ChemDraw User's Manual - CambridgeSoft

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AdministratorTutorial 4: Fischer Projections . . . . . . . . . . . . . . . . . . 44Tutorial 5: Perspective Drawings . . . . . . . . . . . . . . . . 49Tutorial 6: Newman Projections. . . . . . . . . . . . . . . . . 53Tutorial 7: Showing Stereochemistry . . . . . . . . . . . . . 56Chapter 3: Drawing Chemical StructuresDrawing Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59Configuring Settings for Documents . . . . . . . . . 61Configuring Settings for Objects . . . . . . . . . . . . . 62Drawing Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62Multiple Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62Double Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . 63.Double Either Bonds . . . . . . . . . . . . . . . . . . . . 63Triple Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63Quadruple Bonds . . . . . . . . . . . . . . . . . . . . . . . . 63Drawing Constrained Bonds . . . . . . . . . . . . . . . . 64Drawing with Fixed Lengths . . . . . . . . . . . . . . 64Drawing with Fixed Angles . . . . . . . . . . . . . . . 64Toggling Fixed Lengths and Fixed Angles . . 64Dative Bonds and Wedged Bonds. . . . . . . . . . . . 64Adding a Bond by Clicking . . . . . . . . . . . . . . . . . . 65Adding Bonds by Dragging . . . . . . . . . . . . . . . . . 65Changing the Highlight Box Size. . . . . . . . . . . . . 65Drawing Rings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66Drawing a Ring . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66Drawing a Ring by Clicking . . . . . . . . . . . . . . . . . 66Drawing Cyclohexane Chair Rings . . . . . . . . . . . 67Drawing Resonance Delocalized Rings . . . . . . . 67Drawing Cyclopentadiene and Benzene Rings .67Drawing Acyclic Chains . . . . . . . . . . . . . . . . . . . . . . . . 68Drawing Chains. . . . . . . . . . . . . . . . . . . . . . . . . . . . 68Adding Chains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68Changing Chain Direction . . . . . . . . . . . . . . . . . . 68Editing Bonds. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69Changing Bond Types . . . . . . . . . . . . . . . . . . . . . . 69Changing Double Bonds . . . . . . . . . . . . . . . . . . . . 69Changing Orientation of Wedged and DativeBonds. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69Changing Alignment of Double Bonds . . . . . . . 70Moving Atoms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70Changing Bond Crossings. . . . . . . . . . . . . . . . . . . 71Changing the Bond Order. . . . . . . . . . . . . . . . . . . 71Automatic Warnings. . . . . . . . . . . . . . . . . . . . . . . . . . . 71Chapter 4: StructNameStruct=Name . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73Auto Update. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74Name=Struct . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74Converting Names to Structures . . . . . . . . . . . . 75Insert Structure . . . . . . . . . . . . . . . . . . . . . . . . . . 75Paste Special . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75Converting Captions to Structures . . . . . . . . . . 75Types of Structures Supported by Struct=Name76Chapter 5: Drawing Captions and AtomLabelsCreating a New Line and Closing Text Boxes . 79Formatting Text . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80Setting Font parameters . . . . . . . . . . . . . . . . . . . . 80Setting the Baseline Style . . . . . . . . . . . . . . . . . . . 80Specifying Line Spacing . . . . . . . . . . . . . . . . . . . . 81Aligning Text. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81Captions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81Atom Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82Automatic Alignment . . . . . . . . . . . . . . . . . . . . 82Changing the Default Caption or Atom Label TextFormat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83Specifying Document Settings for New Text 83Setting an Individual Text Format Before Typing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83Changing the Spacing of Individual Text Objects. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83Fractional Character Widths (Macintosh) . . . 84Coloring Text . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84Creating Captions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84Changing the Caption Width. . . . . . . . . . . . . . . . 85Editing a Caption . . . . . . . . . . . . . . . . . . . . . . . . . . 85Adding Analysis Data to a Caption . . . . . . . . . . 85Labeling Atoms with the Text Tool . . . . . . . . . . . . . 86Specifying the Margin Width . . . . . . . . . . . . . . . . 86Editing Atom Labels . . . . . . . . . . . . . . . . . . . . . . . 87Deleting an Atom Label . . . . . . . . . . . . . . . . . . . . 87Labeling Atoms with HotKeys . . . . . . . . . . . . . . . . . 87Method 1: Labeling the last atom drawn. . . . . . 87<strong>CambridgeSoft</strong>
Method 2: Labeling an atom by pointing . . . . . 87Method 3: Labeling an Atom with a Selection Tool88Method 4: Labeling multiple atoms . . . . . . . . . . 88Creating HotKeys . . . . . . . . . . . . . . . . . . . . . . . . . 88Hard-Coded HotKeys. . . . . . . . . . . . . . . . . . . . . . 89Labeling Atoms With a Bond or Ring Tool . . . . . . 89Repeating an Atom Label . . . . . . . . . . . . . . . . . . . . . . 89Atom Numbering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89Showing and Hiding Atom Numbers . . . . . . . . 90Editing Atom Numbers . . . . . . . . . . . . . . . . . . . . 90Positioning Atom Number Indicators. . . . . . . . 91Using the Text Tool with the Lasso Tool . . . . . . . . 91Using Bitmap Fonts When Available (Macintosh). 92Chapter 6: Drawing Orbitals, Symbols,Arrows, Arcs, and Other ShapesSelecting Tools From a Palette . . . . . . . . . . . . . . 93The Orbital Tools Palette . . . . . . . . . . . . . . . . . . . . . . 94s-orbitals. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94Sigma Orbitals . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94Single Lobe Orbitals . . . . . . . . . . . . . . . . . . . . . . . 94p-orbitals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95Hybrid Orbitals . . . . . . . . . . . . . . . . . . . . . . . . . . . 95d-orbitals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95dz2-orbitals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96The Chemical Symbols Tools Palette . . . . . . . . . . . . 96H-dot and H-dash . . . . . . . . . . . . . . . . . . . . . . . . . 96Lone Pair . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97Radical . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97Radical Cation and Radical Anion . . . . . . . . . . . 97Charge Symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . 98Attachment Points . . . . . . . . . . . . . . . . . . . . . . . . . 98Rotating a Symbol . . . . . . . . . . . . . . . . . . . . . . . . . 98The Arrow Tools Palette . . . . . . . . . . . . . . . . . . . . . . . 99Drawing an Arrow. . . . . . . . . . . . . . . . . . . . . . . . . 99Editing an Arrow . . . . . . . . . . . . . . . . . . . . . . . . . . 99The Drawing Elements Tools Palette. . . . . . . . . . . . 99Drawing Boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . 100Drawing Circles and Ovals. . . . . . . . . . . . . . . . . 100Resizing or Rotating Drawing Elements . . . . . 100Distorting Circle and Ovals . . . . . . . . . . . . . . . . 100Drawing Lines . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101The Brackets Tools Palette. . . . . . . . . . . . . . . . . . . . . 101Drawing Single Brackets . . . . . . . . . . . . . . . . . . . 101Drawing Paired Brackets . . . . . . . . . . . . . . . . . . . 101Drawing Daggers . . . . . . . . . . . . . . . . . . . . . . . . . 101Framing Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101The Arc Tools Palette . . . . . . . . . . . . . . . . . . . . . . . . . 102Drawing Arcs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102Editing Arcs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102The Pen Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102Drawing Bézier Curves by Dragging . . . . . . . . 103Drawing Segments by Clicking. . . . . . . . . . . . . . 103Editing a Curve . . . . . . . . . . . . . . . . . . . . . . . . . . . 104Changing the Shape of a Curve . . . . . . . . . . . 104Adding a Segment . . . . . . . . . . . . . . . . . . . . . . . 104Deleting a Segment . . . . . . . . . . . . . . . . . . . . . 105Applying a Style to a Shape. . . . . . . . . . . . . . . . . 105Filled and Closed Styles . . . . . . . . . . . . . . . . . . 105Shaded Style . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105Plain Style . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105The TLC Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105R f Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107Resizing Spots. . . . . . . . . . . . . . . . . . . . . . . . . . . . 108Custom Spots . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108Chapter 7: Manipulating DrawingsUsing a Selection Tool . . . . . . . . . . . . . . . . . . . . . . . . 109Selecting Objects with the Lasso Tool . . . . . . . 109Selecting Objects with the Marquee Tool . . . . 109Toggling Between Selection Tools. . . . . . . . . . . 110Toggling Between Other Tools . . . . . . . . . . . . . 110Selecting Objects by Clicking . . . . . . . . . . . . . . . 110Setting the Highlight Box Tolerance . . . . . . . . . 110Selecting Entire Structures . . . . . . . . . . . . . . . . . 111Making Multiple Selections . . . . . . . . . . . . . . . . . 111Removing Objects from the Selection . . . . . . . 111Selecting All Objects . . . . . . . . . . . . . . . . . . . . . . 111Deselecting All Objects . . . . . . . . . . . . . . . . . . . . 111Deleting Objects . . . . . . . . . . . . . . . . . . . . . . . . . . 111Moving Objects. . . . . . . . . . . . . . . . . . . . . . . . . . . 111Using the Clipboard . . . . . . . . . . . . . . . . . . . . . . . 112Cutting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112<strong>ChemDraw</strong> 9
Page 1 and 2: ChemOffice.Com®ChemDraw®Chemical
Page 3 and 4: License InformationChemOffice, Chem
Page 5 and 6: · Licensed users of ChemOffice Ent
Page 7 and 8: computer, except as provided below.
Page 9 and 10: Q: IS IT OK TO COPY MY COLLEAGUE’
Page 11 and 12: A Guide to CambridgeSoft ManualsAnd
Page 13: ContentsIntroductionWhat’s New in
Page 17 and 18: Chapter 10: Drawing Query Structure
Page 19 and 20: Searching. . . . . . . . . . . . .
Page 21 and 22: Administratorthey are presented. Ex
Page 23 and 24: Administrator12•IntroductionCambr
Page 25 and 26: The Mac GUI is shown below.Administ
Page 27 and 28: ToolUse to…AdministratorQueryTool
Page 29 and 30: AdministratorChemDraw window. Undoc
Page 31: AdministratorDouble-clicking on an
Page 36 and 37: 3. Click the checkbox next to Autos
Page 38 and 39: a file as a different format is use
Page 40 and 41: QuickDraw is the graphical format t
Page 42 and 43: Chapter 2: TutorialsOverviewThe tut
Page 44 and 45: .2. Double-click the atom.The hand
Page 46 and 47: 3. Click the third arrow from the l
Page 48 and 49: 2. Press the Enter or Return key to
Page 50 and 51: .Add second and third bonds:1. Poin
Page 52 and 53: Refine the shape of the arrow:1. Po
Page 54 and 55: 4. Click each of the atoms shown be
Page 56 and 57: 4. Select a folder in which to save
Page 58 and 59: Add labels to C1 and C6:3. Point to
Page 60 and 61: 3. Click Paste to paste the informa
Page 62 and 63: 2. Hold the mouse button and drag u
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Save and close the document:1. From
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The size of the orbital is constrai
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8. Click the Wedged Bond tool, poin
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Chapter 3: Drawing ChemicalStructur
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Adjustthis…If you want to …The
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You can use the tools on the Multip
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To draw a wedged bond:1. Click one
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If you click an atom in a ring, a s
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• Press the Ctrl or Command key w
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To convert ring types:1. With a bon
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Chapter 4:UltraStructNameStructName
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Converting Names toStructuresThere
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category ChemDraw 8 supports... Che
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Chapter 5: Drawing Captions andAtom
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• Subscript—Reduces the text by
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If you label C4, the second and thi
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5. To close the text box, click out
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4. The margin width is applied to a
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Hard-Coded HotKeysYou cannot edit h
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To edit atom number text:1. Click t
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Chapter 6: Drawing Orbitals,Symbols
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To draw a single lobe orbital:1. Ho
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To draw an H-dot or an H-dash:1. Ho
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The Arrow ToolsPaletteUse the Arrow
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Drawing LinesLines drawn with the l
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Some examples of shapes that you ca
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Deleting a SegmentTo delete a curve
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If you wantto...then...If you wantt
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Chapter 7: Manipulating DrawingsOve
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Selecting Entire StructuresTo selec
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The unselected bonds that are attac
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Reflecting ObjectsThrough PlanesYou
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3. The current median bond length f
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3. With the group selected, right-c
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Chapter 8: Advanced DrawingTechniqu
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Am Amyl AmericiumNp para-NeptuniumN
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ProExpanding LabelsMulti-Attached L
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3. Double-click on the cyclopentadi
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If you select only part of a struct
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Customizing the ColorPaletteYou can
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2. Click a color in the Color Wheel
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A new and untitled Template window
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Chapter 9: Working WithStructuresOv
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Propertym/zDescriptionMass/charge,
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3. Click the appropriate Position o
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To create a report and view results
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ProExpand GenericStructuresYou can
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The assigned atoms or bonds are hig
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Chapter 10:StructuresProDrawing Que
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• From the Structure menu, choose
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OptionSimple ringSearch ResultFinds
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Abnormal ValenceThe Abnormal Valenc
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The Bond Type options are described
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In the table below, points are may
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To Position …from the atom or bon
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. Not necessarily carbon (a generic
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A structure-based representation of
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Because of its prevalence the No Fl
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However, you are not interested in
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Always Display and PrintAtom Mappin
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ExportedQueryPropertiesISIS Mol Rxn
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ExportedQueryPropertiesISIS Mol Rxn
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Chapter 11: Working With PageLayout
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To create headers and footers:1. Fr
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Saving Page Setup SettingsYou can s
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A check mark appears next to the Sh
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Aligning ObjectsUse the Align comma
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The table appears in the document w
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7. Press Tab again to create a thir
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Chapter 12: Sharing InformationOver
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A clipping file or a scrap file is
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pasted in other types of documents.
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• SMDFormat Import ExportChemDraw
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.opened in versions 3.0, 3.0.1, 3.0
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For single step single or multi-lin
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different computers rather than usi
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Transferring ChemDrawDocuments Acro
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Chapter 13: ChemDraw/ExcelThe ChemD
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mats, but you may get error message
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Adding Structures withChemDrawThe C
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3. Select the search options:If you
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Aligning StructuresA structure may
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FunctionActionCHEM.COMPOSITION Retu
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AppendicesThis section contains the
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Appendix A: Accessing theCambridgeS
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Follow the links to do substructure
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You can search SciStore.Com for che
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Appendix B: Technical SupportOvervi
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4. If the problem still occurs, use
Page 242 and 243:
Appendix C: The Chemistry ofChemDra
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+*/A series of anyCH 2 COOC(OPh) 3c
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Isotopes and ElementsBy default, Ch
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CIP rules are designed to order lig
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• Critical messages that may affe
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MessageThis label has anunrecognize
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Appendix D:WorksUltraHow ChemNMROve
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Appendix E:WorksProHow ChemPropChem
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Appendix F: Shortcuts andHotkeysSho
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Enter...to execute Command...Enter.
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Enter...to execute Command...Enter.
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HotkeyResultHotkeyResultTOTsxX1 n-B
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Appendix G: Document SettingsCreati
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Drawing, Atom Label, and Caption Te
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Appendix H: Chemistry FileFormatsOv
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Double bonds are bit encoded using
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IndexNumerics13C, 1 H shifts, estim
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Bond Propertiesdefining 155descript
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Chemical Warnings (continued)suppre
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Deletingatom labels 87Backspace key
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File format (continued)CTR 198cts 2
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Inserting (continued)rows in tables
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Nicknames (continued)overview 121tr
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Printing (continued)ChemDraw Laser
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Saving customized settings 21Scalec
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System requirements 11TTable tool 1
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Use Defaults (continued)bond proper
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CAMBRIDGESOFTChemOffice Desktop toK
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CS ChemOfficeSoftware SuitesChemOff
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DESKTOPCS E-NotebookElectronic Jour
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DESKTOPCS ChemDrawChemical Structur
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DESKTOPCS Chem3DMolecular Modeling
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DESKTOPCS ChemFinderSearching and I
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DESKTOPCS ChemInfoReference and Che
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ENTERPRISEChemOffice WebServerEnter
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ENTERPRISEOracle CartridgeEnterpris
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KNOWLEDGEE-Notebook EnterpriseDeskt
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KNOWLEDGEDocument ManagerDesktop to
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KNOWLEDGE21CFR11 ComplianceElectron
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RESEARCH&Registration SystemChemica
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RESEARCH&Inventory ManagerChemical
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RESEARCH&CombiChem EnterpriseDeskto
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RESEARCH&BioAssay HTSBiological Ass
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RESEARCH&BioSAR BrowserBiological a
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CHEMICALChemACX DatabaseAvailable C
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CHEMICALThe Merck IndexChemistry’
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CHEMICALChemical DatabasesReference
Page 344 and 345:
CONSULTING &Consulting & ServicesDe
Page 347:
CS Software Problem ReportFor faste
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