Chem3D Users Manual - CambridgeSoft

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Administrator Dragging moves atoms parallel to the X-Y plane, changing only their X- and Y-coordinates. Moving Models with the Translate Tool Use the Translate tool to move a model in the view window. When you use the Translate tool, you move both the focus view and the model coordinates along with the model. Thus, the model’s position does not change relative to the origin. If Automatically Rectify is on, then the unselected rectification atoms that are adjacent to selected atoms move with the selected atoms. To move a model: 1. With the Move Objects tool, drag across the model select it. 2. Drag the model to the new location. Note that the View axis has moved relative to the model coordinates. Rotating Models Chem3D allows you to freely rotate the model around axes. When you select the Trackball tool, four pop-up rotation bars are displayed on the periphery of the model window. You can use these rotation bars to view your model from different angles by rotating around different axes. You can also open the Rotate dialog box where you can use the rotate dial or type the number of degrees to rotate. To display the Rotation bars: • Select the Trackball tool from the Building toolbar. 96 •Manipulating Models CambridgeSoft Rotating Models
When you mouse over an edge of the model window, the Rotation bars appear on the edges of the Model window. Internal Rotation Bar Y-Axis Rotation Bar Z-Axis Rotation Bar X-Axis Rotation Bar X- Y- or Z-Axis Rotations To perform a rotation about the X-, Y-, or Z-axis: 1. Point to the appropriate Rotation bar. 2. Drag the pointer along the Rotation bar. The number of degrees of rotation appears in the Status bar. Trackball Tool Use the Trackball tool to freely rotate a model. • Starting anywhere in the model window, drag the pointer in any direction The Status bar displays the X and Y axis rotation. Internal Rotations Internal rotations alter a dihedral angle and create another conformation of your model. You can rotate an internal angle using the Internal Rotation bar. To perform internal rotations in a model, you must select at least two atoms or one bond. Internal rotation is typically specified by a bond. The fragment at one end of the bond is stationary while the fragment attached to the other end rotates. The order in which you select the atoms determines which fragment rotates. (See the following examples.) For example, consider ethoxybenzene (phenetole): Rotating Fragments If more than one model (fragment) is in the model window, you can rotate a single fragment or rotate all fragments in the model window. To rotate only one fragment: 1. Select an atom in the fragment you want to rotate. 2. Drag a rotation bar. To rotate all fragments, do one of the following: • With an atom selected, Shift+drag a Rotation bar. • With no atoms selected, drag a rotation bar. To perform a rotation about the C-O bond where the phenyl group moves: 1. Select the Trackball tool. 2. Hold down the S key, and select the O atom. ChemOffice 2005/Chem3D Manipulating Models • 97 Rotating Models
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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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Administrator • CambridgeSoft
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Administrator the activation each t
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Administrator The following table d
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Administrator • Bond Angles—Dis
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Administrator The Building Toolbar
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Administrator The Calculation Toolb
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Administrator 1. Right-click in the
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Administrator • In the Model Sett
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Administrator modes and color setti
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Administrator 30 •Chem3D Basics C
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Administrator 2. Click the ChemDraw
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3. Move the pointer over the C-C bo
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Administrator Add serial numbers an
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Administrator 5. Press the Enter ke
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Administrator In the Measurements t
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A molecule of Epinephrine appears.
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Administrator A variety of other ba
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Administrator Molecular wave functi
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Administrator activation barriers.
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3. From the Calculations menu, poin
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minimizing a second model, the mini
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Administrator move to lower the ene
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. Administrator Molecular Dynamics
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Administrator If you want to … Th
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Administrator The Compute Propertie
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Administrator To run a previously c
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Administrator The procedures assume
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Administrator improvements in each
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Administrator • Overall errors in
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Administrator The following table c
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Administrator TRIPLET QUARTET QUINT
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Administrator Chemical symbol ++ ba
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Administrator 4. Click Run. A new m
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Administrator Minimizing Energy Min
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Administrator criteria, to optimize
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Administrator 6. Hold down the S ke
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Administrator Dipole Moment The dip
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Administrator Molecular Surfaces Mo
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Administrator 3. Click in the model
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Keyword Description 7. On the Prope
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Administrator Hyperfine Coupling Co
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Administrator 198•MOPAC Computati
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Administrator If you want to … re
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Administrator In the Results In tex
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Administrator Repeating a Gaussian
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Property Description Property Descr
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Property Description Error Message
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Administrator Property Electronic E
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Administrator To specify the calcul
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Administrator 3. Click Open. The ap
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Administrator • Server—limits t
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Administrator To perform property c
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Administrator • From the ChemOffi
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Administrator Accessing the Online
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Administrator To find a structure t
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Administrator 228• Accessing the
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Administrator Performance Below are
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Administrator Defining Substructure
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Administrator If an atom can be ass
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Key Drag Shift+Drag Administrator Q
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Administrator 238• Keyboard Modif
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Administrator Example 3 In Example
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Administrator Connection tables by
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Administrator 32 3 12 1 0 0 0 33 3
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Administrator 13 * 3D displacement
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Administrator The field value for C
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Administrator Line 4e: C 1.53597 1
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Administrator CONECT 4 2 9 10 11 CO
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Administrator COMPND ATOM HETATM CO
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Administrator 7 2 10 1 8 3 6 1 9 3
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Administrator 12. Line 30, “@BOND
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Parameter Table Use Parameter Table
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Administrator 3. Type the informati
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Administrator Geometry The geometry
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Administrator KS The KS, or bond st
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Administrator one attached hydrogen
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Administrator bond length between t
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Administrator R* The R* field is th
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Administrator The V1 torsional cons
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Administrator VDW Interactions The
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Administrator Editing Parameters Yo
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Administrator 6. The pi molecular o
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Administrator Adding Parameters to
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Administrator fragments 84 paramete
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Administrator CC1 see Cartesian coo
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Administrator Copy As Bitmap comman
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Administrator Examining angles, tut
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Administrator density 67 editing 67
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Administrator editing 107 non-bonde
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Administrator repeating jobs 178 RH
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Administrator Rectification, when d
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Administrator all atoms 95 atoms or
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Administrator Translucent surface t
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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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