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Administrator • From the Computations menu, point to Extended Hückel, and choose Calculate Charges. For each atom in the model, a message is created listing the atom and its partial charge. If you have selected Partial Charge in the Pop-up Information tab of the Model Settings dialog box, then the partial charges will appear as part of the pop-up information when you point to an atom. 4. From the Surfaces menu point to Choose Surface, and select one of the surface types. NOTE: The Choose Surface commands are toggle switches–click once to display, click again to turn off the display. You can display more than one surface at a time. When a surface is displayed, its icon is highlighted with a light blue background. Displaying Molecular Surfaces To display a surface: 1. Decide what surface type to display. 2. Perform a suitable calculation using Extended Hückel, CS MOPAC, or Gaussian 03. Include the Molecular Surfaces property calculation whenever it is available. NOTE: CS MOPAC and Gaussian 03 surfaces calculations are only available in Chem3D Ultra. Different calculation types can provide different results. If you have performed more than one calculation on a model, for example, both an Extended Hückel and an AM1 calculation, you must choose which calculation to use when generating the surface. 3. From the Calculations menu, point to Choose Result and select one of your calculations. Displayed surfaces 5. Adjust the display using the surface display tools. TIP: If you are making a lot of adjustments to the display, activate the Surfaces toolbar and tear off the specific tools you will be using often. For a review of the surface display tools, see “The Surfaces Toolbar” on page 17. Not all surfaces can be displayed from all calculations. For example, a Molecular Electrostatic Potential surface may be displayed only following a Gaussian or MOPAC calculation. If a surface is unavailable, the command is grayed out in the submenu. 92 •Displaying Models CambridgeSoft Molecular Surface Displays
To generate surfaces from MOPAC or Gaussian, you must choose Molecular Surfaces as one of the properties calculated by these programs. The surface types and the calculations necessary to display them are summarized in the following table. NOTE: Spin Density map requires that MOPAC or Gaussian computations be performed with an open shell wavefunction. Surface Type Extended Hückel MOPAC Solvent NA NA NA Accessible a Connolly Molecular Yes Yes Yes Gaussian Surface Type with Partial Charges with Molecular Electrostatic Potential map Total Spin Density Molecular Electrostatic Potential Extended Hückel MOPAC Yes Yes Yes No Yes Yes No Yes Yes No Yes Yes Gaussian Total Charge Density with Molecular Orbital map with Spin Density map Yes Yes Yes Yes Yes Yes No Yes Yes Molecular Orbitals Yes Yes Yes a. Calculated automatically from parameters stored in the Chem3D parameters tables. This surface is always available with no further calculation. Setting Molecular Surface Types Chem3D offers four different types of surface displays, each with its own properties. These types are shown in the following table: ChemOffice 2005/Chem3D Displaying Models • 93 Molecular Surface Displays
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ChemOffice.Com ® ChemOffice ® Che
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License Information ChemOffice, Che
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· Licensed users of ChemOffice Ent
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computer, except as provided below.
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Q: IS IT OK TO COPY MY COLLEAGUE’
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A Guide to CambridgeSoft Manuals An
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Chapter 31: Changes and Audit Trail
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Administrator Tutorial 7: Docking M
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Administrator Connection Table . .
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Administrator Specifying Properties
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Administrator Undoing Changes . . .
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Administrator Chapter 28: Introduci
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Administrator Atom Properties . . .
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Administrator Deleting a Field Type
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Administrator Example 2. . . . . .
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Administrator Reaction Center . . .
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Administrator In addition to browsi
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Administrator Microsoft®Windows®
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Administrator Truncated-Newton-Raph
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Administrator the activation each t
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Administrator The following table d
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Administrator • Stereo Pairs—A
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Administrator • Bond Angles—Dis
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Administrator The Building Toolbar
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Administrator The Calculation Toolb
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Administrator 1. Right-click in the
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Administrator • In the Model Sett
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Administrator modes and color setti
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Administrator 26 •Chem3D Basics C
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Administrator 2. Click the ChemDraw
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3. Move the pointer over the C-C bo
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Administrator Add serial numbers an
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Administrator 5. Press the Enter ke
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. Administrator 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 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 The procedures assume
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Administrator improvements in each
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Administrator • Overall errors in
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Administrator The following table c
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Administrator TRIPLET QUARTET QUINT
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Administrator Chemical symbol ++ ba
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Administrator 4. Click Run. A new m
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Administrator Minimizing Energy Min
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Administrator criteria, to optimize
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Administrator 6. Hold down the S ke
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Administrator Dipole Moment The dip
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Administrator Molecular Surfaces Mo
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The following table contains the ke
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Administrator 3. Click in the model
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Keyword Description 7. On the Prope
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Administrator Hyperfine Coupling Co
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Administrator 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 Repeating a Gaussian
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Administrator To specify the calcul
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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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Administrator • From the ChemOffi
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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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9. Click the Form tab. There should
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to see some of the information avai
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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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To disable security and reset defau
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Administrator • In the new dialog
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To search: Administrator 8. Take th
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Administrator 282•Relational Data
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Administrator The following table s
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1. Click one of the column headers
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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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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 rather difficult, but
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Administrator 360•ChemFinder/Orac
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Administrator Reactant List Format
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Administrator • You can configure
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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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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 Working with the User
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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 Ethanol was selected,
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Administrator Type in the AutoText
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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 • In searching subs
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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 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 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 2. To expand the coll
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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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A new Transition Listener appears,
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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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To change the Transition Security P
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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 To find a structure t
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Administrator The CS ChemOffice SDK
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Administrator Troubleshooting This
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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 FORTRAN Formats The F
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Administrator 32 3 12 1 0 0 0 33 3
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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 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 KS The KS, or bond st
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Administrator VDW Interactions The
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Key Drag Shift+Drag Administrator Q
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Administrator 670• Keyboard Modif
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Administrator 6. The pi molecular o
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Administrator Bond Type Wavy specif
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Administrator HO HO HO N H H N N H
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O O Bond Type Description Administr
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Administrator 686• Structural Que
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Formula Chemfinder Interpretation A
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Administrator You do not need to sp
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Administrator boxes it contains. Th
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Administrator GET retrieves a value
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Administrator You may concatenate v
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Administrator Script-Only Commands
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Administrator 702• CAL Commands C
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Administrator open a large table an
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Administrator 706• CS Oracle Cart
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Administrator Access (continued) re
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Administrator Atom-to-Atom mapping
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Administrator Combi experiments 367
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Administrator Dihedral type field 6
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Administrator Exporting (continued)
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Administrator Frame interval contro
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Administrator Importing (continued)
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Administrator Managing (continued)
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Administrator Mol_ID field 287 Mola
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Administrator Opening (continued) p
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Administrator Property query and ta
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Administrator Redo command 269, 299
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Administrator Search Details prefer
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Administrator Sextic bending consta
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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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