Chem3D Users Manual - CambridgeSoft

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Setting Serial Numbers this step, you will see different numbers on the tree control and the model. If this happens, simply hide the serial numbers momentarily and redisplay them. Administrator Atoms are assigned serial numbers when they are created. You can view the serial numbers in the following ways: • Point to the atom to display the pop-up information. • From the Model Display submenu of the View menu, choose Show Serial Numbers. • In the Chem 3D Model Settings dialog box, choose the Atom Labels tab, and then check the Show Serial Numbers checkbox. • Click the Serial Number toggle on the Model Display Toolbar. Serial numbers are initially assigned based on the order in which you add atoms to your model. To change the serial number of an atom: 1. If you are using the Model Explorer, select the atoms you want to re-number, and select Hide Atom Serial Number from the Atom Serial Numbers submenu of the context menu. 2. Click the Text tool. 3. Click the atom to reserialize. A text box appears. 4. Type the serial number. 5. Press the Enter key. If the serial numbers of any unselected atoms conflict with the new serial numbers, then those unselected atoms are renumbered also. To reserialize another atom with the next sequential number: • Double-click the next atom you want to reserialize. To reserialize several atoms at once: 1. Click the Text tool. 2. Hold down Shift and select several atoms. 3. Type the starting serial number. 4. Press the Enter key. Normally, the selected atoms are reserialized in the order of their current serial numbers. However, the first four atoms selected are reserialized in the order you selected them. Changing Stereochemistry NOTE: The Model Explorer cannot update its numbering to match the changes you are making on the model when Serial Numbers are displayed. If you forget You can alter the stereochemistry of your model by inversion or reflection. Inversion The Invert command performs an inversion symmetry operation about a selected chiral atom. 88 •Building and Editing Models CambridgeSoft Setting Serial Numbers
To perform an inversion: 1. Select the atom. 2. From the Structure menu, choose Invert. The Invert command only repositions side chains extending from an atom. For example, if you choose Invert for the structure below when C(1) is selected: The following structure appears. Plane, all of the X coordinates are negated. You can choose Reflect Through X-Z Plane to negate all of the Y coordinates. Likewise, you can choose Reflect Through X-Y Plane to negate all of the Z coordinates. You can choose Invert through Origin to negate all of the Cartesian coordinates of the model. If the model contains any chiral centers, each of these commands change the model into its enantiomer. If this is done, all of the Pro-R positioned atoms become Pro-S and all of the Pro-S positioned atoms become Pro-R. All dihedral angles used to position atoms are negated. NOTE: Pro-R and Pro-S within Chem3D are not equivalent to the specifications R and S used in standard chemistry terminology. For example, for the structure below, when any atom is selected: • From the Structure menu, point to Reflect Model and choose Through X-Z Plane. To invert several dihedral angles (such as all of the dihedral angles in a ring) simultaneously: 1. Select the dihedral angles to invert. 2. From the Structure menu, choose Invert stereochemistry. All of the dihedral angles that make up the ring are negated. Atoms positioned axial to the ring are repositioned equatorial. Atoms positioned equatorial to the ring are repositioned axial. Chem3D produces the following structure (an enantiomer): Reflection use the Reflect command to perform reflections on your model through any of the specified planes. When you choose the Reflect commands certain Cartesian coordinates of each of the atoms are negated. When you choose Reflect Through Y-Z ChemOffice 2005/Chem3D Building and Editing Models • 89 Changing Stereochemistry
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ChemOffice.Com ® ChemOffice ® Che
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License Information ChemOffice, Che
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· Licensed users of ChemOffice Ent
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computer, except as provided below.
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Q: IS IT OK TO COPY MY COLLEAGUE’
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A Guide to CambridgeSoft Manuals An
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Administrator Setting Molecular Sur
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Administrator Methods Available in
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Administrator Defining Atom Types.
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Desktop Software Enterprise Solutio
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SOLUTIONS Enterprise Solutions APPL
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Desktop to Enterprise Solutions Che
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SOFTWARE E-Notebook Ultra Ultimate
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SOFTWARE ChemDraw Ultra Ultimate Dr
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SOFTWARE Chem3D Ultra Ultimate Mode
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SOFTWARE ChemFinder/Word • Search
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SOFTWARE The Merck Index • Encycl
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SOLUTIONS •Development and deploy
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SOLUTIONS •Adds chemical data typ
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MANAGEMENT •Custom organization o
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MANAGEMENT • Indexes chemical str
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MANAGEMENT • E-Notebook Enterpris
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DISCOVERY • Accessed through your
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DISCOVERY • Integrated with Regis
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DISCOVERY • Reagent lists can be
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DISCOVERY •Effectively manages da
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DISCOVERY • Catalog driven data m
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DATABASES • Fully structure-searc
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DATABASES • Encyclopedic referenc
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DATABASES • Extensive collection
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SERVICES · Business Case Developme
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CS ChemOffice ® Desktop to Enterpr
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Chem3D Users Manual - CambridgeSoft

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