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Administrator 3. Type the information for the new parameter. 4. Close and Save the file. The new parameter is added to the file. NOTE: Do not include duplicate parameters. If duplicate parameters exist in a parameter table it is indeterminate which parameter will be used when called for in a calculation. NOTE: If you do want to make changes to any of the parameters used in Chem3D, we strongly recommend that you make a back up copy of the original parameter table and remove it from the C3DTABLE directory. Color The colors of elements are used when the Color by Element check box is selected in the control panel. To change the color of an element: • Double-click the current color. The Color Picker dialog box appears in which you can specify a new color for the element. Atom Types The Atom Types table Atom Types.xml) contains the atom types for use in building your models. The Elements The Elements table (Elements.xml) contains the elements for use in building your models. To use an element in a model, type its symbol in the Replacement text box (or paste it, after copying the cell in the “Symbol” field to the Clipboard) and press the Enter key when an atom is selected, or double-click an atom. If no atom is selected, a fragment is added. Four fields comprise a record in the Elements table: the symbol, the covalent radius, the color, and the atomic number. Symbol Normally you use only the first column of the Elements table while building models. If you are not currently editing a text cell, you can quickly move from one element to another by typing the first letter or letters of the element symbol. Covalent Radius The covalent radius is used to approximate bond lengths between atoms. Normally you use only the first column of the Atom Types table while building models. To use an atom type in a model, type its name in the Replacement text box (or paste it, after copying the name cell to the Clipboard) and press the Enter key when an atom is selected, or when you double-click an atom. If no atom is selected, a fragment is added. Twelve fields comprise an atom type record: name, symbol, van der Waals radius, text number, charge, the maximum ring size, rectification type, geometry, number of double bonds, number of triple bonds, number of delocalized bonds, bound-to order and bound-to type. Name The records in the Atom Types table are ordered alphabetically by atom type name. Atom type names must be unique. Symbol This field contains the element symbol associated with the atom type. The symbol links the Atom Type table and the Elements table. The element symbol is used in atom labels and when you save files in file formats that do not support atom types, such as MDL MolFile. 652• Parameter Tables <strong>CambridgeSoft</strong> The Elements
van der Waals Radius The van der Waals (VDW) radius is used to specify the size of atom balls and dot surfaces when displaying the Ball & Stick, Cylindrical Bonds or Space Filling models. The Close Contacts command in the Measurements submenu of the Structure menu determines close contacts by comparing the distance between pairs of non-bonded atoms to the sum of their van der Waals radii. The van der Waals radii specified in the Atom Types table do not affect the results of an MM2 computation. The radii used in MM2 computations are specified in the MM2 Atom Types table. NOTE: The space filling model display is set in the Model Display tab of the Model Settings dialog box. The appearance of VDW dot surfaces is specified for the entire model in the Atom Display tab of the Model Settings dialog box, or for individual atoms using the Right-click Atom Dots submenu in the Model Explorer. Text Number (Atom Type) Text numbers are used to determine which measurements apply to a given group of atoms in other parameter tables. For example, C Alkane has an atom type number of 1and O Alcohol has an atom type number of 6. To determine the standard bond length of a bond between a C Alkane atom and an O Alcohol atom , you should look at the 1-6 record in the Bond Stretching table. Charge The charge of an atom type is used when assigning atom types to atoms in a model. When the information about an atom is displayed, the atom symbol is always followed by the charge. Charges can be fractional. For example, the charge of a carbon atom in a cyclopentadienyl ring should be 0.200. Maximum Ring Size The maximum ring size field indicates whether the corresponding atom type should be restricted to atoms found in rings of a certain size. If this cell is zero or empty, then this atom type is not restricted. For example, the maximum ring size of C Cyclopropane is 3. Rectification Type Possible rectification types are: • D • H • H Alcohol • H Amide • H Amine • H Ammonium • H Carboxyl • H Enol • H Guanidine • H Thiol NOTE: When you specify a rectification type, the bound-to type of the rectification type should not conflict with the atom type. If there is no rectification type for an atom, it is never rectified. For example, if the rectification type of O Carboxyl is H Carboxyl, the bound-to type of H Carboxyl should be either O Carboxyl or empty. Otherwise, when assigning atom types, hydrogen atoms bound to O Carboxyl atoms are not assigned H Carboxyl. Appendices <strong>ChemOffice</strong> 2005/Appendix Parameter Tables • 653 Atom Types
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A Guide to CambridgeSoft Manuals An
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Administrator Tutorial 7: Docking M
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KNOWLEDGE E-Notebook Enterprise Des
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KNOWLEDGE 21CFR11 Compliance Electr
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