Chem3D Users Manual - CambridgeSoft

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Administrator • Stereo Pairs—A toggle switch to enhance three dimensional effect by displaying a model with two slightly different orientations. It can also create orthogonal (simultaneous front and side) views. The degree of separation is set on the Stereo View tab of the Settings dialog box. • Perspective—A toggle switch to create a perspective rendering of the model by consistent scaling of bond lengths and atom sizes by depth. The degree of scaling is controlled by the Perspective “Field of View” slider on the Model Display tab of the Settings dialog box. • Depth Fading—A toggle switch to create a realistic depth effect, where more distant parts of the model fade into the background. The degree of fading is controlled by the Depth Fading “Field of View” slider on the Model Display tab of the Settings dialog box. • Model Axes—Displays or hides the Model axes. • View Axes—Displays or hides the view axes. NOTE: When both axes overlap and the Model axes are displayed, the View axes are not visible. • Background Color—Displays the Background color select toolbar. Dark backgrounds are best for viewing protein ribbon or cartoon displays. Selecting redblue or Chromatek 3D display will automatically override the background color to display the optimal black background. Background colors are not used when printing, except for Ribbon displays. When saving a model as a GIF file, the background will be transparent, if you have selected that option for Image Export in the Preferences dialog box. • Color By—Selects the model coloring scheme. See “Coloring Displays” on page 58 for more information. • Toolbars—Click the name of a toolbar to select it for display. Click again to deselect. You can attach a toolbar to any side of the GUI by dragging it to where you want it attached. If you are using a floating toolbar, you can change its shape by dragging any of its edges. • Standard toolbar—Contains standard file, edit, and print tools. The commands are duplicated on the File and Edit menus. • Building toolbar—Contains the Select, Translate, Rotate, and Zoom tools in addition to the model building tools— bonds, text building tool, and eraser. These tools are not duplicated on any menu. This toolbar is divided into “safe” and “unsafe” tools. The four “safe” tools on the left control only the view – they do not affect the model in any way. This includes the new “safe” select tool and the new translate tool . The old select tool is now called the Move tool. Although it can also be used to select, it’s primary use is to move atoms and fragments. • Model Display toolbar—Contains tools to control the display of the model. These tools are duplicated on the View menu. • Surfaces toolbar—Contains tools to calculate and display a molecular surface. Molecular Surface displays provide information about entire molecules, as opposed to the atom and bond information provided by Structure displays. • Movies toolbar—Contains tools for the creation and playback of movies. Chem3D movies are animations of certain visualization operations, such as iterations from a computation. They can be viewed in 16 •Chem3D Basics CambridgeSoft The Graphical User Interface
Chem3D, or saved in Windows AVI movie format. The commands are reproduced on the Movie menu. • Calculation toolbar—Performs MM2 minimization from a desktop icon. The spinning- arrow icon shows when any calculation is running, and the Stop icon can be used to stop a calculation before it’s preset termination. • Status bar—Displays the Status bar, which displays information about the active frame of your model. • Customize—Displays the Customize dialog box. Customizing toolbars is a standard MS Windows operation, and is not described in Chem3D documentation. • Model Explorer—Displays a hierarchical tree representation of the model. Most useful when working with complex molecules such as proteins, the Model Explorer gives you highly granular control over the model display. • ChemDraw Panel—Displays the ChemDraw Panel. Use the ChemDraw Panel to build molecules quickly and easily with familiar ChemDraw drawing tools. You can import, export, edit, or create small molecules quickly and easily using the ChemDraw ActiveX tools palette. • Cartesian Table—Displays the Cartesian Coordinates table. Cartesian Coordinates describe atomic position in terms of X-, Y-, and Z-coordinates relative to an arbitrary origin. • Z-Matrix Table—Displays the internal coordinates, or Z-Matrix, table. Internal coordinates are the most commonly used coordinates for preparing a model for further computation. • Measurements Table—Displays the Measurements table.The Measurements table displays bond lengths, bond angles, dihedral angles, and ring closures. • Parameters Tables—Displays a list of external tables that are used by Chem3D to construct models, perform computations and display results. • Output Box—Displays the Output box, which presents textual information about the model, iterations, etc. • Comments Box—Displays the Comments box, a place for user comments that is stored with the file. • Dihedral Chart—Opens the window displaying results of Dihedral Driver MM2 computation. See “Tutorial 5: Mapping Conformations with the Dihedral Driver” on page 42 for more information. • Status Bar—Displays or hides the Status Bar. • Start Spinning Model Demo—Spins the model on the Y axis. Use stop calculation on the Calculations toolbar to stop the demo. • Full Screen—Activates the full screen display. The Structure Menu The Structure menu commands populate the Measurements table and control movement of the model. The Measurements submenu • Set… Measurements—Sets a measurement—bond length, angle, or distance—according to what is selected. • Bond Lengths—Displays bond lengths in the Measurements Table. The Actual values come from the model and the Optimal values come from the Bond Stretching Parameters external table. ChemOffice 2005/Chem3D Chem3D Basics • 17 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: Administrator Setting Molecular Sur
Page 16 and 17: Administrator Methods Available in
Page 18 and 19: Administrator Defining Atom Types.
Page 20 and 21: Administrator • CambridgeSoft
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Page 26 and 27: Administrator The following table d
Page 30 and 31: Administrator • Bond Angles—Dis
Page 32 and 33: Administrator The Building Toolbar
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Page 36 and 37: Administrator 1. Right-click in the
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Page 44 and 45: Administrator 2. Click the ChemDraw
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Administrator Surface Type Solid De
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Administrator 2. Adjust the slider
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Administrator Density surface is ca
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Administrator 72 •Displaying Mode
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Administrator The following table d
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Administrator When Correct Atom Typ
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Administrator To use the same text
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Administrator Example 2. Building a
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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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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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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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If you want the file to … Then cl
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Molecular Design Limited MolFile (.
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Administrator 7. Leave the last lin
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Administrator 128•Printing and Ex
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Administrator • Semiempirical Ext
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Method Type Advantages Disadvantage
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Administrator • A single point ca
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Administrator • Molecular mechani
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Administrator constant), while θ 0
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Administrator The van der Waals int
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Administrator 6. The modified value
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the same wave function and a consta
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Administrator A variety of other ba
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Administrator Molecular wave functi
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Administrator activation barriers.
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3. From the Calculations menu, poin
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minimizing a second model, the mini
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Administrator move to lower the ene
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. Administrator Molecular Dynamics
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Administrator If you want to … Th
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Administrator The Compute Propertie
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Administrator To run a previously c
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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 198•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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Property Description Property Descr
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Property Description Error Message
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Administrator Property Electronic E
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Administrator To specify the calcul
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Administrator 3. Click Open. The ap
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Administrator • Server—limits t
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Administrator To perform property c
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The Step 4 of 4 dialog box appears.
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Administrator • From the ChemOffi
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Administrator Accessing the Online
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Administrator To find a structure t
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Administrator 228• Accessing the
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Administrator Performance Below are
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Administrator Defining Substructure
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Administrator If an atom can be ass
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Key Drag Shift+Drag Administrator Q
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Administrator 238• Keyboard Modif
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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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5 6 1.11606 3 109.41 5 109.41 -1 21
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Administrator 41 4 1 0 0 0 0 0 0 0
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Administrator 32 3 12 1 0 0 0 33 3
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Administrator 13 * 3D displacement
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Administrator The field value for C
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Administrator Line 4e: C 1.53597 1
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Administrator CONECT 4 2 9 10 11 CO
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Administrator COMPND ATOM HETATM CO
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Administrator Line 56 -2794 21139 6
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Administrator 7 2 10 1 8 3 6 1 9 3
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Administrator Line 16 6 C -0.559 1.
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Administrator 12. Line 30, “@BOND
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Parameter Table Use Parameter Table
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Administrator 3. Type the informati
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Administrator Geometry The geometry
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Administrator KS The KS, or bond st
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Administrator one attached hydrogen
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Administrator bond length between t
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Administrator R* The R* field is th
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Administrator The V1 torsional cons
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Administrator VDW Interactions The
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Administrator Editing Parameters Yo
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Administrator 6. The pi molecular o
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Administrator Adding Parameters to
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Administrator fragments 84 paramete
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Administrator CC1 see Cartesian coo
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Administrator Copy As Bitmap comman
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Administrator Examining angles, tut
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Administrator density 67 editing 67
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Administrator editing 107 non-bonde
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Administrator repeating jobs 178 RH
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Administrator Rectification, when d
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Administrator all atoms 95 atoms or
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Administrator Translucent surface t
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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
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Chem3D Users Manual - CambridgeSoft

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