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Administrator Clean Up Structure or MM2 computation alters these values. To use values you set in these computations, you must apply a constraint. Setting Bond Lengths To set the length of a bond between two bonded atoms: 1. Select two adjacent atoms. 2. From the Structure menu, point to Measurement and choose Set Bond Length Measurement. The Measurements table appears, displaying distance between the two atoms. The Actual value is highlighted. 3. Edit the highlighted text. 4. Press the Enter key. Setting Bond Angles To set a bond angle: 1. Select three contiguous atoms for a bond angle. 2. From the Structure menu, point to Measurement and choose Set Bond Angle Measurement. The Measurements table appears, displaying the angle value. The Actual value is highlighted. 3. Edit the highlighted text. 4. Press the Enter key. Setting Dihedral Angles To set a dihedral angle: 1. Select four contiguous atoms. 2. From the Structure menu, point to Measurement and choose Set Dihedral Measurement. The Measurements table appears, displaying the angle value. The Actual value is highlighted. 3. Edit the highlighted text. 4. Press the Enter key. Setting Non-Bonded Distances (Atom Pairs) To set the distance between two non-bonded atoms (an atom pair): 1. Select two unbonded atoms. 2. From the Structure menu, point to Measurement and choose Set Distance Measurement. The Measurements table appears, displaying the distance. The Actual value is highlighted. 3. Edit the highlighted text. 4. Press the Enter key. Atom Movement When Setting Measurements When you change the value of a measurement, the last atom selected moves. Chem3D determines which other atoms in the same fragment also move by repositioning the atoms that are attached to the moving atom and excluding the atoms that are attached to the other selected atoms. If all of the atoms in a measurement are within a ring, the set of moving atoms is generated as follows: • Only one selected end atom that describes the measurement moves while other atoms describing the measurement remain in the same position. • If you are setting a bond length or the distance between two atoms, all atoms bonded to the non-moving selected atom do not move. This set of non-moving atoms is extended through all bonds. From among the remaining atoms, any atoms which are bonded to the moving atom move; this set of moving atoms is also extended through all bonds. 64 •Building and Editing Models <strong>CambridgeSoft</strong> Setting Measurements
• If the Automatically Rectify check box in the Building control panel is selected, rectification atoms that are positioned relative to an atom that moves may also be repositioned. For example, consider the following structure: • Enter a new value for the constraint in the Optimal field of the Measurements table. In the case of dihedral angles and non-bonded distances, a constraint will have the effect of keeping that measurement constant (or nearly so) while the remainder of the model is changed by the computation. The constraint doesn’t remove the atoms from a computation. Setting Charges Atoms are assigned a formal charge based on the atom type parameter for that atom and its bonding. You can display the charge by pointing to the atom. To set the formal charge of an atom: If you set the bond angle C(1)-C(2)-C(3) to 108 degrees, C(3) becomes the end moving atom. C(1) and C(2) remain stationary. H(11) and H(12) move because they are not part of the ring but are bonded to the moving atom. If the Automatically Rectify check box is selected, H(10) may move because it is a rectification atom and is positioned relative to C(3). Setting Constraints You can override the standard measurements which Chem3D uses to position atoms by setting constraints. Constraints can be used to set an optimal value for a particular bond length, bond angle, dihedral angle, or non-bonded distance, which is then applied instead of the standard measurement when you use Clean Up Structure or perform a Docking, Overlay, or MM2 computation. To set constraints: 1. Click the Text tool. 2. Select the atom or atoms to change. 3. Type + or - followed by the number of the formal charge. 4. Press the Enter key. To set the formal charge of an atom in a molecular fragment as you build you can add the charge after the element in the text as you build. To add the charge: 1. Type PhO- into a text box with no atoms selected. 2. Press the Enter key. The phenoxide ion molecule appears. To remove the formal charge from an atom: 1. Click the Text tool. 2. Select the atom or atoms whose formal charge you want to remove. 3. Type +0. 4. Press the Enter key. <strong>ChemOffice</strong> 2005/Chem3D Building and Editing Models • 65 Setting Charges
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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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