Torsion Angle Restraints

This visualization shows the 3D structure of the relevant molecule, in combination with the torsion angle restraint data.

Main Visualization Window (angle mode)

The visualization is laid out as shown below; the view names are referred to in the text.

The structure (main) view shows the 3D structure (rendered by Jmol). Note that you can control many options in the structure view with the popup menus in that view and the Jmol menu in the JavaScreen menu bar.

The atoms corresponding to the angles selected in the data view or atoms and residues selected in the the atom select tree (see below) are highlighted in green. You have the option of highlighting the atoms with a "selection halo" or by coloring the atoms themselves (Jmol->View->Highlight in the menu bar). Atoms not colored for highlighting are colored as follows:

Atom type colors
Element Color
Carbon Gray
Hydrogen White
Oxygen Red
Nitrogen Blue
Sulfur Yellow
Phosphorus Orange

The atom color legend shows the colors for the elements.

The data view shows one of the data sets available for this entry (selected by the data select view). The DEVise cursor in this view selects angles according to the data values -- an angle for which the red tip of the bar (for violations) or the red average line (for angles) is enclosed in the cursor are selected. By default, angles selected in this view are selected in the atom select tree (see below). The way the data is displayed in this view is slightly different according to whether you are displaying the actual torsion angle values or the violations (see the angle mode and violation mode explanations below).

The data scroll view scrolls the X axis of the data view. The DEVise cursor selects the range of residues shown in the data view -- you can drag the entire cursor, or drag the left or right edge to change its size.

The entity assembly select view selects the entity assembly for which data is shown in the data select view. If the entry being visualized has only one entity assembly, this view has no effect.

The data select view selects the data set shown in the data view. All available data sets for the currently-selected entity assembly are listed in this view; by dragging the DEVise cursor you select which data set is shown in the data view.

The info view shows the BMRB accession number and PDB ID, and the generation date of the visualization; show the view help (F1 key) to see the Peptide-CGI version and exact generation timestamp.

Main Visualization Window (violation mode)

When a violation data set is selected, the data is displayed as a bar graph, with the value of the bar being the maximum violation found for any model in the data. Each bar has a red tip on top, indicating the location that must be enclosed by the cursor to select that angle for highlighting in the structure view. Unselected angles are displayed with an orange bar, while selected angles are displayed with a green bar.

Main Visualization Window (angle mode, data view closeup)

When an angle data set is selected, the lower bound, upper bound, and average value are displayed for each torsion angle. The upper and lower bound are displayed as a vertical bar, with horizontal lines at the lower and upper bounds; the average is displayed as a horizontal red line. To select a given angle for highlighting in the structure view, the average line for that angle must be enclosed in the cursor. Unselected angles are displayed with an orange bar, while selected angles are displayed with a green bar. Angles that "wrap around" the 180 degree/-180 degree boundary are displayed as two separate bars (you can see this with the psi angle for residue 43 below, for example).

Main Visualization Window (violation mode, structure closeup)

For each angle selected in the data view (as long as the selection is not modified in the selection tree) the four atoms making up the torsion angle are highlighted in the structure view. In this case, for a phi angle, C, N, CA, and C atoms are highlighted.

Structure Selection Window

Selection of which atoms to display and highlight is done in a separate window, to allow more space in the main window to be used for the structure view and data view.

The structure type tree selects which atoms are shown in the structure view by structure type (backbone, backbone and side chains, or backbone, side chains, and hydrogens). Changing what's selected in this tree also changes what is displayed in the atom display tree and the atom select tree.

The atom display tree selects which atoms are displayed in the structure view. The atom display tree allows selection of the entire molecule, or parts of the molecule by residue and individual atom. Changing what's selected in this tree also changes what is displayed in the atom select tree.

The atom select tree enables you to modify the selections made with the data view cursor. The atom select tree allows selection of the entire molecule, or parts of the molecule by residue and individual atom.

By default, the atoms corresponding to the angles selected in the data view are also selected in the atom select tree. You can change which residues and atoms are selected by manipulating the tree. The Reset button sets the selection in the tree back to the atoms selected in the data view.

JavaScreen Menubar Jmol Menu

Left-clicking the Jmol button in the JavaScreen menu bar brings up this menu.

Jmol Popup Menu

Right-clicking in the structure (Jmol) view brings up this menu.

Jmol Mouse Functions