- Page 1 and 2: ChemOffice.Com®ChemOffice®Chem3D,
- Page 3 and 4: CS Product RegistrationRegistering
- Page 5 and 6: User’s GuideCS Chem3D 8.0for Wind
- Page 7 and 8: CambridgeSoft Software License1. Gr
- Page 9 and 10: No Waiver. The failure of either pa
- Page 11 and 12: The failure of either party to asse
- Page 13 and 14: ContentsIntroduction . . . . . . .
- Page 15 and 16: Rotating Fragments. . . . . . . . .
- Page 17 and 18: Choosing a Hamiltonian . . . . . .
- Page 19 and 20: Appendix D: MM2 . . . . . . . . . .
- Page 22 and 23: Administrator• Faster graphics-3D
- Page 24 and 25: AdministratorInstallation and Syste
- Page 28 and 29: Table ElementDescriptionObjectDescr
- Page 30 and 31: To specify the rendering type, atom
- Page 32 and 33: AdministratorYou can also build mod
- Page 34 and 35: AdministratorElementBound-to orderS
- Page 36 and 37: Customizing the UserInterfaceAdmini
- Page 38 and 39: AdministratoroptionUse BackBuffer f
- Page 40 and 41: AdministratorExamine the atoms and
- Page 42 and 43: Administrator2. Release the mouse b
- Page 44 and 45: AdministratorReplacing AtomsTo chan
- Page 46 and 47: Change the model display type:Build
- Page 48 and 49: You will also save the frames you c
- Page 50 and 51: Tutorial 4: SearchingFor Conformati
- Page 52 and 53: Administrator3. Click in the model
- Page 54 and 55: Administrator5. In the Theory tab,
- Page 56 and 57: AdministratorFor phenol, the greate
- Page 58 and 59: Creating a Model UsingTemplatesChem
- Page 60 and 61: The Cartesian Coordinates Options d
- Page 62 and 63: Saving a Model with a Different Nam
- Page 64 and 65: Administrator44 • Chapter 3: Crea
- Page 66 and 67: AdministratorThe following table de
- Page 68 and 69: After you have the backbone, you ca
- Page 70 and 71: AdministratorThe interpretation of
- Page 72 and 73: AdministratorTo use a substructure
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AdministratorTo change the bond ord
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Administratorvalues are the standar
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AdministratorTo remove the formal c
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AdministratorRefining a ModelAfter
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AdministratorSelecting Atoms in a G
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AdministratorWhen you choose Show A
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AdministratorTo perform a rotation
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To move three atoms to a plane and
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Administratorit and other atoms. Al
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AdministratorIf an atom is position
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AdministratorModel TypesThe followi
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AdministratorColoring DisplaysYou c
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To change one of the colors in the
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AdministratorAll atoms currently in
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AdministratorDisplaying MolecularSu
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AdministratorMolecular Surface Colo
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AdministratorSolvent Accessible Sur
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AdministratorTo display a Connolly
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previously computed surface. If you
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If you want todisplay …Then Selec
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Administrator• From the Edit menu
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AdministratorShowing Dihedral Angle
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Administrator5. Select the C(2)-C(3
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AdministratorThe color of the atoms
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AdministratorTo begin the docking c
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AdministratorTo perform an overlay,
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To remove all frames after the fram
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Administrator106 • Chapter 7: Ins
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If you want to …Then select …Fi
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AdministratorBMPThe Bitmap file for
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When you save a file as a Connectio
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AdministratorIf you want to …buil
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Administratorexports .PDB. The .PDB
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Administrator116 • Chapter 8: Pri
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AdministratorComputational Chemistr
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AdministratorThe following table su
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Administrator• A single point cal
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Administrator• Potential energy f
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AdministratorE Stretch= 71.94 ∑ K
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Administratorinclude interactions w
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Administratorwhich are used to scal
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AdministratorQuantum mechanical met
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AdministratorLinear Combination of
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AdministratorUHFThe UHF method trea
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Administrator• Hypervalent compou
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Administrator138 • Chapter 9: Com
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AdministratorIf you want to …spec
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AdministratorThe Total Steric Energ
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AdministratorThe conformation you c
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.AdministratorSticks < Ball and Sti
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AdministratorThe simulation ends wh
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AdministratorThe units are kcal/mol
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AdministratorRepeating an MM2Comput
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AdministratorChoose the appropriate
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AdministratorTo determine the appro
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AdministratorFirst excited quintet:
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AdministratorMOPAC uses its default
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AdministratorThe following contains
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The heat of formation is composed o
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AdministratorComparing Cation Stabi
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Administratormeta>para>ortho, where
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Administrator3. Click in the model
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Form ofglycine∆H(kcal/mole)Solven
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AdministratorThe following table co
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AdministratorThe Message window dis
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AdministratorDescriptionVibrational
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You can create a structure from the
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AdministratorIf you want to …reco
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AdministratorSave a customized job
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Administrator2. Type the full path
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Administrator3. From the Basis Set
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AdministratorA new model window is
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PropertyDescriptionPropertyDescript
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PropertyDescriptionError MessageCau
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PropertyDescriptionThe GAMESS serve
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The property filters are:Administra
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AdministratorTo perform property ca
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The Select Descriptors dialog box a
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Administrator• Sum• Standard de
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To access Browse ChemStore.com:The
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AdministratorTo access the ChemOffi
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AdministratorDefining Substructures
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AdministratorA4 • CambridgeSoftDe
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AdministratorIf an atom can be assi
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AdministratorExample 3In Example 3,
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AdministratorEditing ParametersYou
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Administrator5. A matrix called the
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AdministratorAdding Parameters toMO
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AdministratorParameter Table UseEle
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AdministratorThe ElementsThe Elemen
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AdministratorTo view the menu of ge
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AdministratorFinally, the 1-19 bond
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AdministratorPi AtomsThe Pi Atoms t
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AdministratorCubic and Quartic Stre
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potential well increases, as does t
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AdministratorThe counterintuitive f
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Administratorcorrespondence between
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AdministratorAlchemy FileThe follow
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Administrator2. The first line of a
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H 102 2.127594 1.865631 1.48999 21
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Administrator6 1 1.40195 2 107.6989
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41 3 1 0 0 0 0 0 0 0 0 0 0 1.222366
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Administrator21 -1.2615 2.1277 0.01
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Administrator24-42 Bond id, fromato
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Administrator51 2 1 1 6 0 0.000 0 0
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Administrator18. Line 49 contains a
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AdministratorFORTRAN FormatsThe des
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22 Chain Identifier No12-16 Serial
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AdministratorLine 18 H 0 0 0Line 19
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Administratorof hydrogens attached
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AdministratorNumberof AtomsNumberof
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AdministratorLine 30 @BONDLine 31 1
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11-29 Atom type, name,coordinates a
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AdministratorA66 • CambridgeSoftW
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AdministratorTroubleshootingThis se
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4. If the problem still occurs, Fax
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AdministratorAtom typesassigning au
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Administratorchem3d.h 17chem3d.tlb
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AdministratorDisplay Stereo View 80
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AdministratorFont 16Font size 16For
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Administratorjdt file format 114, 1
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AdministratorMolecular Surfacescalc
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AdministratorParameters 12bond angl
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AdministratorSelect Fragment comman
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AdministratorTools palette 6, 44Too
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Administratorxx • IndexCambridgeS
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CAMBRIDGESOFTChemOffice Desktop toK
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CS ChemOfficeSoftware SuitesChemOff
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DESKTOPCS E-NotebookElectronic Jour
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DESKTOPCS ChemDrawChemical Structur
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DESKTOPCS Chem3DMolecular Modeling
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DESKTOPCS ChemFinderSearching and I
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DESKTOPCS ChemInfoReference and Che
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ENTERPRISEChemOffice WebServerEnter
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ENTERPRISEOracle CartridgeEnterpris
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KNOWLEDGEE-Notebook EnterpriseDeskt
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KNOWLEDGEDocument ManagerDesktop to
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KNOWLEDGE21CFR11 ComplianceElectron
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RESEARCH&Registration SystemChemica
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RESEARCH&Inventory ManagerChemical
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RESEARCH&CombiChem EnterpriseDeskto
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RESEARCH&BioAssay HTSBiological Ass
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RESEARCH&BioSAR BrowserBiological a
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CHEMICALChemACX DatabaseAvailable C
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CHEMICALThe Merck IndexChemistry’
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CHEMICALChemical DatabasesReference
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CONSULTING &Consulting & ServicesDe
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Administrator
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MENUSCreate a new model window.Open
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WORKING WITH SELECTIONSIf you want
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CS ChemOffice®Desktop to Enterpris