoms are not actually moved. Only the parameters for rotation and translation are found and saved in programs memory. The parameters can be shown with a SHOW RMS or SAVE RMS. The rotational matrix used for the fitting procedure is the matrix number 8.
Remember: ROTATION is performed before TRANSLATION.
The two RMS choices (SELECT and PAIR) are equivalent.
> rms coordinates all select MOL_A end select MOL_B end
> make pair select MOL_A end select MOL_B end > rms coordinates all pair
Related coomands:
> save rms
The coordinates of the atoms and points can be ROTATED and TRANSLATED into the position found by the RMS fit routine, by first using ROTATION and later TRANSLATION and not vice versa. Center of rotation is implicit (coordinate system origin).
> rotate atom sele MOL_A end rms > translate atom sele MOL_A end rms
ROTATIONAL and TRASLATIONAL fit is performed. BOTH is a synonym of ALL.
ROTATIONAL and TRASLATIONAL fit is performed. BOTH is a synonym of ALL. See "RMS COORDINATES ALL".
Only ROTATIONAL atrix is optimized.
Only TRANSLATIONAL vector is optimized.
ROTATION angles are by default rotations about X, Y and X. POLAR keyword switches to POLAR rotational axis description (phi, psi, kappa) instead of the default choice.
Sometimes the procedure does not converge. In such cases it makes sense to start with some other INITIAL GUESS values. A common problem are 2-fold axis.... GUESS 6*real
Is a synonym of GUESS. See "RMS COORDINATES GUESS".
... FLAGS 6*inte
With flags you can fix some fitting parameters. For example you know that your rotational axis is a perfect 2-fold and you want to enforce it. ZERO means that a variable is kept fixed and 1 that it is optimized during the RMS optimisation procedure.
> rms coor all polar pairs guess 0. 0. 180. 0. 0. 0. \ > flags 1 1 0 1 1 1
... EIGEN
When EIGEN values based rotation matrix construction is performed then always all 6 parameters are fitted. Currently this option is not capable to extract rotation angles. The resulting rotation matrix is the number 8.
... CHARGES ...
Calculates RMS deviation of atomic CHARGES between the two atomic SELECTIONS.
... TEMPERATURE ...
Calculates RMS deviation of atomic TEMPERATURE factors (B-VALUES) between the two atomic SELECTIONS.
... B-VALUES ...
Calculates RMS deviation of atomic TEMPERATURE factors (B-VALUES) between the two atomic SELECTIONS.
... RADII ...
Calculates RMS deviation of atomic RADII between the two SELECTED coordinate lists.
... INTERNAL DISTANCE
ANGLES
DIHEDRALS
Calculates RMS deviation between the two specified INTERNAL coordinate lists.
... POINTS SURFACE
POTENTIAL
Compares pairs of points (SURFACE or POTENTIAL) according to their values.
... 2*inte
RMS deviation of density values between two specified maps can be calculated. It is required that the maps are identical in grids and box.