ChemDraw User's Manual - CambridgeSoft

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RESEARCH&BioSAR BrowserBiological and Chemical Meta Data CatalogBioSAR BrowserBioSAR Browser, a strategic must for any discovery organization interested in serious data mining, is a data-dictionarydriven structure-activity analysis program. Users may choose among assays registered in the dictionary orsearch for assays of interest.Providing Catalog CapabilitiesThe power of BioSAR Browser lies in the researcher’s freedom from dependence on IT support. Once an assayis registered into the data-dictionary it is automatically included in the powerful analysis framework. By reducingthe time between question and answer, BioSAR Browser gives researchers the freedom to explore newideas—the bottom line for discovery information systems. Systems that provide answers after questions havebecome irrelevant are of no use. BioSAR Browser avoids this by placing application development in theresearcher’s control.Forms & Tables in a Unified InterfaceWhile most SAR tools provide only a table-based interface, BioSAR Browser provides a forms-based interface inaddition to a tabular view. Researchers have demonstrated that both form and tabular views are essential. Formsprovide highly detailed information about one compound, whereas tabular views make comparisons betweenForm and Table ViewsData DictionaryOrganizes Reports
DISCOVERY• Catalog driven data mining and analysis operation• Both form and table views available within simpleweb interface; ChemDraw for Spotfire• Role based security specifies operations allowed foradministrators, publishers and browserscompounds more feasible. There is often a tradeoff between power and simplicity, and most SAR tools opt forthe former at the expense of the latter. BioSAR Browser, however, merges the sophistication of a powerful datacatalog technique with knowledge gained through years of working closely with users. The result is a SARapplication that is as intuitive as it is powerful.Security & ConvenienceSecurity within BioSAR Browser is highly granular. Different roles exist for administrators, publishers, andbrowsers. Administrators may add assays to the data catalog engine, publishers may create reports and publishthem, and browsers may use data query and analysis. Most data mining tools provide a mechanism to storequeries, but the interface for creating queries is too complex. With BioSAR Browser, each set of assays is a completereport with a query form, a view form, and a table view, combining the convenience of a ChemFinder orISIS application with the power and flexibility of a data catalog-driven mining program.ChemDraw for SpotfireChemDraw for Spotfire is a powerful add-in for the Spotfire DecisionSite software. Spotfire makes industrystandard applications for high-dimensional visual data analysis, and is used to explore large biological datasets.ChemDraw for Spotfire adds chemistry to DecisionSite, providing structure visualization and searching services.Highlight a spot in Spotfire’s DecisionSite, and a structure is displayed directly in the window. If you drawa structure and click Search, the matching records are displayed right in the Spotfire window. The structuresare retrieved from a chemical database such as Registration System, ChemFinder, or Oracle Cartridge, and arereturned directly over the network. In this way, structures can be linked by registry number, CAS number, orEMAIL info@cambridgesoft.com WWW www.cambridgesoft.comTEL 1 800 315–7300 INT’L 1 617 588–9300 FAX 1 617 588–9390MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USAChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft ©2002.All other trademarks are the property of their respective holders. All specifications subject to change without notice.
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ChemOffice.Com®ChemDraw®Chemical
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License InformationChemOffice, Chem
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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 ManualsAnd
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ContentsIntroductionWhat’s New in
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Method 2: Labeling an atom by point
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Chapter 10: Drawing Query Structure
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Searching. . . . . . . . . . . . .
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Administratorthey are presented. Ex
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Administrator12•IntroductionCambr
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The Mac GUI is shown below.Administ
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ToolUse to…AdministratorQueryTool
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AdministratorChemDraw window. Undoc
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AdministratorDouble-clicking on an
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3. Click the checkbox next to Autos
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a file as a different format is use
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QuickDraw is the graphical format t
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Chapter 2: TutorialsOverviewThe tut
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.2. Double-click the atom.The hand
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3. Click the third arrow from the l
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2. Press the Enter or Return key to
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.Add second and third bonds:1. Poin
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Refine the shape of the arrow:1. Po
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4. Click each of the atoms shown be
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4. Select a folder in which to save
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Add labels to C1 and C6:3. Point to
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3. Click Paste to paste the informa
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2. Hold the mouse button and drag u
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Save and close the document:1. From
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The size of the orbital is constrai
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8. Click the Wedged Bond tool, poin
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Chapter 3: Drawing ChemicalStructur
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Adjustthis…If you want to …The
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You can use the tools on the Multip
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To draw a wedged bond:1. Click one
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If you click an atom in a ring, a s
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• Press the Ctrl or Command key w
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To convert ring types:1. With a bon
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Chapter 4:UltraStructNameStructName
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Converting Names toStructuresThere
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category ChemDraw 8 supports... Che
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Chapter 5: Drawing Captions andAtom
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• Subscript—Reduces the text by
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If you label C4, the second and thi
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5. To close the text box, click out
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4. The margin width is applied to a
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Hard-Coded HotKeysYou cannot edit h
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To edit atom number text:1. Click t
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Chapter 6: Drawing Orbitals,Symbols
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To draw a single lobe orbital:1. Ho
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To draw an H-dot or an H-dash:1. Ho
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The Arrow ToolsPaletteUse the Arrow
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Drawing LinesLines drawn with the l
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Some examples of shapes that you ca
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Deleting a SegmentTo delete a curve
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If you wantto...then...If you wantt
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Chapter 7: Manipulating DrawingsOve
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Selecting Entire StructuresTo selec
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The unselected bonds that are attac
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Reflecting ObjectsThrough PlanesYou
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3. The current median bond length f
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3. With the group selected, right-c
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Chapter 8: Advanced DrawingTechniqu
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Am Amyl AmericiumNp para-NeptuniumN
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ProExpanding LabelsMulti-Attached L
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3. Double-click on the cyclopentadi
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If you select only part of a struct
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Customizing the ColorPaletteYou can
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2. Click a color in the Color Wheel
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A new and untitled Template window
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Chapter 9: Working WithStructuresOv
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Propertym/zDescriptionMass/charge,
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3. Click the appropriate Position o
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To create a report and view results
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ProExpand GenericStructuresYou can
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The assigned atoms or bonds are hig
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Chapter 10:StructuresProDrawing Que
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• From the Structure menu, choose
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OptionSimple ringSearch ResultFinds
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Abnormal ValenceThe Abnormal Valenc
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The Bond Type options are described
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In the table below, points are may
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To Position …from the atom or bon
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. Not necessarily carbon (a generic
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A structure-based representation of
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Because of its prevalence the No Fl
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However, you are not interested in
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Always Display and PrintAtom Mappin
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ExportedQueryPropertiesISIS Mol Rxn
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ExportedQueryPropertiesISIS Mol Rxn
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Chapter 11: Working With PageLayout
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To create headers and footers:1. Fr
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Saving Page Setup SettingsYou can s
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A check mark appears next to the Sh
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Aligning ObjectsUse the Align comma
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The table appears in the document w
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7. Press Tab again to create a thir
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Chapter 12: Sharing InformationOver
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A clipping file or a scrap file is
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pasted in other types of documents.
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• SMDFormat Import ExportChemDraw
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.opened in versions 3.0, 3.0.1, 3.0
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For single step single or multi-lin
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different computers rather than usi
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Transferring ChemDrawDocuments Acro
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Chapter 13: ChemDraw/ExcelThe ChemD
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mats, but you may get error message
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Adding Structures withChemDrawThe C
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3. Select the search options:If you
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Aligning StructuresA structure may
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FunctionActionCHEM.COMPOSITION Retu
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AppendicesThis section contains the
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Appendix A: Accessing theCambridgeS
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Follow the links to do substructure
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You can search SciStore.Com for che
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Appendix B: Technical SupportOvervi
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4. If the problem still occurs, use
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Appendix C: The Chemistry ofChemDra
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+*/A series of anyCH 2 COOC(OPh) 3c
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Isotopes and ElementsBy default, Ch
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CIP rules are designed to order lig
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• Critical messages that may affe
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MessageThis label has anunrecognize
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Appendix D:WorksUltraHow ChemNMROve
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Appendix E:WorksProHow ChemPropChem
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Appendix F: Shortcuts andHotkeysSho
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Enter...to execute Command...Enter.
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Enter...to execute Command...Enter.
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HotkeyResultHotkeyResultTOTsxX1 n-B
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Appendix G: Document SettingsCreati
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Drawing, Atom Label, and Caption Te
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Appendix H: Chemistry FileFormatsOv
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Double bonds are bit encoded using
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IndexNumerics13C, 1 H shifts, estim
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Bond Propertiesdefining 155descript
Page 286 and 287: Chemical Warnings (continued)suppre
Page 288 and 289: Deletingatom labels 87Backspace key
Page 290 and 291: File format (continued)CTR 198cts 2
Page 292 and 293: Inserting (continued)rows in tables
Page 294 and 295: Nicknames (continued)overview 121tr
Page 296 and 297: Printing (continued)ChemDraw Laser
Page 298 and 299: Saving customized settings 21Scalec
Page 300 and 301: System requirements 11TTable tool 1
Page 302 and 303: Use Defaults (continued)bond proper
Page 304 and 305: CAMBRIDGESOFTChemOffice Desktop toK
Page 306 and 307: CS ChemOfficeSoftware SuitesChemOff
Page 308 and 309: DESKTOPCS E-NotebookElectronic Jour
Page 310 and 311: DESKTOPCS ChemDrawChemical Structur
Page 312 and 313: DESKTOPCS Chem3DMolecular Modeling
Page 314 and 315: DESKTOPCS ChemFinderSearching and I
Page 316 and 317: DESKTOPCS ChemInfoReference and Che
Page 318 and 319: ENTERPRISEChemOffice WebServerEnter
Page 320 and 321: ENTERPRISEOracle CartridgeEnterpris
Page 322 and 323: KNOWLEDGEE-Notebook EnterpriseDeskt
Page 324 and 325: KNOWLEDGEDocument ManagerDesktop to
Page 326 and 327: KNOWLEDGE21CFR11 ComplianceElectron
Page 328 and 329: RESEARCH&Registration SystemChemica
Page 330 and 331: RESEARCH&Inventory ManagerChemical
Page 332 and 333: RESEARCH&CombiChem EnterpriseDeskto
Page 334 and 335: RESEARCH&BioAssay HTSBiological Ass
Page 338 and 339: CHEMICALChemACX DatabaseAvailable C
Page 340 and 341: CHEMICALThe Merck IndexChemistry’
Page 342 and 343: CHEMICALChemical DatabasesReference
Page 344 and 345: CONSULTING &Consulting & ServicesDe
Page 347: CS Software Problem ReportFor faste
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