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Administrator Example 2. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 617 Example 3. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 618 Example 4. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 618 Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 618 Appendix F: File Formats Editing File Format Atom Types . . . . . . . . . . . . . 619 Name . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 619 Description. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 619 File Format Examples . . . . . . . . . . . . . . . . . . . . . . . 619 Alchemy File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 619 FORTRAN Formats . . . . . . . . . . . . . . . . . . . . 620 Cartesian Coordinate Files . . . . . . . . . . . . . . . . . 621 Atom Types in Cartesian Coordinate Files . 621 The Cartesian Coordinate File Format . . . . 621 FORTRAN Formats . . . . . . . . . . . . . . . . . . . . 624 Cambridge Crystal Data Bank Files . . . . . . . . . 624 Internal Coordinates File. . . . . . . . . . . . . . . . . . . 624 Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 626 FORTRAN Formats . . . . . . . . . . . . . . . . . . . . 627 MacroModel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 627 FORTRAN Formats . . . . . . . . . . . . . . . . . . . . 628 MDL MolFile. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 628 Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 631 FORTRAN Formats . . . . . . . . . . . . . . . . . . . . 631 MSI MolFile. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 631 FORTRAN Formats . . . . . . . . . . . . . . . . . . . . 635 MOPAC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 635 FORTRAN Formats . . . . . . . . . . . . . . . . . . . . 637 Protein Data Bank Files . . . . . . . . . . . . . . . . . . . . . 637 FORTRAN Formats . . . . . . . . . . . . . . . . . . . . 638 ROSDAL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 640 SMD. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 640 SYBYL MOL File. . . . . . . . . . . . . . . . . . . . . . . . . 643 FORTRAN Formats . . . . . . . . . . . . . . . . . . . . 645 SYBYL MOL2 File. . . . . . . . . . . . . . . . . . . . . . . . 645 FORTRAN Formats . . . . . . . . . . . . . . . . . . . . 648 Appendix G: Parameter Tables Parameter Table Use . . . . . . . . . . . . . . . . . . . . . . . . 649 Parameter Table Fields . . . . . . . . . . . . . . . . . . . . . . 650 Atom Type Numbers . . . . . . . . . . . . . . . . . . . . . . 650 Quality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 651 Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 651 Estimating Parameters . . . . . . . . . . . . . . . . . . . . . . 651 Creating Parameters . . . . . . . . . . . . . . . . . . . . . . . . 651 The Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 652 Symbol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 652 Covalent Radius . . . . . . . . . . . . . . . . . . . . . . . . . . 652 Color. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 652 Atom Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 652 Name . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 652 Symbol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 652 van der Waals Radius. . . . . . . . . . . . . . . . . . . . . . 653 Text Number (Atom Type) . . . . . . . . . . . . . . . . 653 Charge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 653 Maximum Ring Size. . . . . . . . . . . . . . . . . . . . . . . 653 Rectification Type . . . . . . . . . . . . . . . . . . . . . . . . 653 Geometry. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 654 Number of Double Bonds, Triple Bonds, and Delocalized Bonds . . . . . . . . . . . . . . . . . . . 654 Bound-to Order . . . . . . . . . . . . . . . . . . . . . . . . . . 654 Bound-to Type . . . . . . . . . . . . . . . . . . . . . . . . . . . 654 Substructures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 655 References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 655 Reference Number. . . . . . . . . . . . . . . . . . . . . . . . 655 Reference Description. . . . . . . . . . . . . . . . . . . . . 655 Bond Stretching Parameters . . . . . . . . . . . . . . . . . 655 Bond Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 655 KS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 656 Length . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 656 Bond Dipole . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 656 Record Order . . . . . . . . . . . . . . . . . . . . . . . . . . . . 656 Angle Bending, 4-Membered Ring Angle Bending, 3-Membered Ring Angle Bending . . 656 Angle Type. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 657 KB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 657 –XR2– . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 657 –XRH–. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 657 –XH2– . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 658 Record Order . . . . . . . . . . . . . . . . . . . . . . . . . . . . 658 Pi Atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 658 Atom Type. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 658 Electron . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 658 CambridgeSoft
Ionization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 658 Repulsion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 658 Pi Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 659 Bond Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 659 dForce. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 659 dLength . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 659 Record Order . . . . . . . . . . . . . . . . . . . . . . . . . . . . 659 Electronegativity Adjustments . . . . . . . . . . . . . . . 659 MM2 Constants . . . . . . . . . . . . . . . . . . . . . . . . . . . . 660 Cubic and Quartic Stretch Constants . . . . . . . 660 Type 2 (-CHR-) Bending Force Parameters for C-C-C Angles . . . . . . . . . . . . . . . . . . . . . . . . 660 Stretch-Bend Parameters . . . . . . . . . . . . . . . . . . 661 Sextic Bending Constant . . . . . . . . . . . . . . . . . . 661 Dielectric Constants . . . . . . . . . . . . . . . . . . . . . . 661 Electrostatic and van der Waals Cutoff Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 661 MM2 Atom Types . . . . . . . . . . . . . . . . . . . . . . . . . . 661 Atom type number . . . . . . . . . . . . . . . . . . . . . . . 661 R* . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 662 Eps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 662 Reduct. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 662 Atomic Weight . . . . . . . . . . . . . . . . . . . . . . . . . . . 662 Lone Pairs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 662 Torsional Parameters . . . . . . . . . . . . . . . . . . . . . . . 662 Dihedral Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . 663 V1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 663 V2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 663 V3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 664 Record Order . . . . . . . . . . . . . . . . . . . . . . . . . . . . 665 Out-of-Plane Bending . . . . . . . . . . . . . . . . . . . . . . 665 Bond Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 665 Force Constant . . . . . . . . . . . . . . . . . . . . . . . . . . . 665 Record Order . . . . . . . . . . . . . . . . . . . . . . . . . . . . 665 VDW Interactions . . . . . . . . . . . . . . . . . . . . . . . . . 666 Record Order . . . . . . . . . . . . . . . . . . . . . . . . . . . . 666 Appendix H: Keyboard Modifiers Rotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 667 Zoom and Translate . . . . . . . . . . . . . . . . . . . . . . . 667 Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 668 Standard Selection . . . . . . . . . . . . . . . . . . . . . . 668 Radial Selection . . . . . . . . . . . . . . . . . . . . . . . . . 668 Appendix I: MM2 MM2 Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . 671 Other Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . 671 Viewing Parameters . . . . . . . . . . . . . . . . . . . . . . . . . 671 Editing Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . 672 The MM2 Force Field in Chem3D. . . . . . . . . . . . 672 Chem3D Changes to Allinger’s Force Field . . . . 672 Charge-Dipole Interaction Term. . . . . . . . . . . . 673 Quartic Stretching Term . . . . . . . . . . . . . . . . . . . 673 Electrostatic and van der Waals Cutoff Terms 673 Pi Orbital SCF Computation . . . . . . . . . . . . . . . 673 Appendix J: MOPAC MOPAC Background . . . . . . . . . . . . . . . . . . . . . 675 Potential Functions Parameters. . . . . . . . . . . . . . . 675 Adding Parameters to MOPAC. . . . . . . . . . . . . . . 676 Appendix K: Structural Query Features General Properties . . . . . . . . . . . . . . . . . . . . . . . . . . 677 Atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 677 Bonds. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 677 Substituents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 678 Charges and Radicals . . . . . . . . . . . . . . . . . . . . . . 678 Isotopes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 679 Stereochemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . 679 Relative Tetrahedral Stereochemistry . . . . . . 680 MDL File Formats . . . . . . . . . . . . . . . . . . . . . . 680 Normalization . . . . . . . . . . . . . . . . . . . . . . . . . . . . 681 Atom Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . 681 Special Atom Types . . . . . . . . . . . . . . . . . . . . . . . 681 Atom Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 681 Atom Not-Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . 682 Substituents: Exactly . . . . . . . . . . . . . . . . . . . . . . 682 Substituents: Up To . . . . . . . . . . . . . . . . . . . . . . . 682 Substituents: Free Sites . . . . . . . . . . . . . . . . . . . . 683 Implicit Hydrogens. . . . . . . . . . . . . . . . . . . . . . . . 683 Unsaturation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 683 Bond Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . 684 Special Bond Types. . . . . . . . . . . . . . . . . . . . . . . . 684 Topology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 684 ChemOffice 2005
Page 1: ChemOffice.Com ® ChemOffice ® Che
Page 4 and 5: License Information ChemOffice, Che
Page 6 and 7: · Licensed users of ChemOffice Ent
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Page 10 and 11: Q: IS IT OK TO COPY MY COLLEAGUE’
Page 12 and 13: A Guide to CambridgeSoft Manuals An
Page 14 and 15: Chapter 31: Changes and Audit Trail
Page 16 and 17: Administrator Tutorial 7: Docking M
Page 18 and 19: Administrator Connection Table . .
Page 20 and 21: Administrator Specifying Properties
Page 22 and 23: Administrator Undoing Changes . . .
Page 24 and 25: Administrator Chapter 28: Introduci
Page 26 and 27: Administrator Atom Properties . . .
Page 28 and 29: Administrator Deleting a Field Type
Page 32 and 33: Administrator Reaction Center . . .
Page 34 and 35: Administrator In addition to browsi
Page 36 and 37: Administrator Microsoft®Windows®
Page 38 and 39: Administrator Truncated-Newton-Raph
Page 40 and 41: Administrator the activation each t
Page 42 and 43: Administrator The following table d
Page 44 and 45: Administrator • Stereo Pairs—A
Page 46 and 47: Administrator • Bond Angles—Dis
Page 48 and 49: Administrator The Building Toolbar
Page 50 and 51: Administrator The Calculation Toolb
Page 52 and 53: Administrator 1. Right-click in the
Page 54 and 55: Administrator • In the Model Sett
Page 56 and 57: Administrator modes and color setti
Page 58 and 59: Administrator 26 •Chem3D Basics C
Page 60 and 61: Administrator 2. Click the ChemDraw
Page 62 and 63: 3. Move the pointer over the C-C bo
Page 64 and 65: Administrator Add serial numbers an
Page 66 and 67: Administrator 5. Press the Enter ke
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Page 72 and 73: A molecule of Epinephrine appears.
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Administrator Determine the raw spi
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Administrator atoms are relatively
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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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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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Surface Type Description Surface Ty
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Administrator 2. Adjust the slider
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Administrator Density surface is ca
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Administrator 100•Displaying Mode
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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 124•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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Administrator Intermediate status m
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Administrator staggered form. The m
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Administrator During dragging, the
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If you want to … Then Click … A
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Compute Properties The Compute Prop
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Administrator C(2)-C(3)-C(4) bond a
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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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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 194•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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Administrator To specify the calcul
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Administrator 3. Click Open. The ap
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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 • 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 220•Introduction Ca
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. The components of the ChemFinder
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Administrator Screen Element Table
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Administrator • From the View men
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Administrator A form displays data
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. In this tutorial, you learn to cr
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A selected data box is designated b
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Administrator The database opens, a
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9. Click the Form tab. There should
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to see some of the information avai
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• From the Record menu, choose Fi
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Administrator The Table view appear
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+ The ISICCR database opens in Chem
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Administrator To search over a list
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When you release the mouse button,
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Administrator 250•ChemFinder Tuto
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The Open dialog box appears. To cho
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A data source tree appears, contain
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ChemFinder saves the form with a .c
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The framed data box is labeled. NOT
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Administrator To save a metafile fr
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Administrator • Rich Text—displ
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Administrator Adding a Data Box Men
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Administrator Customizing Numbers U
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Administrator When the selection to
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To line up objects on a form: Admin
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Administrator to those usernames. M
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Administrator • Take the appropri
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To disable security and reset defau
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Administrator • In the new dialog
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To search: Administrator 8. Take th
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Administrator 282•Relational Data
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Administrator The following table s
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1. Click one of the column headers
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Administrator Creating Tables There
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Creating Fields Administrator 4. Fr
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The name of the new field appears i
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Administrator ChemFinder creates a
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Administrator atoms contained in th
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Administrator • If you are editin
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Administrator The record is permane
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Administrator The plot appears in a
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Administrator Context menu options
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Administrator In the bottom diagram
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Administrator 308•Visualizing Dat
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The general procedure for importing
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Administrator Using Log Files Durin
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Administrator d. The input file has
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Administrator Export to SDFile When
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Administrator benz OR *bromo* Benze
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Search Type Administrator Normal Se
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Administrator The hit list will inc
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Administrator as part of the data a
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Administrator • Setting the searc
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If you want to Then click Administr
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Administrator ChemFinder searches o
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Administrator • With Stereo Cente
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Administrator Managing Queries Chem
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To reset searches to the full datab
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Administrator To create the hitlist
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Administrator Using ChemDraw's Atom
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Administrator With reaction centers
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To set the options for what ChemFin
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Administrator To return all the too
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Administrator Creating a Script To
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Administrator rather difficult, but
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Administrator 352•Customizing Che
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Administrator Opening an Oracle Dat
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Administrator • Restore Previous
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Administrator 6. Set other options
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Administrator 360•ChemFinder/Orac
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To activate CombiChem/Excel: The Co
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Administrator Adding a Reaction Tem
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Administrator Reactant List Format
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Administrator • You can configure
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An analysis of the reaction steps a
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Administrator ChemFinder/Office tit
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Administrator For more information
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Administrator The Open Chemical Str
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Administrator 3. From the Molecules
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Administrator To use the Search Opt
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Changing the Chem- Finder/Office Pr
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Administrator • Enhanced table of
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Administrator In addition, this gui
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Administrator To export to MS Word:
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Administrator Type in the AutoText
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Administrator Advanced Text Searchi
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Administrator Managing the Audit Se
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Administrator In the form we are sh
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Administrator Several fields types
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Administrator Example 1 In this exa
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Administrator • Username - An opt
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Administrator from the Property dro
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Administrator • SupplierID - the
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Administrator reactants and product
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Administrator • Certain types of
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Administrator To access the Add-In
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Administrator In the query table fi
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Administrator 546• Managing Field
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Administrator A menu appears with t
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Administrator Adding a Collection L
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Administrator A menu appears. 4. Se
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Administrator contained collection
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Administrator Creating a Search Typ
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Administrator Chemical Structure Se
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Administrator If the user wants to
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Administrator To view the export te
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Administrator To edit this data, 1.
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Administrator 604 • CambridgeSoft
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Page 648 and 649:
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Page 746 and 747:
Administrator Combi experiments 367
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Administrator Creating (continued)
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Administrator Exporting (continued)
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Administrator Search Details prefer
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Administrator xxxviii• CambridgeS
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CAMBRIDGESOFT ChemOffice Desktop to
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Page 784 and 785:
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Page 786 and 787:
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Page 794 and 795:
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Page 796 and 797:
KNOWLEDGE E-Notebook Enterprise Des
Page 798 and 799:
KNOWLEDGE Document Manager Desktop
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KNOWLEDGE 21CFR11 Compliance Electr
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RESEARCH & Registration System Chem
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Page 806 and 807:
RESEARCH & CombiChem Enterprise Des
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Page 810 and 811:
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Page 812 and 813:
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Page 814 and 815:
CHEMICAL The Merck Index Chemistry
Page 816 and 817:
CHEMICAL Chemical Databases Referen
Page 818 and 819:
CONSULTING & Consulting & Services
Page 821:
CS Software Problem Report For fast
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