Once you have imported and visualized your sequence you can associate it with a layout (based on the type of sequence) before drawing the residue based diagrams. [Note: This feature is presently only available in the beta version of RbDe]

Once you have selected a layout you can draw and modify your residue based diagram in advanced mode using the Secondary Structure Editor which allows you to modify secondary structure element positions in your sequence.

If you select either of the GPCR or transporter layouts, you have the option of selecting the "Fast diagram mode" which assumes that your sequence has helical transmembrane domains. You can still modify secondary structure element positions (but not the topology) by clicking the "Secondary Structure" button in the menubar to access the Secondary Structure Editor.

[Note: When you select a layout other than "old-rbde"you can't access the Topology Editor that was available in previous versions of RbDe, since the topology is now dictated by the selected layout. To modify your diagram using the Topology Editor select "old-rbde" as your layout option.]