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<title>GAMGI Interfaces: Atom Modify</title>
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<h1>Atom Modify</h1>
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<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><span>View</span></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 visual representation for a single atom or a list of atoms.
<p/>
To modify a atom, click over its graphic image, or write its id 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>Style</h3>
The <b>Style</b> option menu is to select the atom visual representation.
Currently supported styles are: 1) a sphere, for <b>Solid</b>; 2) a cross, for
<b>Wired</b>. The sphere gives a hight visual quality, when coupled with lights
and perhaps a perspective projection. A sphere uses considerable screen space
though and is time consuming.
<p/>
The cross uses much less screen space and computing time. Moreover, when atoms
are bonded, crosses are not represented at all, and atoms are identified just
by the ends of the bond lines, decreasing even further computation needs.
However, wired objects do not have a 3D representation, so diffuse and
specular lights are not reflected, becoming poorly visible when using
lights, unless the ambient component is important, about (0.5, 0.5, 0.5).
<h3>Size</h3>
In <b>Solid</b> mode, this parameter controls the size of the atom spheres.
Combining atom <b>Size</b> and <b>Variancy</b> with bond <b>Size</b>, it is
possible to obtain a wide range of styles to represent atomic structures.
<p/>
In <b>Solid</b> mode, the default is to represent atoms as constant
spheres (<b>Variancy</b> = <b>0.0</b> and <b>Size</b> = <b>0.8</b>),
slightly larger than the bonds (<b>Size</b> = <b>0.5</b>). An elegant
style is to represent atoms as constant spheres with the same <b>Size</b>
as bonds (<b>0.5</b>).
<p/>
To represent compact cristalline structures, atom <b>Size</b>
and <b>Variancy</b> must be <b>1.0</b>, to be consistent with
cell dimensions. This style can also be used to represent molecules,
in order to emphasize the atomic radius and electronic distribution.
To change the default <b>Size</b> select <b>Atom->Config</b>.
<h3>Variancy</h3>
The intrinsic size of an atom is given by:
<pre>Size x (Variancy x Radius + (1 - Variancy) x Min)</pre>
where <b>Radius</b> is the atom radius and <b>Min</b> is the minimum
radius, by default the H covalent radius (currently 0.37). To change
this default select <b>Atom->Config</b>.
<p/>
In <b>Wired</b> mode, <b>Variancy</b> is always <b>0.0</b> so
all atom crosses have a constant size, given by <b>Size</b> x <b>Min</b>.
<p/>
In <b>Solid</b> mode, when <b>Variancy</b> is <b>0.0</b> the atom spheres
have all the same size, when <b>Variancy</b> is <b>1.0</b> the atom spheres
are scaled directly by the atom radius.
<h3>R, G, B</h3>
The <b>R</b>, <b>G</b>, <b>B</b> entries define the atom color,
from black (0.0, 0.0, 0.0) to white (1.0, 1.0, 1.0).
<h3>Scale</h3>
Set the atom size, including its child objects. Atom objects are
scaled around the atom center. The visual representation of an object
is always scaled by its own scale factor multiplied by the scale factor
of all its parent objects until layer, inclusive.
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