6.4 Centroids
VEGA ZZ can manage pseudo-atoms which
coordinates are calculated in real time from the positions of other atoms as symmetry
center. They are called centroids. A centroid can be used to measure
distance, angle, torsion, angle between two planes as a normal atom. In
molecular dynamics analysis the centroid position is recalculated for each
frame.
To define a new centroid, the user must select the Edit -> Add ->
Centroid menu item:
Picking the molecule atoms, the user can add a new centroid. The maximum number of pickable atoms is six (6). Clicking the New button, a new centroid is added and clicking the Reset button, the atom selection restarts from the beginning:
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Clicking the Keep fixed checkbox,
it's possible to fix the centroid coordinates that so aren't updated dynamically
when the coordinates of the other atoms are changed (e.g. during the trajectory
analysis or the torsion edit).
To close the dialog box, click Close
and to remove all centroids, select Edit -> Remove -> Centroids.
The centroids can be removed as normal atoms also. An application example can be
the distance measure between two rings: