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Administrator Subforms (continued) using scripts 281 Subforms, tutorial 248 Submitting queries 329 Substituents 459, 678 exactly 460, 682 free sites 461, 683 in queries 678, 682 up to 461, 682 Substructure searching 242, 321 Substructure similarity 690 Substructures 613 Substructures table 34, 655 Substructures, adding to model 59 Summary file see MOPAC out file Summary of the standard add-ins 597 Supported file formats 309 Surface types 92 Surfaces toolbar 17 Surfaces, mapping properties onto 45 SYBYL file format 122 SYBYL MOL File 643 SYBYL MOL2 File 645 FORTRAN format 648 SYBYL MOLFile 643 FORTRAN format 645 SYBYL2 seeSYBYL MOL2 File Symbol 652 Symmetry, MOPAC 210 Synchronization 306 Synchronizing ChemDraw and Chem3D 52 System requirements 4, 7 T Table editor 56 numerical units, working with 437 organizing columns and rows 434 pivoting 435 removing columns and rows 433 resizing columns and rows 435 structures and images, working with 436 Tables 422 adding 281, 300, 351 changing names 351 creating 288 deleting 288 exporting 351 headers 224 importing 351 internal and external 20 Tabs, creating and editing 260 Tabs, renaming 260 Tanimoto similarity 689 Technical support 611 Temporary database 293 Terminate After control 155 Terminology 384 Tetrahedral stereo center hits 328 Text as structures 298 building tool 55 building tool, tutorial example 32 creating 258 customizing 265 fields 290 format toolbar 265, 299 number (atom type) 653 queries 317 searches 239, 317 sorting 295 styled 299 tool, specifying order of attachment 56 Text files, importing 313 Theory tab 196, 201 Thermal Capacity, ChemProp Pro 207 TIF file format 116 Time settings 543 Tinker file formats 122 Title bar 224 Toolbars building 16 calculation 18 customizing 345 description 223 xxxiv• <strong>CambridgeSoft</strong>
Toolbars (continued) form 224 main 224 model display 11, 16 movie 17 record 225 search 225 standard 15 surfaces 17 text 225, 299 Tools data box 256 eraser 54 frame 257 framed box 257 grid 256 layout 256 picture 259 plain text 258 record 285 select 69 select, hotkey 34 Tools palette see Building toolbar Topology 463, 684 Torsion energy 134 Torsion energy, constraints 138 Torsion energy, MM2 209 Torsional parameters table 663 Torsional parameters table, 4-membered ring 663 Torsionals table 650 Torsion-stretch energy, MM2 209 Total charge density 97 Total charge density surface, calculation types required 93 Total charge density surface, definition 97 Total spin calculation types required 93 definition 98 density 98 density surface dialog 98 Trackball tool overview 75 tutorial example 27 Trackball tool (continued) Z-axis rotation 75 Transferring information to ChemDraw 123 to other applications 123 to other computers 293 Transition listeners 597 Transition security 406, 587 Transition state 129 Translate 74, 667 Translate tool 74 Translucent surface type 94 Trigger scripts 349 Triple bonds field 654 Troubleshooting atoms shift on MOPAC input 173 background color 88 Chem3D 612 MOPAC quits 172 Type 2 (-CHR-) bending force parameters for C-C- C angles 660 U UHF 141, 143, 162 UHF spin density 185 UHF spin density, example 192 Uncoordinated bonds, creating 54 Understanding forms and databases 228 Undo 269 Undoing changes 299 Undoing data entry 295 Uniform bond length 342 Union with current list 337 Unix, Gaussian files 99 Unsaturation 462, 683 Unsaturation, in queries 683 Use Current Z-Matrix button 119 Use tight convergence criteria 196, 202 User administration 581 User collection adding a new collection to 391 adding a reference within 391 working with 390 Chem3D <strong>ChemOffice</strong> 2005- Index • xxxv
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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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Chapter 31: Changes and Audit Trail
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Administrator Tutorial 7: Docking M
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Administrator Connection Table . .
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Administrator Specifying Properties
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Administrator Undoing Changes . . .
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Administrator Chapter 28: Introduci
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Administrator Atom Properties . . .
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Administrator Deleting a Field Type
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Administrator Example 2. . . . . .
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Administrator Reaction Center . . .
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Administrator In addition to browsi
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Administrator Microsoft®Windows®
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Administrator Truncated-Newton-Raph
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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 26 •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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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 388• Introducing E-
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Administrator You can organize coll
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Creating a Page or Experiment Admin
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Administrator Working with the User
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Administrator Showing and Hiding Co
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Administrator • Right-click any b
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Administrator If your system config
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Administrator Your system configura
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Administrator Working with Template
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Administrator Desired Result Change
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Administrator To export to MS Word:
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Administrator 410• E-Notebook Use
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Administrator NO 2 NO 2 Me Me HC(OE
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Administrator • Top of Arrow as R
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Administrator • Equivalents - the
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The example below shows the Prepara
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Administrator Ethanol was selected,
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Administrator Type in the AutoText
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Adding Properties to Property Lists
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Type of Measurement Permitted Units
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3. Enter the URL and click OK. Work
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Administrator A new Ancillary Data
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Administrator Replacing a Spectrum
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The row is removed from the Table.
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Administrator you enter an invalid
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Administrator Type of Measurement m
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Administrator 4. The spreadsheet ap
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5. Click the section menu icon. The
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Administrator Printing Sections You
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Administrator Clicking the Changes
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. Administrator The version of the
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Administrator In some configuration
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Administrator 452• Changes and Au
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Administrator 2. If no form appears
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Administrator Query Text Field The
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Administrator • In searching subs
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Administrator Isotopes Isotopic lab
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Finds: Cl Does not find: Finds: O D
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Administrator either side) is part
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Administrator • Browse to the roo
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Administrator 2. Select Remove Prop
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Administrator Advanced Text Searchi
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For example, the following searches
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Administrator Searching For ... Ret
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3. Click the Search In... checkbox
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Administrator The Collection Tree a
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2. Select Session Manager.... The S
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Administrator A new section type ap
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Administrator See the following top
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Administrator 3. If necessary, clic
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compute the checksum for the upload
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Administrator 4. A new Section List
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Administrator Managing the Audit Se
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Administrator The field appears in
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A menu appears. 2. Select Box Prope
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Showing the Name of a Box To show t
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Administrator contained box accordi
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Administrator In the form we are sh
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Administrator For example, if there
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Administrator 506• Managing Secti
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Administrator Several fields types
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Administrator • Default Font - yo
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The Section Type Configuration dial
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Administrator Example 1 In this exa
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Administrator See the following top
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Administrator Associating a list of
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Administrator • Username - An opt
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Administrator To add a property lis
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Administrator from the Property dro
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Administrator The Field Properties
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Administrator Another feature of ta
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Administrator 3. Right-click the Ta
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Administrator • SupplierID - the
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Administrator reactants and product
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Managing Search Fields Administrato
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Administrator • Certain types of
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4. Enter a name for the field and s
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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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Creating a New Collection Type The
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Administrator 5. Click the Add>> bu
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Administrator A menu appears with t
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Administrator 2. To expand the coll
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Administrator Adding a Collection L
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Administrator A menu appears. 4. Se
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Administrator the Rename command in
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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 To add states to a co
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• Removing a Transition Listener
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Administrator • Unlocked Contents
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Administrator If the user wants to
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A new Transition Listener appears,
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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 Setting the Region fo
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Administrator 584• User Administr
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Administrator 2. If Inherits Securi
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To change the Transition Security P
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Administrator The Security tab appe
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Administrator To disable inherited
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Administrator Desired Result Remove
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Administrator 596• Managing E-Not
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Administrator Section Listeners E-N
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Administrator • Add Reactant tabl
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Administrator have an OK button onl
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Administrator 604 • CambridgeSoft
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Administrator Accessing the Online
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Administrator To find a structure t
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Administrator The CS ChemOffice SDK
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Administrator Troubleshooting This
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Administrator Defining Substructure
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Administrator If an atom can be ass
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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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Key Drag Shift+Drag Administrator Q
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Administrator 670• Keyboard Modif
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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 Bond Type Wavy specif
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Administrator HO HO HO N H H N N H
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Administrator Atom lists may contai
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O O Bond Type Description Administr
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Administrator 686• Structural Que
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Formula Chemfinder Interpretation A
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Page 728 and 729: Administrator GET retrieves a value
Page 730 and 731: Administrator You may concatenate v
Page 732 and 733: Administrator Script-Only Commands
Page 734 and 735: Administrator 702• CAL Commands C
Page 736 and 737: Administrator open a large table an
Page 738 and 739: Administrator 706• CS Oracle Cart
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Page 742 and 743: Administrator Atom-to-Atom mapping
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Page 746 and 747: Administrator Combi experiments 367
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Page 752 and 753: Administrator Exporting (continued)
Page 754 and 755: Administrator Frame interval contro
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Page 760 and 761: Administrator Mol_ID field 287 Mola
Page 762 and 763: Administrator Opening (continued) p
Page 764 and 765: Administrator Property query and ta
Page 766 and 767: Administrator Redo command 269, 299
Page 768 and 769: Administrator Search Details prefer
Page 770 and 771: Administrator Sextic bending consta
Page 774 and 775: Administrator User interface 9 User
Page 776 and 777: Administrator xxxviii• CambridgeS
Page 778 and 779: CAMBRIDGESOFT ChemOffice Desktop to
Page 780 and 781: CS ChemOffice Software Suites ChemO
Page 782 and 783: DESKTOP CS E-Notebook Electronic Jo
Page 784 and 785: DESKTOP CS ChemDraw Chemical Struct
Page 786 and 787: DESKTOP CS Chem3D Molecular Modelin
Page 788 and 789: DESKTOP CS ChemFinder Searching and
Page 790 and 791: DESKTOP CS ChemInfo Reference and C
Page 792 and 793: ENTERPRISE ChemOffice WebServer Ent
Page 794 and 795: ENTERPRISE Oracle Cartridge Enterpr
Page 796 and 797: KNOWLEDGE E-Notebook Enterprise Des
Page 798 and 799: KNOWLEDGE Document Manager Desktop
Page 800 and 801: KNOWLEDGE 21CFR11 Compliance Electr
Page 802 and 803: RESEARCH & Registration System Chem
Page 804 and 805: RESEARCH & Inventory Manager Chemic
Page 806 and 807: RESEARCH & CombiChem Enterprise Des
Page 808 and 809: RESEARCH & BioAssay HTS Biological
Page 810 and 811: RESEARCH & BioSAR Browser Biologica
Page 812 and 813: CHEMICAL ChemACX Database Available
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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