Chem3D Users Manual - CambridgeSoft

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Administrator EPS The PostScript file format saves models as encapsulated postscript file (EPS). EPS files are ASCII text files containing the scaleable PostScript representation of a Chem3D picture. You can open EPS files using other applications such as PageMaker. You can transfer EPS files among platforms, including Macintosh, Windows, and UNIX. TIF The Tagged Image File Format (TIFF) contains binary data describing a bitmap image of the model. TIFF is a high resolution format commonly used for saving graphics for cross-platform importing into desktop publishing applications. TIFF images can be saved using a variety of resolution, color, and compression options. As TIFF images can get large, choosing appropriate options is important. When you save a file as .TIF, an option button appears in the Save As dialog box. If you want to … Then choose … store colors using computer monitor style of color encoding. use printing press style of color encoding. RGB Indexed. CMYK Contiguous. Stores colors nonsequentially. For example: CMYKCMYK. The PackBits compression type provides no compression for this type of file. NOTE: If objects in your document are black and white they are saved as black and white regardless of which Color options you set. If you import drawings from other applications and want them to print Black and White you must set the Color option to Monochrome. To specify the save options: 1. Click Options: The TIFF Options dialog box appears. 4. Choose a compression option: If you want to … Then choose … 2. Choose a resolution. The size of the file increases as the square of the resolution. 3. Choose a color option. If you want to … Then choose … reduce file size by encoding repeating bytes of information as output. For example, for a line of color information such as: CCCCCMMMMMYYYY YKKKKK, the compression yields a smaller file by representing the information as C5M5Y5K5. PackBits. force objects to black and white. Monochrome. fax transmissions of images CCITT Group 3 or CCITT Group 4. 120•Printing and Exporting Models CambridgeSoft Exporting Models Using Different File Formats
GIF and PNG and JPG Use the Graphics Interchange Format (GIF), Portable Network Graphics (PNG) file format, or the JPEG format to publish a Chem3D model on the world wide web. Each of these formats uses a compression algorithm to reduce the size of the file. Applications that can import GIF, PNG, and JPG files include Netscape Communicator and Microsoft Internet Explorer. The model window background color is used as the transparent color in the GIF format graphic. NOTE: The size of the image in Chem3D when you save the file will be the size of the image as it appears in your web page. If you turn on the “Fit Model to Window” building preference in Chem3D, you can resize the Chem3D window (in Chem3D) to resize the model to the desired size and then save. Alchemy Use the ALC file format to interface with TRIPOS© applications such as Alchemy©. This is supported only for input. Cartesian Coordinates Use Cartesian Coordinates 1 (.CC1) or 2 (.CC2) to import or export the X, Y, and Z Cartesian coordinates for your model. When you save a file as Cartesian Coordinates, an option button appears in the Save As dialog box. To specify the save options: 1. Click Options: The Cartesian Coordinates Options dialog box appears. 3DM The QuickDraw 3D MetaFile (3DM) file format contains 3-dimensional object data describing the model. You can import 3DM files into many 3D modeling applications. You can transfer 3DM files between Macintosh and Windows platforms. AVI Use this file format to save a movie you have created for the active model. You can import the resulting movie file into any application that supports the AVI file format. Formats for Chemistry Modeling Applications The following file formats are used to export models to chemistry modeling application other than Chem3D. Most of the formats also support import. 2. Select the appropriate options: If you want the file to … Then click … contain a connection table for each atom with serial numbers contain a connection table for each atom that describes adjacent atoms by their positions in the file By Serial Number. By Position. not contain a connection table Missing. ChemOffice 2005/Chem3D Printing and Exporting Models • 121 Exporting Models Using Different File Formats
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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 • 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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