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<title>GAMGI Interfaces: Atom Modify</title>
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<h1>Atom Modify</h1>
<div id="notebook">
<ul>
<li><a href="modify_element.html">Element</a></li>
<li><a href="modify_property.html">Property</a></li>
<li><a href="modify_analysis.html">Analysis</a></li>
<li><a href="modify_position.html">Position</a></li>
<li><a href="modify_view.html">View</a></li>
<li><a href="modify_length.html">Length</a></li>
<li><span>Angle</span></li>
</ul>
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<div class="contents">
Change here <b>Angle</b> properties between atoms and other objects.
<h3>Property</h3>
The supported <b>Angle</b> properties, the same as for <b>Atom->Measure</b>,
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.
<p/>
An easy technique to select the objects is to click the mouse
sucessively over their visual representations, in the sequence
shown in the dialog.
<p/><b>3-Atom Angle</b><p/>
The valence angle between directions Atom2-Atom1 and Atom2-Atom3.
<p/>
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.
<p/><b>4-Atom Angle</b><p/>
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.
<p/>
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.
<p/>
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.
<h3>Value</h3>
After selecting the property and the objects, set <b>Value</b>
to the desired angle and press <b>Ok</b> 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.
<p/>
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!).
<p/>
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.
<p/>
<b>Value</b> can take negative values, with the meaning described
above for <b>3-Atom</b> and <b>4-Atom</b> rotations.
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