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<title>Measuring</title>
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<h1>2.1.7 Measuring Tools</h1>
<p>Ghemical can measure the distance between atoms, the angle formed by three
atoms and the dihedral angle formed by four atoms. In molecular mechanics
models ghemical will can also measure an approximate charge on an atom.</p>
<a name="measure_charge"></a>
<h2>Measuring Charges</h2>
<p>To find the approximate charge of an atom, click on the Measure button
on the left toolbar. Now left click on the atom you want to measure the charge
of. The approximate charge will be displayed in the log box automatically.
The output in the log box at the bottom of the window will look something like this: <br>
<br>
<kbd>charge: -0.25</kbd> <br>
<br>
Note this only applies to molecular mechanics models; in the current version
it is not possible to measure charges in quantum mechanical models.</p>
<p></p>
<a name="measure_distance"></a>
<h2>Measuring Distances</h2>
<p>To measure the distance between two atoms (such as a bond length), click
on the Measure button on the left toolbar. Now left click on the atoms you
want to measure the distance between. The color of the atoms selected for
measurement will be changed to pink. The distance between the two atoms will
automatically be displayed in the log box once the second atom is
selected. The output in the log box will look something like this:
<br>
<br>
<kbd>distance: 0.150697 nm</kbd> <br>
<br>
The atoms do not have to be bonded; the distance between any two atoms in
a molecule can be measured. </p>
<a name="measure_angle"></a>
<h2>Measuring Angles</h2>
<p> To measure the angle formed by three atoms, click on the measure button
on the left toolbar. Now left click on the three atoms that form the angle
you want to measure. The order that they are selected is important; the first
edge of angle that is measured are the the line between the first and second
atoms and the second edge is between the second and third atoms, making the
second atom the central atom. When the third atom is selected, the angle is
automatically displayed in the log box. The output in the log box will look
something like this: <br>
<br>
<kbd>angle: 109.471 deg</kbd> <br>
<br>
As with distances, the atoms forming the angle to not have to bonded to
each other. </p>
<a name="measure_torsion"></a>
<h2>Measuring Torsions</h2>
<p> To measure the torsion angle formed by four atoms click on the measure
button on the left toolbar. Now select the four atoms for the torsion angle.
The first three atoms selected will define a plane. The angle displayed
is the angle between this plane and a line from the fourth atom to the second.
The torsion angle is displayed in the log box as soon as the fourth
angle is selected. The output in the log box will look something
like this: <br>
<br>
<kdb>torsion: 120 deg <br>
<br>
</kdb></p>
<a name="measure_notes"></a>
<h2>Notes</h2>
<p> Atoms that have been selected can be unselected by clicking on them again.
All atoms are automatically unselected when a fourth atom is selected. There
are toggle buttons on the top toolbar labeled "The distance measuring mode,"
"The angle measuring mode," and "The torsion measuring mode" In the current
release these toggle buttons have no effect on the measuring tool. </p>
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