| vision: | |
| 1. Camera Position: Is the image centered on a protein complex composed of clearly distinguishable half red RAS and half blue RAF components? | |
| 2. Membrane Placement: Is a lipid bilayer clearly visible above the protein? | |
| 3. Correct Leaflet Ordering: Is the inner leaflet of the bilayer closer to the protein and the outer leaflet positioned farther away? | |
| text: | |
| 1. Q1 correct answer: Yes | |
| 2. Q2 correct answer: C. 3-5 | |
| # Q1 reason: quite some gray dots from cholesterol ROH headgroup bead can be seen in the center of the bilayer, so the answer is YES. | |
| # Q2 reason: if you run the flowing VMD selection command (name PO4 ROH) and within 15 of (index 3457 to 35009 and resid 188 to 329) | |
| # You will find 4 lipids head group beads, so the answer is C. 3-5 | |
| # Note here it’s important to only count each lipid once, e.g. either use a single reference bead per lipid or center of mass, also selecting the protein can be tricky as the lipids and water also if resid’s in the 188 to 329 range so either exclude other molecule or sub select only the protein residues |