Molecular Visualization
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.
Example Scripts
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.
3D Molecular Model Representations
- Cartoon: Shows the secondary structure of proteins and the backbone of nucleic acids. Very common representation. Not applicable to small molecules, sugars, lipids, or ions.
- Backbone: Shows the backbone trace of proteins and the backbone of nucleic acids. Not applicable to small molecules, sugars, lipids, or ions.
- Spheres (or Spacefill): Shows each atom as a sphere with a radius based on the van der Waals radius. Size can be customized. Emphasizes the atom and hides the bonds.
- Ball and Stick: Shows each atom as a small sphere and each bond as a stick. Emphasis split between the atom and the bond.
- Licorice (or Sticks): Show each bond as a stick. Atoms can be seen by color, but not by shape alone. Emphasis is on bonds. For ions, the result is a small sphere.
- Surface: Shows a thin envelope around a molecule. Emphasizes the overall shape. Often used with different opacity levels to layer with other representations.
- Mesh: Shows a thin mesh envelope around a molecule that is semi-transparent. Setting the level of the mesh to be lower results in more detail.
Show sphere.
Change to licorice and surface with opacity 0.1
Smart Color Customization
Built in
- By Element: Colors atoms by standard conventions. C: gray, O: red, N: blue, H: white, S: yellow, ...
- Secondary Structure: Colors according to helices, sheets, turns, and other.
- Residue name: Colors reach residue name a different color.
- b-Factor: Uses a gradient based on the b-factor column
- pLDDT: Very low: orange, Low: yellow, High: cyan, Very high: blue. Assumes b-factor column is pLDDT values.
Custom
- By Name: Red, blue, peach, moonlight green, ...
- Custom: #78FF00, #0078FF, ...
Color by secondary structure
Color by plddt
Quick Selection
- Structure: Helix, sheet, turn (not helix and not sheet), all, sidechain, backbone, polymer
- Residue type: nucleophilic, hydrophobic, aromatic, amid, acidic, basic, charged, polar, nonpolar, cyclic, aliphatic, small
- Residue name: Alanine or ala or A, arginine or arg or R, ...
- Chain name: A, B, C, ...
- Molecule type: protein, nucleic, dna, rna, hetero, ligand, ion, saccharide/sugar, polymer, water
- Atoms/Elements: carbon or .C, c alpha or .CA, oxygen or .O, nitrogen or .N, hydrogen, ...
- Residue numbers:: 1, 2, 100 or 300-500, ...
- Model number: 0, 1, 2, ... (for NMR structures)
Labels
- Residue: Show the residue name and number for specified residues or atoms.
- Distance: Show a dotted line and label the distance between 2 specific atoms. Default is anstroms, but you can ask for nm.
- Angle: Show and label the angle, in degrees, between 3 specific atoms.
Label residues 1-2, and 7O
Label the distance between 11 SG and 8 OD1
Show the distances between 1 and 70-75 in tiffany blue
Label the angle between 3NH2, 3 CZ, and 3.NH1
