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Chapter 31: Changes and Audit Trail . . 445 Chapter 32: Searching . . . . . . . . . . . . . . 453 Appendix J: MOPAC . . . . . . . . . . . . . . . 675 Appendix K: Structural Query Features 677 Administrator Chapter 33: Viewing User Information 479 Using the Session Manager . . . . . . . . . . 479 Refreshing E-Notebook . . . . . . . . . . . . . 480 Chapter 34: Managing Section Types and Forms . . . . . . . . . . . . . . . . . . . . . . . 481 Appendix L: Formula Input Rules . . . . 687 Appendix M: Similarity Rules . . . . . . . . 689 Appendix N: CAL Commands. . . . . . . . 691 Appendix O: CS Oracle Cartridge . . . . 703 Chapter 35: Managing Fields . . . . . . . . 507 Chapter 36: Managing Collection Types547 Chapter 37: User Administration . . . . . 581 Chapter 38: Managing E-Notebook Security . . . . . . . . . . . . . . . . . . . . . . . . . 585 Chapter 39: Summary of the Standard Add-Ins . . . . . . . . . . . . . . . . . . . . . . . . . 597 Using the Batch Import Facility . . . . . . 600 Section V: Appendices Appendix A: Accessing the CambridgeSoft Web Site . . . . . . . . . . . . . . . . . . . . . . . . . 605 Appendix B: Technical Support . . . . . . 611 Appendix C: Substructures . . . . . . . . . . 613 Appendix D: Atom Types . . . . . . . . . . . 615 Appendix E: 2D to 3D Conversion . . . . 617 Appendix F: File Formats . . . . . . . . . . . 619 Appendix G: Parameter Tables . . . . . . . 649 Appendix H: Keyboard Modifiers . . . . . 667 Appendix I: MM2. . . . . . . . . . . . . . . . . . 671 CambridgeSoft
Contents Introduction About Chem3D . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 ChemSAR/Excel . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 About ChemFinder. . . . . . . . . . . . . . . . . . . . . . . . . . . 1 ChemFinder/Office . . . . . . . . . . . . . . . . . . . . . . . . 1 About CombiChem/Excel . . . . . . . . . . . . . . . . . . . . 2 About E-Notebook. . . . . . . . . . . . . . . . . . . . . . . . . . . 2 About This User’s Guide . . . . . . . . . . . . . . . . . . . . . . 2 Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 Additional Information . . . . . . . . . . . . . . . . . . . . . . . 3 Quick Reference Card. . . . . . . . . . . . . . . . . . . . . . . 3 Help System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 CambridgeSoft Web Pages. . . . . . . . . . . . . . . . . . . 3 Installation and System Requirements . . . . . . . . . . 3 Microsoft®Windows® Requirements. . . . . . . . . 4 Site License Network Installation Instructions . 4 Chem3D Introduction About CS MOPAC . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 About Gaussian . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 About CS Mechanics . . . . . . . . . . . . . . . . . . . . . . . . . 5 What’s New in Chem3D 9.0? . . . . . . . . . . . . . . . . . . 6 What’s New in Chem3D 9.0.1?. . . . . . . . . . . . . . . 6 For Users of Previous Versions of Chem3D . . . 7 CambridgeSoft Web Pages. . . . . . . . . . . . . . . . . . . 7 Installation and System Requirements . . . . . . . . . . 7 Microsoft®Windows® Requirements. . . . . . . . . 7 Site License Network Installation Instructions . 8 Chapter 1: Chem3D Basics The Graphical User Interface . . . . . . . . . . . . . . . . . . 9 Model Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Rotation Bars . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 Menus and Toolbars . . . . . . . . . . . . . . . . . . . . . . . 10 The File Menu . . . . . . . . . . . . . . . . . . . . . . . . . . 10 The Edit Menu . . . . . . . . . . . . . . . . . . . . . . . . . . 11 The View Menu/Model Display Toolbar . . . 11 The Structure Menu . . . . . . . . . . . . . . . . . . . . . 13 The Standard Toolbar . . . . . . . . . . . . . . . . . . . . 15 The Building Toolbar . . . . . . . . . . . . . . . . . . . . 16 The Model Display Toolbar . . . . . . . . . . . . . . . 16 The Surfaces Toolbar . . . . . . . . . . . . . . . . . . . . . 17 The Movie Toolbar . . . . . . . . . . . . . . . . . . . . . . 17 The Calculation Toolbar . . . . . . . . . . . . . . . . . . 18 The ChemDraw Panel . . . . . . . . . . . . . . . . . . . . . . 18 The Model Information Panel . . . . . . . . . . . . . . . 19 The Output and Comments Windows. . . . . . . . 19 Model Building Basics . . . . . . . . . . . . . . . . . . . . . . . . 20 Internal and External Tables . . . . . . . . . . . . . . . . 20 The Model Setting Dialog Box . . . . . . . . . . . . . . 21 Model Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 Model Data Labels . . . . . . . . . . . . . . . . . . . . . . . 22 Atom Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 Rectification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 Bond Lengths and Bond Angles . . . . . . . . . . . 23 The Model Explorer. . . . . . . . . . . . . . . . . . . . . . . . 23 Model Coordinates . . . . . . . . . . . . . . . . . . . . . . . . . 24 Z-matrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 Cartesian Coordinates . . . . . . . . . . . . . . . . . . . . 24 The Measurements Table . . . . . . . . . . . . . . . . . 25 Chapter 2: Chem3D Tutorials Tutorial 1: Working with ChemDraw. . . . . . . . . . . 27 Tutorial 2: Building Models with the Bond Tools. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 Tutorial 3: Building Models with the Text Building Tool . . . . . . . . . . . . . . . . . . . . . . . . . . 32 Replacing Atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 Using Labels to Create Models . . . . . . . . . . . . . . 33 Using Substructures . . . . . . . . . . . . . . . . . . . . . . . . 34 Tutorial 4: Examining Conformations. . . . . . . . . . 35 Tutorial 5: Mapping Conformations with the Dihedral Driver . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 Rotating two dihedrals . . . . . . . . . . . . . . . . . . . . 39 Customizing the Graph . . . . . . . . . . . . . . . . . . . 39 Tutorial 6: Overlaying Models . . . . . . . . . . . . . . . . 39 ChemOffice 2005
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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
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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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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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Administrator • Semiempirical Ext
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Method Type Advantages Disadvantage
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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 A variety of other ba
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Compute Properties The Compute Prop
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Administrator C(2)-C(3)-C(4) bond a
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Administrator improvements in each
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Administrator Chemical symbol ++ ba
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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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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 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 Property Electronic E
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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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to see some of the information avai
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+ The ISICCR database opens in Chem
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When you release the mouse button,
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Administrator 250•ChemFinder Tuto
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The Open dialog box appears. To cho
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A data source tree appears, contain
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ChemFinder saves the form with a .c
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To line up objects on a form: Admin
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Administrator to those usernames. M
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To disable security and reset defau
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To search: Administrator 8. Take th
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1. Click one of the column headers
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Administrator Creating Tables There
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Creating Fields Administrator 4. Fr
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The name of the new field appears i
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Administrator ChemFinder creates a
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Administrator atoms contained in th
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The general procedure for importing
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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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If you want to Then click Administr
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To reset searches to the full datab
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To set the options for what ChemFin
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To activate CombiChem/Excel: The Co
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Administrator • You can configure
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An analysis of the reaction steps a
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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 If your system config
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Administrator Your system configura
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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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The example below shows the Prepara
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Administrator Ethanol was selected,
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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 Replacing a Spectrum
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The row is removed from the Table.
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Showing the Name of a Box To show t
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Managing Search Fields Administrato
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Creating a New Collection Type The
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Key Drag Shift+Drag Administrator Q
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O O Bond Type Description Administr
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Formula Chemfinder Interpretation A
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Administrator For the two compounds
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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
Page 730 and 731:
Administrator You may concatenate v
Page 732 and 733:
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
Page 740 and 741:
Administrator Access (continued) re
Page 742 and 743:
Administrator Atom-to-Atom mapping
Page 744 and 745:
Administrator Changing (continued)
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Administrator Combi experiments 367
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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 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 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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DESKTOP CS E-Notebook Electronic Jo
Page 784 and 785:
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Page 786 and 787:
DESKTOP CS Chem3D Molecular Modelin
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DESKTOP CS ChemFinder Searching and
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RESEARCH & Registration System Chem
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RESEARCH & Inventory Manager Chemic
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RESEARCH & BioAssay HTS Biological
Page 810 and 811:
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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
Page 821:
CS Software Problem Report For fast
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