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Administrator • Stereo Pairs—A toggle switch to enhance three dimensional effect by displaying a model with two slightly different orientations. It can also create orthogonal (simultaneous front and side) views. The degree of separation is set on the Stereo View tab of the Settings dialog box. • Perspective—A toggle switch to create a perspective rendering of the model by consistent scaling of bond lengths and atom sizes by depth. The degree of scaling is controlled by the Perspective “Field of View” slider on the Model Display tab of the Settings dialog box. • Depth Fading—A toggle switch to create a realistic depth effect, where more distant parts of the model fade into the background. The degree of fading is controlled by the Depth Fading “Field of View” slider on the Model Display tab of the Settings dialog box. • Model Axes—Displays or hides the Model axes. • View Axes—Displays or hides the view axes. NOTE: When both axes overlap and the Model axes are displayed, the View axes are not visible. • Background Color—Displays the Background color select toolbar. Dark backgrounds are best for viewing protein ribbon or cartoon displays. Selecting redblue or Chromatek 3D display will automatically override the background color to display the optimal black background. Background colors are not used when printing, except for Ribbon displays. When saving a model as a GIF file, the background will be transparent, if you have selected that option for Image Export in the Preferences dialog box. • Color By—Selects the model coloring scheme. See “Coloring Displays” on page 86 for more information. • Toolbars—Click the name of a toolbar to select it for display. Click again to deselect. You can attach a toolbar to any side of the GUI by dragging it to where you want it attached. If you are using a floating toolbar, you can change its shape by dragging any of its edges. • Standard toolbar—Contains standard file, edit, and print tools. The commands are duplicated on the File and Edit menus. • Building toolbar—Contains the Select, Translate, Rotate, and Zoom tools in addition to the model building tools— bonds, text building tool, and eraser. These tools are not duplicated on any menu. This toolbar is divided into “safe” and “unsafe” tools. The four “safe” tools on the left control only the view – they do not affect the model in any way. This includes the new “safe” select tool and the new translate tool . The old select tool is now called the Move tool. Although it can also be used to select, it’s primary use is to move atoms and fragments. • Model Display toolbar—Contains tools to control the display of the model. These tools are duplicated on the View menu. • Surfaces toolbar—Contains tools to calculate and display a molecular surface. Molecular Surface displays provide information about entire molecules, as opposed to the atom and bond information provided by Structure displays. • Movies toolbar—Contains tools for the creation and playback of movies. Chem3D movies are animations of certain visualization operations, such as iterations from a computation. They can be viewed in 12 •Chem3D Basics CambridgeSoft The Graphical User Interface
Chem3D, or saved in Windows AVI movie format. The commands are reproduced on the Movie menu. • Calculation toolbar—Performs MM2 minimization from a desktop icon. The spinning- arrow icon shows when any calculation is running, and the Stop icon can be used to stop a calculation before it’s preset termination. • Status bar—Displays the Status bar, which displays information about the active frame of your model. • Customize—Displays the Customize dialog box. Customizing toolbars is a standard MS Windows operation, and is not described in Chem3D documentation. • Model Explorer—Displays a hierarchical tree representation of the model. Most useful when working with complex molecules such as proteins, the Model Explorer gives you highly granular control over the model display. • ChemDraw Panel—Displays the ChemDraw Panel. Use the ChemDraw Panel to build molecules quickly and easily with familiar ChemDraw drawing tools. You can import, export, edit, or create small molecules quickly and easily using the ChemDraw ActiveX tools palette. • Cartesian Table—Displays the Cartesian Coordinates table. Cartesian Coordinates describe atomic position in terms of X-, Y-, and Z-coordinates relative to an arbitrary origin. • Z-Matrix Table—Displays the internal coordinates, or Z-Matrix, table. Internal coordinates are the most commonly used coordinates for preparing a model for further computation. • Measurements Table—Displays the Measurements table.The Measurements table displays bond lengths, bond angles, dihedral angles, and ring closures. • Parameters Tables—Displays a list of external tables that are used by Chem3D to construct models, perform computations and display results. • Output Box—Displays the Output box, which presents textual information about the model, iterations, etc. • Comments Box—Displays the Comments box, a place for user comments that is stored with the file. • Dihedral Chart—Opens the window displaying results of Dihedral Driver MM2 computation. See “Tutorial 5: Mapping Conformations with the Dihedral Driver” on page 38 for more information. • Status Bar—Displays or hides the Status Bar. • Start Spinning Model Demo—Spins the model on the Y axis. Use stop calculation on the Calculations toolbar to stop the demo. • Full Screen—Activates the full screen display. The Structure Menu The Structure menu commands populate the Measurements table and control movement of the model. The Measurements submenu • Set… Measurements—Sets a measurement—bond length, angle, or distance—according to what is selected. • Bond Lengths—Displays bond lengths in the Measurements Table. The Actual values come from the model and the Optimal values come from the Bond Stretching Parameters external table. ChemOffice 2005/Chem3D Chem3D Basics • 13 The Graphical User Interface
Page 1: ChemOffice.Com ® ChemOffice ® Che
Page 4 and 5: License Information ChemOffice, Che
Page 6 and 7: · Licensed users of ChemOffice Ent
Page 8 and 9: computer, except as provided below.
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 16 and 17: Administrator Tutorial 7: Docking M
Page 18 and 19: Administrator Connection Table . .
Page 20 and 21: Administrator Specifying Properties
Page 22 and 23: Administrator Undoing Changes . . .
Page 24 and 25: Administrator Chapter 28: Introduci
Page 26 and 27: Administrator Atom Properties . . .
Page 28 and 29: Administrator Deleting a Field Type
Page 30 and 31: Administrator Example 2. . . . . .
Page 32 and 33: Administrator Reaction Center . . .
Page 34 and 35: Administrator In addition to browsi
Page 36 and 37: Administrator Microsoft®Windows®
Page 38 and 39: Administrator Truncated-Newton-Raph
Page 40 and 41: Administrator the activation each t
Page 42 and 43: Administrator The following table d
Page 46 and 47: Administrator • Bond Angles—Dis
Page 48 and 49: Administrator The Building Toolbar
Page 50 and 51: Administrator The Calculation Toolb
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Page 60 and 61: Administrator 2. Click the ChemDraw
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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 Dragging moves atoms
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Administrator 3. Hold down the Shif
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To position a plane in your model p
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Administrator • Second Positioned
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Administrator For example, consider
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To change the structural display ty
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Administrator When sizing by partia
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Administrator Depth Fading3D enhanc
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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 Density surface is ca
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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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Administrator To add to a group: 1.
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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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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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Compute Properties The Compute Prop
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Administrator C(2)-C(3)-C(4) bond a
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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 TRIPLET QUARTET QUINT
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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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Administrator Hyperfine Coupling Co
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Administrator 194•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 To specify the calcul
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Property Description Property Descr
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Property Description Error Message
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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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A selected data box is designated b
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Administrator The database opens, a
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9. Click the Form tab. There should
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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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Administrator To search over a list
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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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The framed data box is labeled. NOT
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Administrator To save a metafile fr
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Administrator • Rich Text—displ
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Administrator Adding a Data Box Men
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Administrator Customizing Numbers U
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Administrator When the selection to
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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 • Take the appropri
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Administrator • In the new dialog
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Administrator 282•Relational Data
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Administrator The following table s
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Administrator Creating Tables There
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Administrator ChemFinder creates a
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Administrator atoms contained in th
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Administrator • If you are editin
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Administrator The record is permane
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Administrator The plot appears in a
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Administrator Context menu options
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Administrator In the bottom diagram
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Administrator 308•Visualizing Dat
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The general procedure for importing
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Administrator Using Log Files Durin
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Administrator d. The input file has
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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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Administrator ChemFinder searches o
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Administrator • With Stereo Cente
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Administrator Managing Queries Chem
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To reset searches to the full datab
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Administrator To create the hitlist
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Administrator Using ChemDraw's Atom
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Administrator With reaction centers
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To set the options for what ChemFin
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Administrator To return all the too
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Administrator Creating a Script To
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Administrator rather difficult, but
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Administrator 352•Customizing Che
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Administrator Opening an Oracle Dat
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Administrator • Restore Previous
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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 For more information
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Administrator The Open Chemical Str
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Administrator 3. From the Molecules
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Administrator To use the Search Opt
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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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Creating a Page or Experiment Admin
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Administrator Working with the User
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Administrator Showing and Hiding Co
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Administrator • Right-click any b
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Administrator If your system config
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Administrator Your system configura
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Administrator Working with Template
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Administrator Desired Result Change
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Administrator To export to MS Word:
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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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Administrator • Top of Arrow as R
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Administrator • Equivalents - the
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The example below shows the Prepara
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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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5. Click the section menu icon. The
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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 • 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 3. If necessary, clic
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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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Showing the Name of a Box To show t
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Administrator contained box accordi
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Administrator In the form we are sh
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Administrator For example, if there
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Administrator 506• Managing Secti
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Administrator Several fields types
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Administrator • Default Font - yo
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The Section Type Configuration dial
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Administrator Example 1 In this exa
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Administrator See the following top
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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 Another feature of ta
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Administrator 3. Right-click the Ta
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Administrator • SupplierID - the
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Administrator reactants and product
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Managing Search Fields Administrato
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Administrator • Certain types of
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4. Enter a name for the field and s
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Administrator To access the Add-In
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Administrator In the query table fi
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Administrator 546• Managing Field
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Creating a New Collection Type The
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Administrator 5. Click the Add>> bu
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Administrator A menu appears with t
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Administrator Adding a Collection L
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Administrator A menu appears. 4. Se
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Administrator the Rename command in
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Administrator contained collection
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Administrator Creating a Search Typ
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Administrator Chemical Structure Se
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Administrator To add states to a co
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• Removing a Transition Listener
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Administrator • Unlocked Contents
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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 Setting the Region fo
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Administrator 584• User Administr
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Administrator 2. If Inherits Securi
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Administrator The Security tab appe
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Administrator To disable inherited
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Administrator Desired Result Remove
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Administrator 596• Managing E-Not
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Administrator Section Listeners E-N
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Administrator • Add Reactant tabl
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Administrator have an OK button onl
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Administrator 604 • CambridgeSoft
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Administrator Accessing the Online
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Administrator Defining Substructure
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Administrator If an atom can be ass
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Administrator Example 3 In Example
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Administrator 14 13 H 2.197 -0.8229
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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 Line 56 -2794 21139 6
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Administrator 7 2 10 1 8 3 6 1 9 3
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Administrator Line 16 6 C -0.559 1.
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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 Adding Parameters to
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Administrator Creating (continued)
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Administrator Dihedral type field 6
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Administrator Exporting (continued)
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Administrator Managing (continued)
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Administrator Search Details prefer
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Administrator Subforms (continued)
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Administrator User interface 9 User
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Administrator xxxviii• CambridgeS
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CAMBRIDGESOFT ChemOffice Desktop to
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CS ChemOffice Software Suites ChemO
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DESKTOP CS E-Notebook Electronic Jo
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DESKTOP CS ChemDraw Chemical Struct
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DESKTOP CS Chem3D Molecular Modelin
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DESKTOP CS ChemFinder Searching and
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ENTERPRISE ChemOffice WebServer Ent
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ENTERPRISE Oracle Cartridge Enterpr
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KNOWLEDGE E-Notebook Enterprise Des
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KNOWLEDGE Document Manager Desktop
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KNOWLEDGE 21CFR11 Compliance Electr
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RESEARCH & Registration System Chem
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RESEARCH & Inventory Manager Chemic
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RESEARCH & CombiChem Enterprise Des
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RESEARCH & BioAssay HTS Biological
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CHEMICAL ChemACX Database Available
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CHEMICAL The Merck Index Chemistry
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CHEMICAL Chemical Databases Referen
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CONSULTING & Consulting & Services
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CS Software Problem Report For fast
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