Graphical view and editing of secondary structure

Side Panel settings
The settings in the Side Panel are a subset of the settings in the normal sequence view described in Sequence settings in Side Panel. However, there is one additional group of settings which is unique to the secondary structure 2D view: Secondary structure.

• Follow structure selection. This setting pertains to the connection between the structures in the secondary structure table. If this option is checked, the structure displayed in the secondary structure 2D view will follow the structure selections made in this table.
• Layout strategy. Specify the strategy used for the layout of the structure. In addition to these strategies, you can modify the layout manually as explained in the next section.
  • Auto. The layout is adjusted to minimize overlapping structure elements. This is the default setting.
  • Proportional. Arc lengths are proportional to the number of residues. Nothing is done to prevent overlap.
  • Even spread. Stems are spread evenly around loops.
  Reset layout. If you have manually modified the layout of the structure, clicking this button will reset the structure to the way it was laid out when it was created.

Selecting and editing

When you are in Selection mode, you can select parts of the structure like in a normal sequence view.

One of the advantages of the secondary structure 2D view is that it is integrated with other views of the same sequence. This means that any selection made in this view will be reflected in other views.

If you make a selection in another sequence view, this will will also be reflected in the secondary structure view.

The Workbenches seek to produce a layout of the structure where none of the elements overlap. However, it may be desirable to manually edit the layout of a structure for ease of understanding or for the purpose of publication.

To edit a structure, first select the Pan mode in the Tool bar. Now place the mouse cursor on the opening of a stem, and a visual indication of the anchor point for turning the substructure will be shown.

Click and drag to rotate the part of the structure represented by the line going from the anchor point. In order to keep the bases in a relatively sequential arrangement, there is a restriction on how much the substructure can be rotated. The highlighted part of the circle represents the angle where rotating is allowed.

Press Reset layout in the Side Panel to reset the layout to the way it looked when the structure was predicted.