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Administrator FORTRAN Formats The FORTRAN format for the records in a Cartesian coordinate file with a connection table by serial number or position and a Cartesian coordinate file with fractional crystal cell parameters are listed in the following tables: Cartesian coordinate File (Connection Table by Serial Number or Position): Line Number Description 1 Number of Atoms FORTRAN Format I3 specifications of the Cambridge Structural Database, Version 1 File Specifications from the Cambridge Crystallographic Data Centre. For further details about the FDAT format, please refer to the above publication or contact the Cambridge Crystallographic Data Centre. As described in the specifications of the Cambridge Crystal Data Bank format, bonds are automatically added between pairs of atoms whose distance is less than that of the sum of the covalent radii of the two atoms. The bond orders are guessed based on the ratio of the actual distance to the sum of the covalent radii. The bond orders, bond angles, and the atom symbols are used to determine the atom types of the atoms in the model. 2 to End Atom coordinates A3, 1X, I4, 3(1X, F11.6), 1X, I4, 10(1X, I4) Bond Type Actual Distance / Sum of Covalent Radii Cartesian coordinate File (Fractional Crystal Cell Parameters): Line Number Description 1 Number of Atoms, Crystal Cell Parameters 2 to End Atom coordinates FORTRAN Format I3, 6(1X, F), I A3, 1X, I4, 3(1X, F11.6), 1X, I4, 10(1X,I4) Cambridge Crystal Data Bank Files The specific format of Cambridge Crystal Data Bank files (CCDB) used by Chem3D is the FDAT format, described on pages 26–42 of the data file Triple 0.81 Double 0.87 Delocalized 0.93 Single 1.00 Internal Coordinates File Internal coordinates files (INT Coords) are text files that describe a single molecule by the internal coordinates used to position each atom. The serial numbers are determined by the order of the atoms in the file. The first atom has a serial number of 1, the second is number 2, etc. 624• File Formats <strong>CambridgeSoft</strong> File Format Examples
The format for Internal coordinates files is as follows: 1. Line 1 is a comment line ignored by Chem3D. Each subsequent line begins with the atom type number of an atom type. 2. Line 2 contains the atom type number of the Origin atom. 3. Beginning with line 3, the atom type number is followed by the serial number of the atom to which the new atom is bonded and the distance to that atom. In an Internal coordinates file, the origin atom is always the first distance-defining atom in the file. All distances are measured in Angstroms. 4. Beginning with line 4, the distance is followed by the serial number of the first angle-defining atom and the angle between the newly defined atom, the distance-defining atom, and the first angle-defining atom. All angles are measured in degrees. 5. Beginning with line 5, the serial number of a second angle-defining atom and a second defining angle follows the first angle. Finally, a number is given that indicates the type of the second angle. If the second angle type is zero, the second angle is a dihedral angle: New Atom – Distance-defining Atom – First Angledefining Atom – Second Angle-defining Atom. Otherwise the third angle is a bond angle: New Atom – Distance-defining Atom – Second Angle-defining Atom. If the second angle type is 1, then the new atom is defined using a Pro-R/Pro-S relationship to the three defining atoms; if the second angle type is -1, the relationship is Pro-S. NOTE: You cannot position an atom in terms of a later-positioned atom. The following is a sample of an Internal coordinates output file for cyclohexanol which was created from within Chem3D: 1 1 1 1.54146 1 2 1.53525 1 111.7729 1 1 1.53967 2 109.7132 3 -55.6959 0 1 4 1.53592 1 111.703 2 55.3112 0 1 3 1.53415 2 110.7535 1 57.0318 0 6 1 1.40195 2 107.6989 3 -172.6532 0 5 1 1.11742 2 109.39 4 109.39 -1 5 2 1.11629 1 109.41 3 109.41 1 5 2 1.11568 1 109.41 3 109.41 -1 5 3 1.11664 2 109.41 6 109.41 -1 5 3 1.11606 2 109.41 6 109.41 1 5 4 1.11542 1 109.41 5 109.41 1 5 4 1.11493 1 109.41 5 109.41 -1 5 5 1.11664 4 109.41 6 109.41 1 5 5 1.11617 4 109.41 6 109.41 -1 5 6 1.11664 3 109.41 5 109.41 1 Appendices <strong>ChemOffice</strong> 2005/Appendix File Formats • 625 File Format Examples
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License Information ChemOffice, Che
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· Licensed users of ChemOffice Ent
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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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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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Page 610 and 611: Administrator To view the export te
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Page 614 and 615: Administrator Setting the Region fo
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Page 654 and 655: Administrator Connection tables by
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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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Administrator For the two compounds
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Administrator You do not need to sp
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Administrator boxes it contains. Th
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Administrator GET retrieves a value
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Administrator You may concatenate v
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Administrator Script-Only Commands
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Administrator 702• CAL Commands C
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Administrator open a large table an
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Administrator 706• CS Oracle Cart
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Administrator Access (continued) re
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Administrator Atom-to-Atom mapping
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Administrator Changing (continued)
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Administrator Combi experiments 367
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Administrator Creating (continued)
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Administrator Dihedral type field 6
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Administrator Exporting (continued)
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Administrator Frame interval contro
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Administrator Importing (continued)
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Administrator Managing (continued)
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Administrator Mol_ID field 287 Mola
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Administrator Opening (continued) p
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Administrator Property query and ta
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Administrator Redo command 269, 299
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Administrator Search Details prefer
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Administrator Sextic bending consta
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Administrator Subforms (continued)
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Administrator User interface 9 User
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Administrator xxxviii• CambridgeS
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CAMBRIDGESOFT ChemOffice Desktop to
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CS ChemOffice Software Suites ChemO
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DESKTOP CS E-Notebook Electronic Jo
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DESKTOP CS ChemDraw Chemical Struct
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DESKTOP CS Chem3D Molecular Modelin
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DESKTOP CS ChemFinder Searching and
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DESKTOP CS ChemInfo Reference and C
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ENTERPRISE ChemOffice WebServer Ent
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ENTERPRISE Oracle Cartridge Enterpr
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KNOWLEDGE E-Notebook Enterprise Des
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KNOWLEDGE Document Manager Desktop
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KNOWLEDGE 21CFR11 Compliance Electr
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RESEARCH & Registration System Chem
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RESEARCH & Inventory Manager Chemic
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RESEARCH & CombiChem Enterprise Des
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RESEARCH & BioAssay HTS Biological
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RESEARCH & BioSAR Browser Biologica
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CHEMICAL ChemACX Database Available
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CHEMICAL The Merck Index Chemistry
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CHEMICAL Chemical Databases Referen
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CONSULTING & Consulting & Services
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CS Software Problem Report For fast
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