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Predict Side Chains - Constraints Dialog Box |
In this dialog box, you can set up constraints on distances and restraints of atoms to initial positions when performing side-chain predictions.
To open the Predict Side Chains - Constraints dialog box, you can:
Click Constraints in the Predict Side Chains panel.
In this tab you can constrain the distance between pairs of atoms. Normally, these constraints are made between nonbonded atoms, but you can pick bonded atoms as well.
Use these picking tools to pick pairs of atoms for which a distance constraint will be applied. When you pick the second atom, a row is added to the constraints table, with the atom-atom distance and a default force constant for the constraint.
This table lists the constraints. It has four columns, which are described below. You can select a single row in the table.
| Atom1 | Index of first atom in constraint. Noneditable. |
| Atom2 | Index of second atom in constraint. Noneditable. |
| Distance | Distance to which atoms are constrained. The initial value is the distance between the atoms in the Workspace structure. You can change the distance by editing the table cell. |
| Force Constant | Coefficient of the harmonic constraint potential (actually half the force constant), in kcal mol-1 Å-2. You can change the value by editing the table cell. The default is 350; if you clear the table cell it is reset to 350. |
Delete the constraint that is selected in the table by clicking Delete; delete all constraints by clicking Delete All.
In this tab you can restrain atoms to within a given distance of their initial coordinates with a flat-bottomed potential.
Use these picking tools to pick atoms for which a flat-bottomed harmonic restraint will be applied.
Coefficient of the harmonic constraint potential (actually half the force constant), in kcal mol-1 Å-2. The default is 10.
Radius of the flat-bottomed part of the restraining potential. This is the distance that any atom can move freely from its initial position before it experiences the restraining potential.
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