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Administrator Tutorial 7: Docking Models . . . . . . . . . . . . . . . . . . . 42 Tutorial 8: Viewing Molecular Surfaces . . . . . . . . . 44 Tutorial 9: Mapping Properties onto Surfaces . . 45 Tutorial 10: Computing Partial Charges . . . . . . . . 48 Chapter 3: Building and Editing Models Setting the Model Building Controls . . . . . . . . . . . 51 Building with the ChemDraw Panel . . . . . . . . . . . . 52 Unsynchronized Mode. . . . . . . . . . . . . . . . . . . . . . 52 Name=Struct . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 Building with Other 2D Programs . . . . . . . . . . . 53 Building With the Bond Tools. . . . . . . . . . . . . . . . . 53 Creating Uncoordinated Bonds . . . . . . . . . . . . . . 54 Removing Bonds and Atoms . . . . . . . . . . . . . . . . 54 Building With The Text Tool. . . . . . . . . . . . . . . . . . 55 Using Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 Changing atom types . . . . . . . . . . . . . . . . . . . . . 56 The Table Editor . . . . . . . . . . . . . . . . . . . . . . . . 56 Specifying Order of Attachment . . . . . . . . . . . 56 Using Substructures . . . . . . . . . . . . . . . . . . . . . . . . 56 Building with Substructures . . . . . . . . . . . . . . . . . 57 Example 1. Building Ethane with Substructures . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 Example 2. Building a Model with a Substructure and Several Other Elements . . 58 Example 3. Polypeptides . . . . . . . . . . . . . . . . . . 58 Example 4. Other Polymers . . . . . . . . . . . . . . . 59 Replacing an Atom with a Substructure. . . . . . . 59 Building From Tables . . . . . . . . . . . . . . . . . . . . . . . . 59 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 Changing an Atom to Another Element . . . . . . . . 60 Changing an Atom to Another Atom Type . . . . . 61 Changing Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 Creating Bonds by Bond Proximate Addition .62 Adding Fragments . . . . . . . . . . . . . . . . . . . . . . . . . . . 62 View Focus. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 Setting Measurements . . . . . . . . . . . . . . . . . . . . . . . . 63 Setting Bond Lengths. . . . . . . . . . . . . . . . . . . . . . . 64 Setting Bond Angles . . . . . . . . . . . . . . . . . . . . . . . . 64 Setting Dihedral Angles . . . . . . . . . . . . . . . . . . . . . 64 Setting Non-Bonded Distances (Atom Pairs) . . 64 Atom Movement When Setting Measurements 64 Setting Constraints. . . . . . . . . . . . . . . . . . . . . . . . . 65 Setting Charges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 Setting Serial Numbers. . . . . . . . . . . . . . . . . . . . . . . 66 Changing Stereochemistry . . . . . . . . . . . . . . . . . . . . 66 Refining a Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68 Chapter 4: Manipulating Models Selecting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 Selecting Single Atoms and Bonds. . . . . . . . . . . 69 Selecting Multiple Atoms and Bonds. . . . . . . . . 70 Deselecting Atoms and Bonds . . . . . . . . . . . . . . 70 Selecting Groups of Atoms and Bonds. . . . . . . 70 Using the Selection Rectangle. . . . . . . . . . . . . 70 Defining Groups . . . . . . . . . . . . . . . . . . . . . . . . 71 Selecting a Group or Fragment . . . . . . . . . . . 71 Selecting Atoms or Groups by Distance. . . . . . 72 Showing and Hiding Atoms . . . . . . . . . . . . . . . . . . 72 Showing Hs and Lps . . . . . . . . . . . . . . . . . . . . . . . 73 Showing All Atoms . . . . . . . . . . . . . . . . . . . . . . . . 73 Moving Atoms or Models . . . . . . . . . . . . . . . . . . . . 73 Rotating Models. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74 X- Y- or Z-Axis Rotations . . . . . . . . . . . . . . . . . . 75 Rotating Fragments . . . . . . . . . . . . . . . . . . . . . . . . 75 Trackball Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 Internal Rotations . . . . . . . . . . . . . . . . . . . . . . . . . 75 Rotating Around a Bond . . . . . . . . . . . . . . . . . 76 Rotating Around a Specific Axis . . . . . . . . . . 76 Rotating a Dihedral Angle . . . . . . . . . . . . . . . . 76 Using the Rotation Dial . . . . . . . . . . . . . . . . . . . . 77 Changing Orientation . . . . . . . . . . . . . . . . . . . . . . . . 77 Aligning to an Axis . . . . . . . . . . . . . . . . . . . . . . . . 77 Aligning to a Plane. . . . . . . . . . . . . . . . . . . . . . . . . 77 Resizing Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78 Centering a Selection. . . . . . . . . . . . . . . . . . . . . . . 78 Using the Zoom Control . . . . . . . . . . . . . . . . . . . 79 Scaling a Model. . . . . . . . . . . . . . . . . . . . . . . . . . . . 79 Changing the Z-matrix . . . . . . . . . . . . . . . . . . . . . . . 79 The First Three Atoms in a Z-matrix . . . . . . . . 79 Atoms Positioned by Three Other Atoms . . . . 80 Positioning Example . . . . . . . . . . . . . . . . . . . . . 81 Positioning by Bond Angles . . . . . . . . . . . . . . 81 Positioning by Dihedral Angle . . . . . . . . . . . . 82 CambridgeSoft
Setting Origin Atoms . . . . . . . . . . . . . . . . . . . . 82 Chapter 5: Displaying Models Structure Displays . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 Model Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84 Displaying Solid Spheres . . . . . . . . . . . . . . . . . . . 85 Setting Solid Sphere Size . . . . . . . . . . . . . . . . . 85 Displaying Dot Surfaces . . . . . . . . . . . . . . . . . . . . 86 Coloring Displays. . . . . . . . . . . . . . . . . . . . . . . . . . 86 Coloring by Element . . . . . . . . . . . . . . . . . . . . . 86 Coloring by Group . . . . . . . . . . . . . . . . . . . . . . 87 Coloring by Partial Charge . . . . . . . . . . . . . . . . 87 Coloring by Depth for Chromatek Stereo Viewers . . . . . . . . . . . . . . . . . . . . . . . . . 87 Red-blue Anaglyphs . . . . . . . . . . . . . . . . . . . . . 87 Depth Fading3D enhancement: . . . . . . . . . . . 88 Perspective Rendering . . . . . . . . . . . . . . . . . . . 88 Coloring the Background Window . . . . . . . . . . 88 Coloring Individual Atoms . . . . . . . . . . . . . . . . . 88 Displaying Atom Labels . . . . . . . . . . . . . . . . . . . . 89 Setting Default Atom Label Display Options 89 Displaying Labels Atom by Atom . . . . . . . . 89 Using Stereo Pairs . . . . . . . . . . . . . . . . . . . . . . . . . 89 Using Hardware Stereo Graphic Enhancement 90 Molecular Surface Displays . . . . . . . . . . . . . . . . . . . 91 Extended Hückel . . . . . . . . . . . . . . . . . . . . . . . . . 91 Displaying Molecular Surfaces . . . . . . . . . . . . . . 92 Setting Molecular Surface Types . . . . . . . . . . 93 Setting Molecular Surface Isovalues . . . . . . . 94 Setting the Surface Resolution . . . . . . . . . . . . 95 Setting Molecular Surface Colors . . . . . . . . . . 95 Setting Solvent Radius . . . . . . . . . . . . . . . . . . . 95 Setting Surface Mapping . . . . . . . . . . . . . . . . . 96 Solvent Accessible Surface. . . . . . . . . . . . . . . . . . 96 Connolly Molecular Surface. . . . . . . . . . . . . . . . . 97 Total Charge Density. . . . . . . . . . . . . . . . . . . . . . . 97 Total Spin Density . . . . . . . . . . . . . . . . . . . . . . . . . 98 Molecular Electrostatic Potential . . . . . . . . . . . . 98 Molecular Orbitals . . . . . . . . . . . . . . . . . . . . . . . . . 98 Visualizing Surfaces from Other Sources. . . . . . . 99 Chapter 6: Inspecting Models Pop-up Information . . . . . . . . . . . . . . . . . . . . . . . . 101 Non-Bonded Distances . . . . . . . . . . . . . . . . . . 102 Measurement Table . . . . . . . . . . . . . . . . . . . . . . . . . 102 Editing Measurements . . . . . . . . . . . . . . . . . . . . . 103 Optimal Measurements . . . . . . . . . . . . . . . . . . . . 103 Non-Bonded Distances in Tables . . . . . . . . . . . 103 Showing the Deviation from Plane . . . . . . . . 103 Removing Measurements from a Table . . . . 104 Displaying the Coordinates Tables . . . . . . . . . . 104 Internal Coordinates . . . . . . . . . . . . . . . . . . . . 104 Cartesian Coordinates . . . . . . . . . . . . . . . . . . . 105 Comparing Models by Overlay . . . . . . . . . . . . . . . 105 Working With the Model Explorer. . . . . . . . . . . . 107 Model Explorer Objects . . . . . . . . . . . . . . . . . . . 108 Creating Groups . . . . . . . . . . . . . . . . . . . . . . . . 109 Adding to Groups . . . . . . . . . . . . . . . . . . . . . . 109 Pasting Substructures . . . . . . . . . . . . . . . . . . . . 110 Deleting Groups . . . . . . . . . . . . . . . . . . . . . . . . 110 Using the Display Mode . . . . . . . . . . . . . . . . . 110 Coloring Groups . . . . . . . . . . . . . . . . . . . . . . . . 110 Resetting Defaults . . . . . . . . . . . . . . . . . . . . . . 111 Animations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111 Creating and Playing Movies . . . . . . . . . . . . . . . 111 Spinning Models . . . . . . . . . . . . . . . . . . . . . . . . . 111 Spin About Selected Axis . . . . . . . . . . . . . . . . 111 Editing a Movie . . . . . . . . . . . . . . . . . . . . . . . . . . . 112 Movie Control Panel . . . . . . . . . . . . . . . . . . . . . . 112 Chapter 7: Printing and Exporting Models Specifying Print Options . . . . . . . . . . . . . . . . . . . 113 Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114 Exporting Models Using Different File Formats114 Publishing Formats. . . . . . . . . . . . . . . . . . . . . . . . 115 WMF and EMF . . . . . . . . . . . . . . . . . . . . . . . . 115 BMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115 EPS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116 TIF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116 GIF and PNG and JPG . . . . . . . . . . . . . . . . . 117 3DM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117 AVI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117 Formats for Chemistry Modeling Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117 Alchemy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117 Cartesian Coordinates . . . . . . . . . . . . . . . . . . . 117 ChemOffice 2005
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Page 10 and 11: Q: IS IT OK TO COPY MY COLLEAGUE’
Page 12 and 13: A Guide to CambridgeSoft Manuals An
Page 14 and 15: Chapter 31: Changes and Audit Trail
Page 18 and 19: Administrator Connection Table . .
Page 20 and 21: Administrator Specifying Properties
Page 22 and 23: Administrator Undoing Changes . . .
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Administrator 5. Press the Enter ke
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. Administrator b. From the Structu
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Administrator In the Measurements t
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A molecule of Epinephrine appears.
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Administrator Tutorial 7: Docking M
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Administrator To save the iteration
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The allyl radical, CH 2 =CHCH 2·,
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Administrator Determine the raw spi
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Administrator atoms are relatively
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Administrator The following table d
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Administrator When Correct Atom Typ
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Administrator To use the same text
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Administrator Example 2. Building a
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Administrator copied into blank tab
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Administrator 3. Type the atom type
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Administrator Clean Up Structure or
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Setting Serial Numbers this step, y
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Administrator Refining a Model Afte
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Administrator Selecting Multiple At
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Administrator New in Chem3D version
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Administrator 3. Hold down the Shif
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To change the structural display ty
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• Select Parallel to rotate the r
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Administrator • From the Computat
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Surface Type Description Surface Ty
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Administrator 2. Adjust the slider
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Administrator 100•Displaying Mode
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Administrator If you want to displa
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Administrator Example: To examine t
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Administrator Chem3D provides two o
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Administrator change a property. By
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To stop spinning: • On the Movie
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Administrator If you want to … Th
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Administrator EPS The PostScript fi
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If you want the file to … Then cl
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Molecular Design Limited MolFile (.
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Administrator 124•Printing and Ex
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Administrator • Semiempirical Ext
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Method Type Advantages Disadvantage
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Administrator • A single point ca
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Administrator • Molecular mechani
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Administrator constant), while θ 0
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Administrator The van der Waals int
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Administrator 6. The modified value
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the same wave function and a consta
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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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Administrator Intermediate status m
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Administrator staggered form. The m
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Administrator During dragging, the
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If you want to … Then Click … A
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Compute Properties The Compute Prop
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Administrator C(2)-C(3)-C(4) bond a
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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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The following table contains the ke
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Keyword Description 7. On the Prope
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Administrator Hyperfine Coupling Co
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Administrator 3. Click Open. The ap
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Property Description Property Descr
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Property Description Error Message
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The Step 4 of 4 dialog box appears.
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Administrator • From the ChemOffi
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Administrator 220•Introduction Ca
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. The components of the ChemFinder
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Administrator Screen Element Table
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Administrator • From the View men
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Administrator A form displays data
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. In this tutorial, you learn to cr
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A selected data box is designated b
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Administrator The database opens, a
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to see some of the information avai
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• From the Record menu, choose Fi
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Administrator The Table view appear
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+ The ISICCR database opens in Chem
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When you release the mouse button,
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Administrator 250•ChemFinder Tuto
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The Open dialog box appears. To cho
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A data source tree appears, contain
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ChemFinder saves the form with a .c
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Administrator • Rich Text—displ
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Administrator Customizing Numbers U
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To line up objects on a form: Admin
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Administrator to those usernames. M
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Administrator 282•Relational Data
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1. Click one of the column headers
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Administrator Creating Tables There
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Creating Fields Administrator 4. Fr
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The name of the new field appears i
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Administrator ChemFinder creates a
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Administrator atoms contained in th
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Administrator Export to SDFile When
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Administrator benz OR *bromo* Benze
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Search Type Administrator Normal Se
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Administrator The hit list will inc
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If you want to Then click Administr
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To reset searches to the full datab
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Administrator 6. Set other options
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Administrator 360•ChemFinder/Orac
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To activate CombiChem/Excel: The Co
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Administrator Adding a Reaction Tem
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Administrator Reactant List Format
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Administrator • You can configure
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An analysis of the reaction steps a
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Administrator ChemFinder/Office tit
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Administrator The Open Chemical Str
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Administrator 3. From the Molecules
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Changing the Chem- Finder/Office Pr
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Administrator • Enhanced table of
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Administrator In addition, this gui
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Administrator 388• Introducing E-
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Administrator You can organize coll
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Administrator If your system config
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Administrator 410• E-Notebook Use
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Administrator NO 2 NO 2 Me Me HC(OE
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The example below shows the Prepara
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Administrator Ethanol was selected,
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Administrator Type in the AutoText
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Adding Properties to Property Lists
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Type of Measurement Permitted Units
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3. Enter the URL and click OK. Work
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Administrator A new Ancillary Data
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Administrator Replacing a Spectrum
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The row is removed from the Table.
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Administrator you enter an invalid
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Administrator Type of Measurement m
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Administrator 4. The spreadsheet ap
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Administrator Printing Sections You
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Administrator Clicking the Changes
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. Administrator The version of the
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Administrator In some configuration
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Administrator 452• Changes and Au
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Administrator 2. If no form appears
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Administrator Query Text Field The
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Administrator • In searching subs
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Administrator Isotopes Isotopic lab
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Finds: Cl Does not find: Finds: O D
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Administrator • Browse to the roo
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Administrator 2. Select Remove Prop
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Administrator Advanced Text Searchi
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For example, the following searches
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Administrator Searching For ... Ret
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3. Click the Search In... checkbox
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Administrator The Collection Tree a
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2. Select Session Manager.... The S
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Administrator A new section type ap
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Administrator See the following top
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Administrator 3. If necessary, clic
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compute the checksum for the upload
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Administrator 4. A new Section List
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Administrator Managing the Audit Se
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Administrator The field appears in
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A menu appears. 2. Select Box Prope
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Administrator Several fields types
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Administrator • Default Font - yo
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Administrator Example 1 In this exa
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Administrator Associating a list of
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Administrator • Username - An opt
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Administrator To add a property lis
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Administrator from the Property dro
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Administrator The Field Properties
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Administrator reactants and product
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Administrator In the query table fi
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Administrator A menu appears. 4. Se
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Administrator contained collection
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Administrator If the user wants to
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Administrator To view the export te
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Administrator To edit this data, 1.
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Administrator Creating (continued)
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Administrator xxxviii• CambridgeS
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CAMBRIDGESOFT ChemOffice Desktop to
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RESEARCH & Registration System Chem
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Page 814 and 815:
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CHEMICAL Chemical Databases Referen
Page 818 and 819:
CONSULTING & Consulting & Services
Page 821:
CS Software Problem Report For fast
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