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Administrator Chem3D provides two overlay techniques. “Tutorial 6: Overlaying Models” on page 39 describes the Fast Overlay method. This section uses the same example—superimposing a molecule of Methamphetamine on a molecule of Epinephrine (Adrenalin) to demonstrate their structural similarities—to describe the Minimization Method. 1. From the File menu, choose New Model. 2. Select the Text Building tool and click in the model window. A text box appears. 3. Type Epinephrine and press the Enter key. A molecule of Epinephrine appears. 4. Click in the model window, below the Epinephrine molecule. A text box appears. 5. Type Methamphetamine and press the Enter key. A molecule of Methamphetamine appears beneath the Epinephrine molecule. 6. From the Model Display submenu of the View menu, deselect Show Hs and Lps. The hydrogen atoms and lone pairs in the molecule are hidden. The two molecules should appear as shown in the following illustration. You may need to move or rotate the models to display them as shown. TIP: To move only one of the models, select an atom in it before rotating. 7. From the Model Display submenu of the View menu, select Show Atom Labels and Show Serial Numbers. The atom labels and serial numbers appear for all the visible atoms. To perform an overlay, you must first identify atom pairs by selecting an atom in each fragment, and then display the atom pairs in the Measurements table. Atom Pair —an atom in one fragment which has a distance specified to an atom in a second fragment. 1. Select C(9) in the Epinephrine molecule. 2. Shift+click C(27) in the Methamphetamine molecule. 3. From the Structure menu, point to Measurements and choose Set Distance. The Measurements table appears. The Actual cell contains the current distance between the two atoms listed in the Atom cell. 4. For an acceptable overlay, you must specify at least three atom pairs, although it can be done with only two pairs. Repeat steps 1 to 3 to create at least three atom pairs. 5. The optimal distances for overlaying two fragments are assumed to be zero for any atom pair that appears in the Measurements table. For each atom pair, type 0 into the Optimal column and press the Enter key. 106•Inspecting Models CambridgeSoft Comparing Models by Overlay
Your measurements table should look something like this: Now perform the overlay computation: NOTE: To help see the two overlaid fragments, you can color a fragment. For more information see “Working With the Model Explorer” on page 107 1. From the Model Display submenu of the View menu, deselect Show Atom Labels and Show Serial Numbers. 2. From the Structure menu point to Overlay, and click Minimize. The Overlay dialog box appears. 3. Type 0.100 for the Minimum RMS Error and 0.010 for the Minimum RMS Gradient. The overlay computation will stop when either the RMS Error becomes less than the Minimum RMS Error or the RMS Gradient becomes less than the Minimum RMS Gradient value. 4. Click Display Every Iteration. 5. Click Start. How the fragments are moved at each iteration of the overlay computation is displayed. To save the iterations as a movie, click the Record Each Iteration check box. To stop the overlay computation before it reaches the preset minima, click Stop Calculation on the toolbar. The Overlay operation stops. Recording is also stopped. The following illustration shows the distances between atom pairs at the completion of the overlay computation. The distances in the Actual cells are quite close to zero. Your results may not exactly match those described. The relative position of the two fragments or molecules at the start of the computation can affect the final results. Working With the Model Explorer The Model Explorer displays a hierarchical tree representation of the model. It provides an easy way to explore the structure of any model, even complex macromolecules, and alter display properties at any level. The Model Explorer defines the model in terms of “objects”. Every object has a set of properties, including a property that defines whether or not it belongs to another object (is a “child” of a higher level “parent” object.) The default setting for all properties is Inherit Setting. This means that “parents” determine the properties of “children”, until you choose to ChemOffice 2005/Chem3D Inspecting Models • 107 Working With the Model Explorer
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Chapter 31: Changes and Audit Trail
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Administrator Tutorial 7: Docking M
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