There are specific View Options for working with ligands. There's "Ligand Specific" coloring option and a "Cartoon Ligand" protein view. The X-ray tunnel for ligand ligand option may also make the ligand easier to see. The "Show Bonds (non-protein)" option shows hydrogen bonds between the ligand and the protein, a key design feature.
The ligand view options use CPK colors. Hydrogen atoms are shown as white caps, nitrogen atoms are blue, and oxygen atoms are red. Carbon atoms are shown in a default color, which can be changed. Other atoms have their CPK colors, such as yellow for sulfur, but it can be difficult to distinguish them.
The ligand design cheat sheet developed by the Foldit science team summarizes the features available in ligand design. The features include:
- adding an atom
- changing an atom to a different element
- deleting an atom
- changing single, double, or triple bonds
- adding fragments
In both the original and selection interfaces, ligand design depends on atoms being selected. In both interfaces, clicking on atoms of the ligand selects them. (In the selection interface, the ligand itself must first be selected as a segment selection.)
Multiple atoms can be selected by clicking on them. In the original interface, a "broom" icon clears the selected atoms. In the selection interface, clicking on the background clears the selected atoms and deselects the ligand. The ligand must be re-selected and the ligand design tool opened again to proceed in the selection interface.
The ligand design options available depend on the atom selected, including what chemical element it is and it's bonding relationship to other atoms. Options that aren't currently available are "grayed out".
The possible elements include:
- C - carbon
- N - nitrogen
- O - oxygen
- P - phosphorous
- S - sulfur
- F - fluorine
- Cl - chlorine
- I - iodine
- Br - boron
- H - hydrogen
Changing a bond requires selecting two adjacent non-hydrogen heavy atoms. The possible bonds between heavy atoms are:
The fragments are themselves small molecules or functional groups, and include: