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Adjust Panel |
The Adjust panel allows the adjustments of dihedral angles, bond angles, atom distances, and inversion at all or selected chiral centers.
To open the Adjust panel, you can:
Choose Edit → Adjust → Distance in the main window.
Choose Edit → Adjust → Angle in the main window.
Choose Edit → Adjust → Dihedral in the main window.
Choose Edit → Adjust → Chirality in the main window.
To adjust a distance, angle or dihedral, follow the steps below. Chirality behaves differently, see Chirality.
To make an adjustment:
Note: You can use the middle and right mouse buttons to rotate and translate the molecule (global transformation) while doing adjustments.
If you are adjusting a dihedral of a protein, you can click Dihedral and choose the dihedral from a list.
To define a geometric parameter to adjust, choose Atoms or Bonds from the Pick menu (see Picking Controls). Then, depending on what you wish to adjust, select the appropriate number of items:
The order in which atoms are selected determines how the adjustment is made. The atom that was picked last is the atom that is moved in the adjustment, and is called the moving atom. The controls in the Move section determine whether only the moving atom is moved, or whether atoms attached to it are moved as well.
When a parameter is defined, it is marked in the Workspace and an entry is created in the table in the Adjust panel.
The marker includes four parts and are color-coded by the type of parameter being adjusted:
| Distance | Angle | Dihedral | |
| Solid lines through atoms | green | red | |
| Dashed lines representing adjustment | purple | green | red |
| An arrow indicating direction | yellow | orange | turquoise |
| Highlight lines for the currently selected parameter | yellow | orange | turquoise |
Once a parameter has been defined, you can adjust it in three ways:
The Adjust panel has four tabs. Three of these, Angle, Distance, and Dihedral, have identical structure. The fourth tab, Chirality, is different. The following sections describe the features of each of the three similar tabs, followed by a description of the Chirality tab.
The three picking controls, Define Atoms For Distance Adjustment, Define Atoms For Angle Adjustment, and Define Atoms For Dihedral Adjustment, are used to define distances (two atoms), angles (three atoms), and dihedrals (four atoms) to be adjusted.
You can choose Atoms or Bonds from the Pick option menu. If you choose Atoms, you must pick two atoms for a distance adjustment, three for an angle adjustment, and four for a dihedral adjustment. The last atom picked is the moving atom. If you choose Bonds, you must pick one bond for a distance adjustment, two for an angle adjustment, and one for a dihedral adjustment. The bond for dihedral adjustment is the bond between the second and third atoms. Maestro chooses the remaining two atoms. The direction of the arrow for adjustment is determined by where you click on the bond, for both dihedral and angle adjustments. The moving atom is the atom closest to where you click. For bond angle adjustments, the moving atom is the atom in the second bond that is not common to the two bonds.
In the dihedral panel, you can also click Dihedral to open the Dihedral Selection dialog box and select dihedrals by standard names.
The table displays all the parameters that have been defined. For example in the Distance tab, the list shows all defined distances. Click on a parameter to select it. If no parameters have been defined, you can define one using the picking controls and selecting atoms or bonds in the Workspace.
Atomn—The atom columns identify the atoms in each defined item, in the order of their selection.
Original—Displays the value of the distance, angle or dihedral at the time it was defined.
Current—Displays the value of the distance, angle or dihedral after adjustment. This field is directly editable. Valid ranges are:
Name: (for dihedrals only) Displays the name of the dihedral if selected from the Dihedral Selection dialog box.
Clicking Delete while a parameter is selected in the table deletes that particular parameter from the table and removes its markers from the Workspace. Clicking Delete All clears the entire table, and removes all the corresponding markers from the Workspace. To undo a delete, choose Undo delete from the Edit menu in the main window, or press Ctrl+Z (⌘Z).
Clicking Reset while a parameter is selected in the table resets the distance, angle or dihedral to its original value.
In this section you can determine how other atoms that are attached to the moving atom are treated. The moving atom is the second atom for distance, third atom for bond angle, and fourth atom for dihedral. There are three options:
Move All Attached Atoms—(Default) All atoms that are attached to the moving atom are moved together with the moving atom. This is the most common action. However, this option is not available in some cases that may cause problems:
Move All Attached Terminal Atoms—Only atoms that are terminally attached to the moving atom are moved together with the moving atom. For example, hydrogen and halogen atoms would be moved, but a methyl group would not.
Move Only Single Atom—Only the moving atom is moved, that is, atom2 (for distance), atom3 (for bond angle), or atom4 (for dihedral). For dihedrals, the moving atom is not the same as in the other two cases.
In the Chirality tab you can change the chirality of chiral centers in the Workspace. The Invert Chirality picking controls allow you to change the chirality of a single center, of all centers in a molecule, or all centers in an entry. When you select Atoms from the Pick menu, you must pick the chiral center first, then pick the two atoms that are to remain in place. After you have picked the third atom, the two atoms that were not picked are interchanged, with their attached groups.
If you want to label stereocenters with their chirality, click Label Chiral Centers. To clear these labels again, click Clear Labels.
Note: You cannot change the chirality of a center at the junction of two fused rings with these controls. To do so, you must perform the change manually, using distance, angle and dihedral adjustments.
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