Gallery
Molecular modeling the 3D placement of atoms relative to each other in biological molecules like proteins, small molecules, nucleic acids, sugars (carbohydrates), and fats (lipids) gives a lot of information about how the molecule works. Visualizing molecule structure in different ways highlights different aspects. For example, emphasizing the overall shape of a virus particle vs the electrostatic pattern around a small molecule drug. Visualization helps scientists understand the molecules they’re studying as well as communicate their findings
Examples
Color by residue index, show ligands as spheres, show white mesh for chain A, and show gray mesh for chain B
Hide cartoon for chain A and chain B. Then, color chain A spheres size 0.3 pink, chain A mesh blue, chain B licorice blue, and chain B cartoon pink
Color chain A #FFB800 and ribbon in gray. Color chain B cartoon gray with ribbon color #FFB800. And show ligands as spheres colored by element
Change 10-50 to spacefill of resname color only for carbon atoms. Change 50-100 to green mesh
change all helices to yellow surface and all M residues to red dots
Change to cartoon to be colored white, then color sheets #FF4747 and helices #38AAEA
Hide cartoon, color the licorice #85DB18 with opacity 0.7, show CA as spheres with size 0.3 in white and label all CA with resno in #FF4747
Show trace in #FF4747, show cartoon in white with opacity 0.5, and label helix CA with resname in yellow
Hide cartoon, show licorice colored by element with opacity 0.8, show ions as surface with opacity 0.1 colored #7000FF, and add label for ZN in white
