Chem3D Users Manual - CambridgeSoft

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Administrator If you want to display … information relative to other selected atoms, such as the distance between two atoms, the angle formed by three atoms, or the dihedral angle formed by four atoms. Then Select… measurement formed by all the selected atoms appears. Measurements • Select two non-bonded atoms and point to one of them. The interatomic non-bonded distance appears in the last line of the pop-up window. For example, in the cyclohexane model below, when you select two non-bonded atoms and point to one of them, the interatomic non-bonded distance appears in the last line of the pop-up window. the distance between the atoms attached by a bond in angstroms the bond orders calculated by Minimize Energy, Steric Energy, or Molecular Dynamics the partial charge according to the currently selected calculation Bond Length. Bond Order. Bond orders are usually 1.000, 1.500, 2.000, or 3.000 depending on whether the bond is a single, delocalized, double, or triple bond. Computed bond orders can be fractional. Partial Charge. See “Displaying Molecular Surfaces” on page 64 for information on how to select a calculation. Non-Bonded Distances To display non-bonded atoms measurements: Measurement Table Another way to view information about your model is to activate the Measurement Table. This table can display internal measurements between atoms in your model in various ways. To display internal measurements: 1. From the View menu, click Measurement Table. A blank table appears in the Tables window. 2. From the Structure menu, point to Measurements and select a measurement to display. The measurement values appear in the table. 106•Inspecting Models CambridgeSoft Measurement Table
You can display several measurements sequentially in the table. The following table shows the bond lengths and angles for Ethene. When the Measurements table is not visible, the standard measurements are taken from the parameter tables. To specify optimal values for particular measurements, edit the value in the Optimal column. bond lengths bond angles { { Chem3D also uses the optimal values with the Dock command. When you choose Dock from the Structure menu, Chem3D reconciles the actual distance between atoms in two fragments to their optimal distances by rigidly moving one fragment relative to the other. Non-Bonded Distances in Tables Editing Measurements If you select a measurement in the Measurements table, the corresponding atoms are selected in the model window. If you select atoms in your model, any corresponding measurements are selected. To change the value of a measurement: 1. Select the text in the Actual column. 2. Type a new measurement value in the selected cell. 3. Press the Enter key The model reflects the new measurement. When atoms are deleted, any measurements that refer to them are removed from the Measurements table. Optimal Measurements Optimal values are used instead of the corresponding standard measurements when a measurement is required in an operation such as Clean Up Structure. Optimal measurements are only used when the Measurements table is visible. To display non-bonded atom measurements: 1. Select the atoms. 2. From the Structure menu, point to Measurements and choose Set Distance Measurement. The measurement between the selected atoms is added to the table. non-bonded distance Showing the Deviation from Plane The Deviation from Plane command allows you to compute the RMS Deviation from the least squares plane fitted to the selected atoms in the model. ChemOffice 2005/Chem3D Inspecting Models • 107 Measurement Table
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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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A Guide to CambridgeSoft Manuals An
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Administrator Setting Molecular Sur
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Administrator Methods Available in
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Administrator Defining Atom Types.
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Administrator Tutorial 7: Docking M
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Parameter Table Use Parameter Table
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Administrator Geometry The geometry
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Administrator R* The R* field is th
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Administrator repeating jobs 178 RH
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Administrator Rectification, when d
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Desktop Software Enterprise Solutio
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SOLUTIONS Enterprise Solutions APPL
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Desktop to Enterprise Solutions Che
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SOFTWARE E-Notebook Ultra Ultimate
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SOFTWARE ChemDraw Ultra Ultimate Dr
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SOFTWARE Chem3D Ultra Ultimate Mode
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SOFTWARE ChemFinder/Word • Search
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SOFTWARE The Merck Index • Encycl
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SOLUTIONS •Development and deploy
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SOLUTIONS •Adds chemical data typ
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MANAGEMENT •Custom organization o
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MANAGEMENT • Indexes chemical str
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MANAGEMENT • E-Notebook Enterpris
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DISCOVERY • Accessed through your
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DISCOVERY • Integrated with Regis
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DISCOVERY • Reagent lists can be
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DISCOVERY •Effectively manages da
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DISCOVERY • Catalog driven data m
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DATABASES • Fully structure-searc
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DATABASES • Encyclopedic referenc
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DATABASES • Extensive collection
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SERVICES · Business Case Developme
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CS ChemOffice ® Desktop to Enterpr
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Chem3D Users Manual - CambridgeSoft

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