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Refine Loops - Constraints Panel |
In this panel, you can set up various kinds of constraints when performing loop refinements: constraints on distances, restraints of atoms to initial positions, restraints of C-alpha atoms to specified positions, constraints of parts of the loop to helical conformation, and constraints on the loop to lie inside or outside an implicit membrane.
To open the Refine Loops - Constraints panel, you can:
Click Constraints in the Refine Loops 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.
In this tab you can constrain part of a loop to helical conformation.
Select this option to constrain a subset of the loop residues to helical conformation during loop prediction.
Specify the residues in which the helix starts and ends in these text boxes. If you do not leave enough residues outside the helical region, the loop prediction might not produce good conformations, because it is too constrained.
In this tab you can define spatial (distance) constraints for Cα atoms in the loop when doing a loop prediction. The constraints are specified in terms of a position and a distance: the Cα atoms are constrained to remain within the given distance of the specified point in space.
Select this option to move the selected constraint in the Workspace. You can either pick the sphere in the Workspace or select the table row. The sphere can be moved by right-clicking and dragging. This action moves the sphere in the current plane (of the screen). You can use the middle mouse button to rotate the structure so that you can move the sphere in another plane.
This table lists the residues in the loop, and allows you to select the residues to constrain and the parameters of the constraint. The initial coordinates in the table are the current positions of the Cα atoms. The table has the following columns:
In this tab you can constrain loop conformations so that the Cα atoms of the loop are inside the membrane or outside the membrane when the loops are built. The tab has three options:
The constraints are applied to the Cα atoms only: other atoms of the residues are not restricted. Side chains can cross the boundary, for example. The constraints are applied only in the building stage, and subsequent minimization can move the residues across the membrane boundary.
There is no requirement that the implicit membrane model, with the adjusted dielectric constant, is actually used in the loop refinement. You can use the membrane to define a spatial exclusion zone, and then the constraints are just spatial constraints.
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