Project Tree Tools
Just below the Project Tree, the following tools are available
- Show Sequence Select molecules which have sequences associated (Protein, DNA, RNA) in the Project Tree, and click this button. Then, a split-view will appear with a sequence list editor for each of the sequence data types (Protein, DNA, RNA). This is described in Sequences associated with the molecules.
- Setup Binding Site Clicking this button will invoke the Binding Site Setup dialog box, which will do an automatic binding site setup, display the setup settings and give access to modify them (see Setup Binding Site).
- Ligand Optimizer This opens an interactive dialogue to use for modifying a ligand or docking result. If a Binding Site Setup is present, the modifications will adjust to the binding site, and the interactions can be visualized. This is further described in The Ligand Optimizer.
- Dock Ligand Select ligands that you wish to dock to the Binding Site Setup, and click this button to start the docking (see Ligand docking from the Project Tree).
- Align Protein Structure This will invoke the dialog for aligning protein structures based on global alignment of whole chains or local alignment of e.g. binding sites defined by atom groups. This is described in Protein structure alignment.