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<title>GAMGI Interfaces: Atom Modify</title>
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<h1>Atom Modify</h1>
<div id="notebook">
<ul>
<li><span>Element</span></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><a href="modify_angle.html">Angle</a></li>
</ul>
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<div class="contents">
Change here the element and label for a single atom or a list of atoms.
<p/>
To modify an atom, click over its graphic image, or write its identification
(name and number) on the <b>Atom</b> entry. To modify a list of atoms, press
the button <b>List</b> (after creating the list of atoms with <b>Atom->Select</b>).
Parameters for empty entries or <b>Local</b> choices remain unchanged.
<p/>
To change an atom name write the new name in the <b>Atom</b> entry,
followed by the atom number (GAMGI needs the number to identify the atom).
To change the name for a list of atoms, press <b>List</b> first
and then write the new common name in the <b>Name</b> entry.
<h3>Element</h3>
Change here the element name, which can be <b>Si</b> but
not <b>si</b>, <b>S i</b> or <b>SI</b>. When a valid name is entered,
the element number is automatically set and default values are
suggested for the atom name, label, mass, radius and color. Choosing
a new element automatically changes these values to the new element.
Selecting non-default values for these parameters should therefore
be done only after setting the element.
<h3>Number</h3>
Change here the element number, which can vary between
0 (Du, a dummy atom) and 111 (Rg, currently the last element with
a two-letter symbol). When a valid number is entered,
the element name is automatically set and default values are
suggested for the atom name, label, mass, radius and color,
as described above.
<h3>Label</h3>
Change here the atom label, commonly used in Molecular
Mechanics to distinguish atoms described by different inter-atomic
potentials. For example, methyl and hydroxyl hydrogen atoms in methanol
molecules might be described by "h3" and "ho" atom labels. Atom labels
can have a maximum of 10 characters, accepted characters are the
same as for atom names.
<h3>Table</h3>
Pressing <b>Table</b> pops up a second window, showing a Periodic
Table of the Elements, with a button for each element. When an element
button is clicked, default data is transported to the first window,
exactly as if the user had written the element name in the <b>Name</b>
entry or the element number in the <b>Number</b> entry.
<p/>
Pressing <b>Table</b> again (or clicking <b>Cancel</b> in the second
window, or using the Window Manager tools) closes the second window.
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