Chem3D Users Manual - CambridgeSoft

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Administrator The Calculation Toolbar The Calculation toolbar provides a desktop icon for performing the most common calculation, MM2 minimization. It also provides a Stop button and a “calculation running” indicator that work with all calculations. Calculation indicator MM2 minimization Stop button Close panel Auto-Hide Synchronize Draw > 3D add Draw>3D replace 3D>Draw Clean up structure Clear Lock Name=Struct The ChemDraw Panel Chem3D 9 makes it easier than ever to create or edit models in ChemDraw. The ChemDraw panel is activated from the View menu. By default it opens on the right side of the GUI, but like the toolbars you can have it “float” or attach it anywhere you like. ChemDraw ActiveX tool palette Use the 3D > Draw icon to drag a Chem3D model into the ChemDraw panel. To create a model in ChemDraw, click in the ChemDraw panel to activate the ChemDraw toolbar. Use the Draw>3D Add or Draw>3D Replace icons to put the model in Chem3D—or select the Synchronize icon to draw in both simultaneously. You can also create a model by typing the name of a compound—or a SMILES string—into the Name=Struct box. When you finish editing, add or replace your Chem3D model by clicking the appropriate icon. 22 •Chem3D Basics CambridgeSoft The Graphical User Interface
The Model Information Panel The Model information panel contains information about the model in the top-most tabbed window and its display. You can display one or more of the following tables in the area: • Model Explorer • Measurements • Cartesian Coordinates • Z-Matrix table Tables are linked to the structure so that selecting an atom, bond, or angle in either will highlight both. Numerical values in the tables can be edited or cut and pasted to/from other documents (text or Excel worksheets), and the changes are displayed in the structure. All of the tables have an Auto-hide feature to minimize their display. For more information on Model Tables, see “Model Coordinates” on page 28. The Z-Matrix table is shown below: Record Selector Column Heading Column Divider Field Name Cell The following table describes the elements of the Measurement table. Table Element Column Heading Record Selector Field Name Column Divider Cell Description Contains field names describing the information in the table. Used to select an entire record. Clicking a record selector highlights the corresponding atoms in the model window. Identifies the type of information in the cells with which it is associated. Used to change the width of the column by dragging. Contains one value of one field in a record. All records in a given table contain the same number of cells. The Output and Comments Windows The Output and Comments boxes are typically found at the bottom of the GUI window. You can have them float if you wish, or move them to another side of the window. You can select Autohide to minimize them. Calculations on models and other operations produce messages that are displayed in the Output window.You can save the information in the Output window either directly or using the clipboard. To save information directly: ChemOffice 2005/Chem3D Chem3D Basics • 23 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
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Page 12 and 13: A Guide to CambridgeSoft Manuals An
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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 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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Administrator 13 * 3D displacement
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Administrator The field value for C
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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 12. Line 30, “@BOND
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Parameter Table Use Parameter Table
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Administrator KS The KS, or bond st
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Administrator R* The R* field is th
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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 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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