- Page 1: ChemOffice.Com ® ChemOffice ® Che
- Page 5 and 6: CambridgeSoft Software License 1. G
- Page 7 and 8: STANDING THE ABOVE, WHERE APPLICABL
- Page 9 and 10: In no event shall CS, Merck, and/or
- Page 11 and 12: Q: Do the same rules apply to bulle
- Page 13 and 14: Contents by Chapter ChemOffice 2005
- Page 15 and 16: Contents Introduction About Chem3D
- Page 17 and 18: Setting Origin Atoms . . . . . . .
- Page 19 and 20: Dynamics Settings . . . . . . . . .
- Page 21 and 22: Saving a Form. . . . . . . . . . .
- Page 23 and 24: Framing Pictures . . . . . . . . .
- Page 25 and 26: Inserting Reactants and Products wi
- Page 27 and 28: Reconfiguring an Existing Form. . .
- Page 29 and 30: Configuring Annotation Options . .
- Page 31 and 32: Ionization. . . . . . . . . . . . .
- Page 33 and 34: Introduction Overview This User’s
- Page 35 and 36: Features that are available in the
- Page 37 and 38: Section I Chem3D: Introduction Abou
- Page 39 and 40: For Users of Previous Versions of C
- Page 41 and 42: Chapter 1: Chem3D Basics The Graphi
- Page 43 and 44: • Preferences—Displays the Pref
- Page 45 and 46: Chem3D, or saved in Windows AVI mov
- Page 47 and 48: • Position by Dihedrals—Positio
- Page 49 and 50: The Surfaces Toolbar The Surfaces t
- Page 51 and 52: The Model Information Panel The Mod
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To view an external table: • Poin
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If you select four contiguous atoms
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The Measurements Table The Measurem
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Chapter 2: Chem3D Tutorials Overvie
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model is centered. You can rotate y
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• On the Model Display submenu of
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Replacing Atoms To change one eleme
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4. Type Ph(NO2) in the text box. 5.
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To examine this result numerically,
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The model display rotates the dihed
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A box or oval indicates the positio
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1. In the Model Explorer, select C(
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3. From the Calculations menu, poin
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To complete this tutorial, you will
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You can graphically display partial
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Chapter 3: Building and Editing Mod
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and in Chem3D. Editing either model
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• Select the atom or bond, and fr
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• Amino Acid substructures come i
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The charge is applied to the oxygen
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For example, to change benzene to p
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If you are using the Text tool: 1.
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• If the Automatically Rectify ch
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To perform an inversion: 1. Select
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Chapter 4: Manipulating Models Over
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Any atoms that fall at least partia
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• Right-click at any level, point
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When you mouse over an edge of the
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Using the Rotation Dial The Rotatio
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To center your model based on a par
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To position Atom D in Pro-S Orienta
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Chapter 5: Displaying Models Overvi
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Model Type Ribbons Description Ribb
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4. Close and Save the table. NOTE:
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To change an atom to a new solid co
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You can use depth fading and perspe
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To generate surfaces from MOPAC or
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Setting the Surface Resolution The
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are too small to affect the overall
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specified for a previously computed
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Chapter 6: Inspecting Models Model
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You can display several measurement
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To display the Internal Coordinates
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Your measurements table should look
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The Model Explorer window appears a
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The Apply Group Color command is au
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Chapter 7: Printing and Exporting M
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File Format Name Extension Molecula
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GIF and PNG and JPG Use the Graphic
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Chem3D displays the surface the fil
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Col. 1 Col. 2 C3 Col. 4 C5 Col. 6 C
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Exporting With the Clipboard The si
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Chapter 8: Computation Concepts Com
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Semiempirical: The time required fo
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• Relative energies for conformat
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occurs because the value of the ene
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• Cutoffs for electrostatic and v
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about the rotation angle axis. The
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or dipole/dipole interactions are r
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The Molecular Dynamics (MM2) comman
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that describe the interaction betwe
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(usually taken as 1.75). The Hamilt
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• Non-classical structures are pr
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Chapter 9: MM2 and MM3 Computations
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If you want to … Then … watch t
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To view the value of one of the dih
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When the minimization is complete,
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. The Molecular Dynamics dialog box
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A text box appears. 4. Type F(C2F4)
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• The Stretch-Bend term represent
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Chapter 10: MOPAC Computations Over
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esults in better estimates of the e
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and other atoms are predicted. In p
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Keyword MMOK Description Automatica
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2. On the General tab, in the Keywo
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Excited State, UHF Only the ground
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The .out and .aax files are saved b
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Delete text through this line Keywo
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Option Display Every Iteration Show
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The Output window displays intermed
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3. On the Properties tab, select th
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matrix (Charges) or Mulliken popula
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The following table contains the ke
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Example 2 Comparing Cation Stabilit
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Example 4 Calculating the Dipole Mo
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Form of glycine ∆H (kcal/mole) So
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Example 8 RHF Spin Density for the
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Chapter 11: Computations Gaussian O
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6. Select a Spin Multiplicity value
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To create a Gaussian Input file: 1.
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Chapter 12 : Computations GAMESS Ov
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2. On the Properties tab, set the f
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Chapter 13: SAR Descriptors SAR Des
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mass of the molecule. In this case,
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The MM2 server provides the followi
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Chapter 14: SAR Descriptor Computat
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Chapter 15: Overview ChemSAR/Excel
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c. Click the icon at the right of t
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To calculate properties for added s
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Section II: ChemFinder Introduction
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Chapter 16: ChemFinder Basics Overv
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Screen Element Description Screen E
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The tools are described in detail i
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The Database Model A database is a
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Chapter 17: ChemFinder Tutorials Ov
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The label appears above the Framed
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1. Draw the form shown below, using
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Tutorial 3: Creating Your Own Datab
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3. Draw benzene. Enter two more rec
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1. Choose Explorer Window from the
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Adjust the height of any form by dr
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In this search you get 123 hits of
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. do not know how to produce it. In
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Before you start, go to the View me
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To test this: 1. Click anywhere out
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Chapter 18: Creating and Editing Fo
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Opening a Secured MS Access Databas
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If you want the boxes to be labeled
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To draw a Data Box: 1. Click the Da
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To change the font or color of the
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A structure box appears in the uppe
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If you want to Then choose Right cl
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The scroll bar appears on the botto
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To set the form background and form
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3. Press an arrow key in the direct
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The Form Generation dialog box appe
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• Take the appropriate action:
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If you want users to Then click use
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Chapter 19: Relational Data and Sub
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3. Select the table to be linked (i
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Using Scripts in Subforms You can s
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Chapter 20: Working with Data Overv
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2. Type your username, password, an
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2. Switch to Data Table view. Creat
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Attaching Tables from Other Applica
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Memo/Rich Text field—Used to disp
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Adding Structures to Non-Chemical D
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Committing the New Data When you fi
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Resetting the Database To reset the
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. The Structure field displays a 3D
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Chapter 21: With BioViz Visualizing
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Dialog Option Description Dialog Op
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Filters are set in the filter windo
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Changing the Display Once you have
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Chapter 22: Importing and Exporting
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7. Optional: Click the Logging tab
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ChemDraw format, you can open them
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The Data Export dialog box is simil
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Chapter 23: Searching Overview You
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• Use the Periodic Table to enter
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another R atom. Moreover, stereoche
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complete reaction implies many subr
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Searching for Intermediates Rarely,
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If you want to Then click 3. Take t
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center hits is set to Same, a query
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structure, substructure, and/or sim
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as a doubly drawn pair, the combine
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if you want to... then choose... if
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To edit a saved hit list, open the
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The “A” label denotes that the
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Chapter 24: Customizing ChemFinder
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• ASCII file export (see “Expor
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To add an item to a folder: 1. Poin
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ChemFinder Automation Language (CAL
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5. Press the Esc key to stop debugg
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and search tasks. This feature allo
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Chapter 25: ChemFinder/Oracle Overv
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contain structures, and ChemFinder/
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• Do not modify data in an existi
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To create a primary key index: •
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Section III: CombiChem Overview Com
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If ChemACX is installed on a hard d
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• If you process a reaction templ
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A file browser appears. CombiChem/E
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To highlight products or reactants:
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Chapter 27: ChemFinder/Office Overv
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To look for a structure in specific
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2. Take the appropriate action: Bro
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3. From the File menu in Notepad, c
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Refining Your Search You can refine
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If you want to... match a relative
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Section IV: E-Notebook Chapter 28:
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• Read & Write privilege - The pr
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From within the Search area, you ca
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Chapter 29: E-Notebook User's Guide
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Adding a New Collection to the User
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2. Drag the template into the Noteb
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3. To rename the section, click the
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Browsing from Home You can browse f
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See the following topics for more i
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The collection menu appears. 4. Sel
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• Last Modified - the date on whi
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Collection Security To change the S
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Desired Result Remove a User or Gro
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• All - prints all of the section
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Chapter 30: Reactions, MS Word, MS
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NOTE: You can access a drawing menu
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Applying a Filter To filter the acr
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2. Select Add Reactant After, to ad
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You may also use the reactants/prod
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The Add AutoText dialog appears. 3.
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Section Names as Categories If you
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Data type Enumerated Value Action t
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were conducted for a property value
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You are select a file to import. 3.
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To create a new Spectrum section fo
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A dialog box appears with a list of
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Resizing Columns and Rows in a Tabl
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Changing Information in a Table Cel
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6. You can click the arrow in the t
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In some cases, you will only have R
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4. In the Collection Tree, click th
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Chapter 31: Changes and Audit Trail
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To Backup and Restore your changes:
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3. To view a particular version, cl
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Type of Data Change Display Example
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Chapter 32: Searching E-Notebook of
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Collection (Metadata) Properties Me
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Chemical Structure Search Substruct
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Bond Type Description Finds: Does n
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With a substructure search, the que
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Bond Type Description Property Desc
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By matching numbers across the arro
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Parameter Options 1. Right-click wi
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• Advanced Text Searching Numeric
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For example, the following searches
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For example, the following searches
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Soundex (!) The soundex operator is
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• Remove from the Previous Search
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Chapter 33: Viewing User Informatio
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Chapter 34: Managing Section Types
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Each type of field has its own, spe
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The dialog closes. The form refresh
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• Table Field with Products Liste
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This will prevent users from draggi
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2. Select Section Type Configuratio
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A box appears on top of the box you
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4. Right-click within the new box,
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2. Select Box Properties. Hiding th
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2. Select Box Properties. Changing
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The Box is no longer visible in the
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See the following topics: • “Cr
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corresponds to the value. a column
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Chapter 35: Managing Fields Fields
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Managing AutoText Fields With AutoT
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5. Enter a name, and select Chemica
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• Password - An optional string u
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4. Type in a name, and select Excel
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6. Select the Type from the drop-do
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The Enumerated List Properties dial
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Example 1 - Database Lookup Configu
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Managing the Person Property List L
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The Section Type Configuration dial
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Managing the Button View Subsection
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4. Type in a Name and Nickname for
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corresponds to a value in the secti
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The attributes of the property appe
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field. In addition, you must associ
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The Add Field dialog appears. The S
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Managing Property Query Fields Prop
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The Add Field dialog appears. 4. En
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that implements the corresponding i
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Type of Measurement Standard Units
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Chapter 36: Managing Collection Typ
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The Collection Type Configuration D
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Removing a Section Type from a Coll
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3. Right-click contained collection
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A message appears, asking you to co
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2. If necessary, click the plus sig
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For example, if a Notebook collecti
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Select the custom properties as sho
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Managing the Print Multiple Form To
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A new search engine appears and you
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1. Right-click the search type in t
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To configure a transition between s
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5. Click the transition listener wh
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Managing the Required Properties Tr
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Enabling Visual Display of Changes
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Configuring Autosave The Autosave f
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8. Select New and then Export Templ
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Chapter 37: User Administration You
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Depending upon your configuration,
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Chapter 38: Managing E-Notebook Sec
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Desired Result Action to take Desir
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Managing the Security Properties of
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Desired Result Action to take Desir
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The Security tab appears. The group
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This dialog shows the Users, Sessio
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Chapter 39: Summary of the Standard
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• Table Fields - enable users to
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element which specifies by position
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Appendices This section contains th
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Appendix A: Accessing the Cambridge
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Follow the links to do substructure
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The SciStore.Com page opens in your
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Appendix B: Technical Support Overv
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Appendix C: Substructures Overview
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Appendix D: Atom Types Overview Che
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Appendix E: 2D to 3D Conversion Ove
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Appendix F: File Formats Editing Fi
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Cartesian Coordinate Files The Cart
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An example of a Cartesian Coordinat
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The format for Internal coordinates
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This portion of the Internal coordi
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of Chemical Information and Compute
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Limitations The MDL MolFile format
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48 * Bond List 49 * Bond# bond_type
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serial numbers for the atoms involv
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FORTRAN Formats The description of
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21 UNUSED No 7-11 Atom Serial Numbe
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Line 20 H 0 0 0 Line 21 H 0 0 0 Lin
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coordinate type specified in line 4
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ecord, which contains the number of
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Each line is either a blank line, a
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Appendix G: Parameter Tables Parame
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Quality The quality of a parameter
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van der Waals Radius The van der Wa
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• N Isonitrile • N Nitro • O
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four membered rings, the parameters
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• The energy required to keep two
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4-membered rings and the -CHR- Bend
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Membered Ring Torsional Parameters
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Record Order When sorted by Dihedra
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Appendix H: Keyboard Modifiers The
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In all cases, multiple selection is
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Appendix I: MM2 Overview This appen
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Charge-Dipole Interaction Term Alli
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Appendix J: MOPAC Overview The appe
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Appendix K: Structural Query Featur
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finds any of: N Br O OH N Isotopes
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• Mol- or SDFiles obtained from I
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Substituents: Free Sites The Substi
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Property Description Property Descr
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Appendix L: Formula Input Rules Ove
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Appendix M: Similarity Rules Overvi
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Appendix N: CAL Commands Overview C
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• A simple name without extension
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The table below shows examples of P
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• R—read-only • E—exclusive
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APPEND ON WRITEVAL output.txt SETVA
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The table below shows examples of S
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Appendix O: Cartridge Pre-Setup Pro
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To designate a BLOB column as a pic
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Index Symbols % wildcard character
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Aligning objects 269 parallel to an
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Boxes changing styles 262 creating
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ChemProp Pro (continued) thermal ca
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Compute Properties dialog box 211 G
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Data Table description 222 sorting
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Electron field 658 Electronegativit
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File formats 640 (continued) .mop 1
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Groups defining 71 mapping colors o
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Labels 618 (continued) using 55 usi
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Measurements (continued) editing 10
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Move column 434 row 434 to X-Y plan
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Pi bonds table 649, 659 PI keyword
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Query operators (continued) < 319 =
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Ribbons display 85 Ring bonds 684 R
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Security (continued) MS Access work
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Standard measurements, applying 23
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Toolbars (continued) form 224 main
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Viewing (continued) Lowest Unoccupi
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Desktop Software Enterprise Solutio
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SOLUTIONS Enterprise Solutions APPL
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Desktop to Enterprise Solutions Che
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SOFTWARE E-Notebook Ultra Ultimate
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SOFTWARE ChemDraw Ultra Ultimate Dr
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SOFTWARE Chem3D Ultra Ultimate Mode
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SOFTWARE ChemFinder/Word • Search
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SOFTWARE The Merck Index • Encycl
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SOLUTIONS •Development and deploy
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SOLUTIONS •Adds chemical data typ
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MANAGEMENT •Custom organization o
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MANAGEMENT • Indexes chemical str
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MANAGEMENT • E-Notebook Enterpris
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DISCOVERY • Accessed through your
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DISCOVERY • Integrated with Regis
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DISCOVERY • Reagent lists can be
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DISCOVERY •Effectively manages da
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DISCOVERY • Catalog driven data m
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DATABASES • Fully structure-searc
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DATABASES • Encyclopedic referenc
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DATABASES • Extensive collection
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SERVICES · Business Case Developme
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CS ChemOffice ® Desktop to Enterpr