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Administrator Sextic bending constant 661 Shift+selecting 70 Show Internal Coordinates command 79 Show Surface button 93 Show Used Parameters command 158, 160, 651 Showing all atoms 73 and hiding collections 396 and hiding the max button for a box 496 and hiding the name of a box 497 annotations 342 atoms or groups 72 data boxes 265 Hs and Lps 73 max button 496 name of a box 498 opening dialog 344 reaction centers 341 serial numbers 66 used parameters 160 Similarity rules 689 Similarity searching 321 Similarity searching, see also Exact searching, Normal searching see also 321 Single point calculations, definition 126 Single point calculations, MOPAC 180 Single Point energy calculations 129 SM2 seeSYBYL MOL2 File SMD 640 SMD files 309, 640 Solid spheres, size by control 85 Solid spheres, size% 86 Solid surface type 94 Solubility, ChemProp Pro 208 Solution effects 184 Solvent accessible surface calculation types required 93 definition 97 map property 97 mapping atom colors 97 mapping group colors 97 mapping hydrophobicity 97 Solvent accessible surface (continued) solvent radius 96 Sorting 304 data 295 data by a property 434 data tables 296 fields 296 formulas 295 from the data table 296 in reverse order 296 languages other than English 296 permanently 351 properties 211 structures 295 text 295 Space filling display 84 Special atom types 460 Special atom types, list of 681 Special bond types 462, 684 Special structure searches 331 Specification of units 545 Specifying annotations through the history pane 449 electronic configuration 168 general settings 203 print options 113 properties to compute 202 Spectra, replacing 432 Speed control 112 Spelling check 429 Spin about selected axis 111 Spin density 185 Spin density, tutorial example 45 Spin functions 141 Spinning models 111 SQL 325 SQL searches 325 Standard field types 504 Standard Gibbs free energy, ChemProp Pro 207 Standard measurement 649 Standard measurements bond angle 25 bond length 25 xxxii• <strong>CambridgeSoft</strong>
Standard measurements, applying 23 Standard measurements, bond angle 657 Standard measurements, bond length 655 Standard Molecular Data file format 122 Start menu login 386 Starting ChemFinder 226 Stationary point 129 Status bar 223, 225 Step Interval control 155 Stereo pairs 89 Stereochemistr , inversion 66 Stereochemistry 322, 679 allenic 679 changing 66 cis/trans double bonds 679 octahedral 679 overview 322 queries 679 relative tetrahedral 329, 680 search preferences 328 square planar 679 stereochemical relationships 617 tetrahedral 679 trigonal bipyrimidal 679 Steric energy computing 158 equations 132 parameters 158 terms 158 tutorial example 37 Sticks display 84 STN Express 122 Stopping minimization 149 molecular dynamics 157 queries 329 Stretch-bend cross terms 138 Stretch-bend energy, MM2 209 Stretch-bend parameters 661 Structural query features 677 Structure columns 292 Structure (continued) deleting 436 display preferences 341 displays, changing 83 displays, overview 83 drawing 412 editing 436 registration options 343 searches 320 Structure field 287 Structure menu 13 Structure-activity relationships 205 Structures adding 294 adding to non-chemical database 293 as pictures 298 checking chemistry 298 chemically-significant text 298 cleaning 297 editing 297 entering 297, 343 file formats 309 importing 309 queries 320 query properties 677 red highlighting in queries 330 scaling 342 sorting 295 viewing related 368 Style, box, changing 262 Style, definition 302 Styled text 299 Subform fields, exporting 316 Subforms changes in ChemFinder 9 277 creating 278 data table 280 description 223 linking fields 277 overview 277 searching 280 switching between forms and data tables 280 tutorial 248 Chem3D <strong>ChemOffice</strong> 2005- Index •xxxiii
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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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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 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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Page 722 and 723: Administrator For the two compounds
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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
Page 740 and 741: Administrator Access (continued) re
Page 742 and 743: Administrator Atom-to-Atom mapping
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Page 746 and 747: Administrator Combi experiments 367
Page 748 and 749: Administrator Creating (continued)
Page 750 and 751: Administrator Dihedral type field 6
Page 752 and 753: Administrator Exporting (continued)
Page 754 and 755: Administrator Frame interval contro
Page 756 and 757: Administrator Importing (continued)
Page 758 and 759: Administrator Managing (continued)
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 772 and 773: Administrator Subforms (continued)
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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