Chem3D Users Manual - CambridgeSoft

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Key Drag Shift+Drag Administrator Q Zoom to rotation center W Zoom to selection center If you have a wheel mouse, you may also use the scroll wheel to zoom. Dragging with the middle button or scroll wheel translates the view. Selection Standard Selection Key Click Shift+Click Drag Shift+Drag S Select atom/bond Multiple select atom/bond Box select atoms /bonds Multiple box select atoms /bonds Notes: • Clicking a bond selects the bond and the two atoms connected to it. • Double-clicking an atom or bond selects the fragment that atom or bond belongs to. • Double-clicking a selected fragment selects the next higher fragment; that is, each double-click moves you up one in the hierarchy until you have selected the entire model. Radial Selection Radial selection is selection of an object or group of objects based on the distance or radius from a selected object or group of objects. This feature is particularly useful for highlighting the binding site of a protein. Radial selection is accessed through the Select submenu of the context menu in the Model Explorer or 3D display. 236• Keyboard Modifiers <strong>CambridgeSoft</strong>
In all cases, multiple selection is specified by holding the shift key down while making the selections. Submenu option Select Atoms within Distance of Selection Select Groups within Distance of Selection Select Atoms within Radius of Selection Centroid Select Groups within Radius of Selection Centroid Effect Selects all atoms (except for those already selected) lying within the specified distance from any part of the current selection. The current selection will be un-selected unless multiple selection is used. Selects all groups (except for those already selected) that contain one or more atoms lying within the specified distance from any part of the current selection. The current selection will be un-selected unless multiple selection is used. Selects all atoms (except for those already selected) lying within the specified distance of the centroid of the current selection. The current selection will be un-selected unless multiple selection is used. Selects all groups (except for those already selected) that contain one or more atoms lying within the specified distance of the centroid of the current selection. The current selection will be un-selected unless multiple selection is used. Appendices ChemOffice 2005/Appendix Keyboard Modifiers • 237
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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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Administrator Setting Molecular Sur
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Administrator Methods Available in
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Administrator Defining Atom Types.
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Administrator • CambridgeSoft
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Administrator provides a balance be
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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 30 •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 Tutorial 7: Docking M
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Administrator To save the iteration
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The allyl radical, CH 2 =CHCH 2·,
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Administrator Determine the raw spi
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Administrator atoms are relatively
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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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• Select Parallel to rotate the r
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Administrator • From the Computat
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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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Page 204 and 205: Administrator 3. Click in the model
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Page 216 and 217: Administrator Repeating a Gaussian
Page 218 and 219: Property Description Property Descr
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Page 224 and 225: Administrator To specify the calcul
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Page 238 and 239: Administrator To find a structure t
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Page 242 and 243: Administrator Performance Below are
Page 244 and 245: Administrator Defining Substructure
Page 246 and 247: Administrator If an atom can be ass
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Page 256 and 257: Administrator Connection tables by
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Page 266 and 267: Administrator 13 * 3D displacement
Page 268 and 269: Administrator The field value for C
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Page 272 and 273: Administrator CONECT 4 2 9 10 11 CO
Page 274 and 275: Administrator COMPND ATOM HETATM CO
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Page 282 and 283: Administrator 12. Line 30, “@BOND
Page 284 and 285: Parameter Table Use Parameter Table
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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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