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<title>Ghemical User Documentation: Objects: ESP Plane</title>
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<h1>2.1.8 Visualization Tools</h1>
<p>The following visualization tools are available:<br>
</p>
<ol>
<li>A ribbon model for polypeptides. Click <a href="ribbon.html">here</a>
for a description of this feature.</li>
<li>An intersection plane object (a 2D plane that displays information
using colour of the plane).</li>
<li>A 3D volume rendering object (made of several stacked transparent
plane objects).</li>
<li>A 3D isosurface object. An isosurface is a surface defined by the
set of points that have a constant value for a function. Ie f(x, y, z)=k.
Only the points for which f(x, y, z)=k are on the surface. For example,
in the case of electrostatic potential, the function f(x,y,z) is an expression
of electrostatic potential for a set of point charges.<br>
</li>
</ol>
<p>The objects are capable to display any continuous mathematical functions.
Currently supported functions are:<br>
</p>
<ul>
<li>Electrostatic potential (in MM models calculated using the atomic
charges, and QM models using calculated electron density).</li>
<li>(in QM models only) Molecular Orbital Wavefunctions.</li>
<li>(in QM models only) Electron Density.</li>
</ul>
<p> </p>
<h2>Examples:</h2>
<p>As an example, let's create an electrostatic potential plane parallel
to the XY plane of the project view. The electrostatic potential of a point
is defined as the energy required to move a unit positive charge from infinity
to the point. The plane is displayed in the project window, superimposed
on the molecule. The plane is colored to indicate the sign and magnitude
of the electrostatic potential at that point. Areas with negative electrostatic
potentials (a unit positive charge moving from infinity to that point is
spontaneous) are colored blue. The move negative the electrostatic potential
is, the lighter the shade of blue is. Areas with positive electrostatic potentials
are colored red, with the more positive areas colored with a lighter shade
of red. </p>
<p> To create an electrostatic potential plane right click on the project
window. Now select Objects and then ESP Plane. </p>
<br>
<img src="images/esp-plane_select.png" width="409" height="427"
alt="Screenshot of selecting the ESP plane object.">
<br>
<p> A window will appear that looks like this:</p>
<br>
<img src="images/ci_plane.png" width="411" height="98"
alt="Screenshot of the ESP plane parameters command interpreter box.">
<br>
<p>Typically only advanced users should modify the text in this box. Click
ok to run the calculation You may change the orientation of the plane if
you want to have it intersect a different section of the molecule. To do
this, make sure the ESP Plane object is selected (after the plane is added
it is automatically selected, although using other features may change the
selection to a different object). To select the object, click on the Project
View tab and then highlight the ESP Plane entry on the list of objects. The
ESP Plane is now selected. </p>
<br>
<img src="images/esp-plane_select_obj.png" width="395" height="184"
alt="Screenshot of selecting the ESP plane object.">
<br>
<p> Click back onto the camera view. Holding the shift key down will cause
any translation, rotation or orbit to only affect the ESP plane. </p>
<h2>Algorithm</h2>
<p> The molecular mechanical model of Ghemical uses a relatively simple algorithm
to generate an electrostatic potential plane. At each point on the plane
the electrostatic potential is calculated. It is calculated by adding together
the electrostatic potential energy between the point and each atom. The
charge used for each atom is the same as the charge displayed by the Measure
tool (an approximate charge based on the type of atom and what it is bonded
to, ie the oxygen of an alcohol is given a charge of -0.25). Once the energy
is calculated, a color for that point is calculated based on the sign and
magnitude of the energy.</p>
<p></p>
<h2>Applications</h2>
<p>Electrostatic potential planes can be used predict the location of an
electrophilic attack. An electrophile will typically attack in areas near
an electrostatic potential minimum, which are colored blue.</p>
<h2>Notes</h2>
<p>The quantum mechanical model can also produce an electrostatic potential
plane. The algorithm used by by the quantum mechanical model is more complex
than the one used by the molecular mechanics model, so the plane produced
may contain different features. The quantum mechanical electrostatic potential
plane of cytosine shows a minimum next to the nitrogen where experimental
data shows an electrophile will attack. The molecular mechanics ESP plane
does not show this minimum. </p>
<img src="images/esp-plane_mm.png" width="410" height="428"
alt="Screenshot of molecular mechanics ESP plane of cytosine.">
<img src="images/esp-plane_qm.png" width="410" height="428"
alt="Screenshot of quantum mechanics ESP plane of cytosine.">
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