GAMGI Interfaces: Atom Modify

# Atom Modify

- Element
- Property
- Analysis
- Position
- View
- Length
- Angle

Change here Angle properties between atoms and other objects.

### Property

The supported Angle properties, the same as for Atom->Measure, are listed below. Atoms and other objects may belong to different parents and may be bonded or not. Only objects in the current layer can be chosen.

An easy technique to select the objects is to click the mouse sucessively over their visual representations, in the sequence shown in the dialog.

3-Atom Angle

The valence angle between directions Atom2-Atom1 and Atom2-Atom3.

The signal convention is: when vector Atom2-Atom1 is rotated from vector Atom2-Atom3 through a direct, counter-clockwise rotation, the angle is positive, otherwise is negative. In 3D space, the direction of this planar rotation depends of the side of the plane where the user is, so the angle signal depends of the user position relatively to the atoms.

4-Atom Angle

The torsion angle between two planes, defined by Atom1-Atom2-Atom3 and Atom2-Atom3-Atom4. An error is shown when Atom1, Atom2, Atom3 or Atom2, Atom3, Atom4 are initially aligned along a common direction, because the plane Atom1-Atom2-Atom3 or Atom2-Atom3-Atom4 is undefined.

The signal convention is: looking along vector Atom2-Atom3 (with Atom1 near the user and Atom4 away from the user), when vector common direction-Atom1 is rotated from vector common direction-Atom4 by a direct, counter-clockwise rotation, the angle is positive, otherwise is negative.

While the signal of the 3-atom angle depends of the user position, the signal of the 4-atom angle is unique, because the four atoms define a 3D construction while the three atoms define only a 2D construction. If the user is looking from the other side, along the common direction Atom3-Atom2 (with Atom4 near the user and Atom1 away from the user), the user now sees the rotation in the opposite direction, which compensates the Atom1, Atom4 swap, so the signal of the torsion angle remains the same.

### Value

After selecting the property and the objects, set Value to the desired angle and press Ok to activate the change. An error is shown when some of the objects are not recognized, or when the angle or axis rotation cannot be determined.

For all properties, of all the objects selected by users only the first atom is actually modified. Atoms bonded to the first atom are also modified, as long as they are not bonded by cyclic structures to any of the other selected objects (without this restriction, all atoms in a ring would be rotated!).

In torsion angles, atoms bonded to the second atom are also modified, as long as they are not bonded to any of the other selected objects.

Value can take negative values, with the meaning described above for 3-Atom and 4-Atom rotations.
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