Puzzle 2020: Olivetolic Acid Ligand Binder Design
Contributors:
- NinjaGreg
- Go Science
- Crossed Sticks
- Bruno Kesteomont
- grogar7
- LociOiling
- nspc
X-ray tunnel[]
Without the X-ray tunnel, the ligand can be hidden by the protein.
In this type of puzzle, it can be difficult to see how the ligand is bonded to the protein. The "X-ray tunnel for ligand" view option may help by cutting away some of the protein. The "Cartoon Ligand" protein view also needs to be selected for the tunnel to behave properly. Setting "Show bonds (non-protein)" is also a good idea.
With the X-ray tunnel, the ligand and its protein bonds can be seen more easily.
If "Cartoon Ligand" is not selected, the X-ray tunnel will be very large, as shown in the first image below.
The size of the tunnel can be adjusted by dragging on the dark wall of the tunnel. In the case of the oversize tunnel, you may need to zoom out in order to adjust the tunnel. Selecting "Cartoon Ligand" is much easier.
Without "Cartoon Ligand", the X-ray tunnel won't follow the ligand correctly when you rotate the protein. The tunnel can end up looking at a point in empty space.
Even with "Cartoon Ligand" set, the X-ray tunnel view has some limitations. You can adjust the size of the tunnel, but not the near and far cutoff. So it may be difficult to see all the bonds between the ligand and the protein in one view.
View options for ligand tunnel. In particular, the "Cartoon Ligand" protein view is needed for the X-ray tunnel to work correctly.