Chem3D Users Manual - CambridgeSoft

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A molecule of Epinephrine appears. TIP: If you leave out the upper case “E”, Chem3D will display an “Invalid Label” error message. 1. Click one of the fragment names in the Model Explorer. The entire fragment is selected. Administrator 4. Click in the model window again to open another text box. 5. Select the entire word Epinephrine, replace it with Methamphetamine, and press the Enter key. The list of atoms in the Model Explorer is replaced with two Fragment objects, labeled Epinephrine and Methamphetamine. Fragment Labels 2. Click the Move Objects tool. 3. Drag the selected fragment away from the other fragment. The two fragments are hopelessly jumbled together at this point, so you might want to separate them before you proceed. 44 •Chem3D Tutorials CambridgeSoft Tutorial 6: Overlaying Models
A box or oval indicates the position of the fragment while you are moving it. TIP: You can rotate a fragment separately from the whole model by selecting at least one atom in it and using the Shift key with the trackball tool. Try this to reorient the fragments as in the illustration below. The icon on the fragment changes to a target. 3. Select the Methamphetamine fragment. TIP: The check in the box next to Methamphetamine does not mean that it is selected, it means that it is visible. (Try it. This is how you work with multiple overlays.) You must click on the fragment name for the Fast Overlay command to become active. At this point, you have to decide which of the fragments will be the target. In this simple example, with only two compounds, it doesn’t really matter. You might, however, have cases where you want to overlay a number of compounds on a specific target. Chem3D allows multiple overlays. The Model Explorer makes it easy to hide compounds you are not actively working with, and to display any combination of compounds you want. 4. Choose Fast Overlay from the Overlay submenu on the context menu. The fragments are overlaid. The numbers show the serial numbers of the target atoms that the matching overlay atoms correspond to. TIP: You can designate a group, rather than the entire fragment, as the target. In some cases, this will give more useful results. 1. Click the Epinephrine fragment to select it. 2. Point to Overlay on the context (right-click) menu, and click Set Target Fragment. To turn off the Fast Overlay mode: • Choose Clear Target Fragment from the Overlay submenu. ChemOffice 2005/Chem3D Chem3D Tutorials • 45 Tutorial 6: Overlaying Models
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ChemOffice.Com ® ChemOffice ® Che
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License Information ChemOffice, Che
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Page 12 and 13: A Guide to CambridgeSoft Manuals An
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Administrator New in Chem3D version
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To position a plane in your model p
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Administrator For example, consider
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Administrator Chem3D provides two o
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Administrator change a property. By
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Administrator To add to a group: 1.
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the same wave function and a consta
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3. From the Calculations menu, poin
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Administrator The following table c
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Administrator TRIPLET QUARTET QUINT
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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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