Chem3D 8.0 Manual - CambridgeSoft

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AdministratorShowing Dihedral AnglesTo display the dihedral angles for a model in theMeasurements table:• From the Analyze menu, point to ShowMeasurements, and then choose ShowDihedral Angles.For example, to display the dihedral angles in apenicillin molecule:1. Click the Text Building tool.2. Click in an empty model window.A text box appears.3. Type Penicillinyl and press Enter.4. From the Object menu, point to Show SerialNumbers, and then choose Show.5. Select the C(7)-N(1)-C(2)-C(8) dihedral angle.6. From the Analyze menu, point to ShowMeasurements, and then choose ShowDihedral Angles.The Measurements table appears with thedihedral angles for the penicillin molecule. TheC(7)-N(1)-C(2)-C(8) dihedral angle isapproximately 107°.Showing Close ContactsTo display the close contacts for a model in theMeasurements table:• From the Analyze menu, point to ShowMeasurements, and then choose Show CloseContacts.Two atoms are considered to be in close contact ifthe distance between them is less than or equal to thesum of their van der Waals radii. The van der Waalsradii used to determine close contacts are located inthe Atom Types table. In general, the van der Waals94 • Chapter 7: Inspecting Models CambridgeSoftPop-up Information
adii in the parameter set supplied withChem3D were computed on the assumption that ahydrogen atom is in close contact with another atomwhen the energy of interaction is greater than orequal to 0.5 kcal/mol.For example, to display the Close Contacts in apenicillin molecule:1. Click the Text Building tool.2. Click in an empty model window.A text box appears.3. Type Penicillinyl and press Enter.4. From the Object menu, point to Show SerialNumbers, and then choose Show.5. From the Analyze menu, point to ShowMeasurements, and then choose Show CloseContacts.The Measurements table appears with the closecontacts records shown between the bondlength records and the bond angle records.Atoms C(7) and H(17) are in close contact; theirdistance apart is approximately 2.4Å.6. Click in a blank area of the Measurementstable to deselect all measurements.7. Click the C(7), H(17) close contact record.When you select any of the close contactrecords in the Measurements table, thecorresponding atoms in the model are selected.In the following illustration, C(8) and H(17) are inclose contact because the distance between them,2.110Å, is less than the sum of their van der Waalsradii, 2.597Å.Showing Ring ClosuresTo display the ring closure bonds and ring closureangles in the Measurements table:• From Analyze menu, point to ShowMeasurements, and then choose Show RingClosures.For example, to display the Ring Closures in apenicillin molecule:1. Click the Text Building tool.2. Click in an empty model window.A text box appears.3. Type Penicillinyl and press Enter.4. From the Analyze menu, point to ShowMeasurements, and then choose Show RingClosures.The Measurements table appears with the ringclosure bonds and ring closure angles in thepenicillin molecule.The C(2)-C(3) and C(6)-C(7) bonds are ringclosure bonds.Chem3D 8 Chapter 7: Inspecting Models • 95Pop-up Information
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ChemOffice.Com®ChemOffice®Chem3D,
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CS Product RegistrationRegistering
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User’s GuideCS Chem3D 8.0for Wind
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CambridgeSoft Software License1. Gr
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No Waiver. The failure of either pa
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The failure of either party to asse
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ContentsIntroduction . . . . . . .
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Rotating Fragments. . . . . . . . .
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Choosing a Hamiltonian . . . . . .
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Appendix D: MM2 . . . . . . . . . .
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Administrator• Faster graphics-3D
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AdministratorInstallation and Syste
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AdministratorModel WindowThe Model
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Table ElementDescriptionObjectDescr
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To specify the rendering type, atom
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AdministratorYou can also build mod
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AdministratorElementBound-to orderS
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Customizing the UserInterfaceAdmini
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AdministratoroptionUse BackBuffer f
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AdministratorExamine the atoms and
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Administrator2. Release the mouse b
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AdministratorReplacing AtomsTo chan
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Change the model display type:Build
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You will also save the frames you c
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Tutorial 4: SearchingFor Conformati
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Administrator3. Click in the model
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Administrator5. In the Theory tab,
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AdministratorFor phenol, the greate
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Creating a Model UsingTemplatesChem
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The Cartesian Coordinates Options d
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Saving a Model with a Different Nam
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Administrator44 • Chapter 3: Crea
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AdministratorThe following table de
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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
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