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Administrator The following table describes the objects in the Model window. Object Model area Active Window tab Rotation Bars Chem3D 9 introduces dynamic (auto-hide) rotation bars. The rotation bars only appear on your screen when you are actually using them. To view the dynamic rotation bars you must do two things: • Activate rotation mode by selecting the Trackball tool. • “Mouse over” the rotation bar area. Bond axis Description The workspace where a molecular model is viewed, built, edited, or analyzed. The origin of the Cartesian axes (0,0,0) is always located at the center of this window, regardless of how the model is moved or scaled. The Cartesian axes do not move relative to the window. Chem3D 9 can open multiple models simultaneously. The tab selects the active window. Z-axis Y-axis X-axis Click on a bar and drag to rotate a model around that axis. The “Rotate About a Bond” bar is only active when a bond or dihedral is selected. Freehand rotation is accomplished by dragging in the main window. The cursor changes to a hand when you are in freehand rotation mode. You can turn off the display (but not the function) of the bars with the Show Mouse Rotation Zones checkbox on the GUI tab of the Preferences dialog box (File > Preferences). Menus and Toolbars All Chem3D commands and functions can be accessed from the menus or toolbars. The toolbars contain icons that offer shortcuts to many commonly used functions. You can activate the Toolbars you want from the Toolbars submenu of the View menu. Toolbars can be attached to any side of the GUI, or can be “torn off ” and placed anywhere on the screen for convenience. TIP: Most Toolbar commands are duplicated from the menus, and are intended as a convenience. If you only use a command infrequently, you can save clutter by using the menu commands. The File Menu In addition to the usual File commands, you use the File menu to access the Chem3D Templates and Preferences, and the Model Settings. • Import File—Import MOL2 and SD files into Chem3D a document. The import utility accurately preserves model coordinates. • Model Settings—Displays the Settings dialog box. Set defaults for display modes and colors, model building, atom and ligand display, atom labels and fonts, movie and stereo pair settings, and atom/bond popup label information. 10 •Chem3D Basics <strong>CambridgeSoft</strong> The Graphical User Interface
• Preferences—Displays the Preferences dialog box. Set defaults for image export, calculation output path, OpenGL settings and including hydrogens in CDX format files. • Sample Files—Accesses example models. The Edit Menu In addition to the usual Edit functions, you can use the Edit menu to copy the model in different formats, to clear the model window, and to select all or part of the model. • Copy as—Puts the model on the Clipboard in ChemDraw format, as a SMILES string, or in bitmap format. • Copy As ChemDraw Structure—Puts the model on the Clipboard in CDX format. You may only paste the structure into an application that can accept this format, for example ChemDraw, ChemFinder, or Chem3D. • Copy As SMILES—Puts the model on the Clipboard as a SMILES string. You may only paste the structure into an application that can accept this format. • Copy As Picture—Puts the model on the Clipboard as a bitmap. You may only paste the structure into an application that can accept bitmaps. NOTE: The application you paste into must recognize the format. For example, you cannot paste a ChemDraw structure into a Microsoft Word document. • Paste Special—Preserves coordinates when pasting a Chem3D model from one document to another. • Clear—Clears the model window of all structures. • Select All—Selects the entire model. • Select Fragment—If you have selected an atom, selects the fragment that atom belongs to. The View Menu/Model Display Toolbar Use the View menu to select the view position and focus, as well as which toolbars, tables, and panels are visible. The Model Display submenu of the View menu duplicates all of the commands in the Model Display toolbar. • View Position—The View Position submenu gives you options for centering the view, fitting the window, and aligning the view with an axis. • View Focus—The View Focus submenus is used to set the focus. See “View Focus” on page 63 • Model Display—Duplicates the Model Display toolbar—Contains tools to control the display of the model. These tools are duplicated on the View menu.. • Show Atom Labels—A toggle switch to display or hide the atom labels. • Show Serial Numbers—A toggle switch to display or hide the atom numbers. • Show Atom Dots—Displays or hides atom dot surfaces for the model. The dot surface is based on VDW radius or Partial Charges, as set in the Atom Display table of the Settings dialog box. • Show Atom Spheres—Displays or hides atom spheres for the model. The radius is based on VDW radius or Partial Charges, as set in the Atom Display table of the Settings dialog box. • Show Hs and Lps—A toggle switch to display or hide hydrogen atoms and lone pairs. • Red and Blue glasses—A toggle switch to set the display for optimal viewing with redblue 3D glasses to create a stereo effect. <strong>ChemOffice</strong> 2005/Chem3D Chem3D Basics • 11 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
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Page 28 and 29: Administrator Deleting a Field Type
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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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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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Administrator • Second Positioned
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Administrator For example, consider
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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 To add to a group: 1.
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Administrator 124•Printing and Ex
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Administrator • A single point ca
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Administrator The van der Waals int
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Administrator 6. The modified value
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Administrator A variety of other ba
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Administrator activation barriers.
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3. From the Calculations menu, poin
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Compute Properties The Compute Prop
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Administrator The following table c
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Administrator TRIPLET QUARTET QUINT
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Administrator criteria, to optimize
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Administrator Dipole Moment The dip
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Administrator Molecular Surfaces Mo
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Administrator 220•Introduction Ca
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Administrator Screen Element Table
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Administrator • From the View men
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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 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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Creating Fields Administrator 4. Fr
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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 Context menu options
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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 as part of the data a
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Administrator • Setting the searc
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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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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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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 See the following top
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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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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 2. To expand the coll
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Administrator Adding a Collection L
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Administrator the Rename command in
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Administrator contained collection
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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 Section Listeners E-N
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Administrator 604 • CambridgeSoft
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Administrator Accessing the Online
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Administrator The CS ChemOffice SDK
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Administrator Troubleshooting This
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Administrator If an atom can be ass
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Administrator 14 13 H 2.197 -0.8229
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Parameter Table Use Parameter Table
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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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DESKTOP CS ChemInfo Reference and C
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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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RESEARCH & BioSAR Browser Biologica
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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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