Mol cheat sheet
Mol* Cheat Sheet
To Navigate the 3D Canvas:
Rotate - Press the left mouse button and move, or use the Shift button + left mouse button and drag.
Translate - Press the right mouse button and move, or use the Control button + the left mouse button and move. On a touchscreen device, use a two-finger drag.
Zoom - Use the mouse wheel. On a touchpad, use a two-finger drag. On a touchscreen device, pinch two fingers.
Center and zoom - Use the right mouse button to click onto the part of the structure you wish to see.
Change clipping planes - Use the Shift button + the mouse wheel. On a touchpad, use the Shift button + a two-finger drag.
First open Selection Mode and change the Picking Level (if needed):
- Click on objects in the 3D canvas, OR
- Click on residues in the Sequence Panel, OR
- Use the Set Operations Menu in the Selection Mode toolbar
To See or Hide
- Create a component of the region you wish to see/hide →
- Go to the Components Panel and press the “eye” icon next to the component you created
N-terminus to C-terminus (rainbow) - Components → Polymer → Set Coloring → Residue Property → Sequence Id
Heteroatom - Components → Polymer → Set Coloring → Atom Property → Element Symbol
Secondary structure - Components → Polymer → Set Coloring → Residue Property → Secondary Structure
Hydrophobicity - Components → Polymer → Set Coloring → Residue Property → Hydrophobicity
Domain - Select domain → Selections Menu → Apply Theme to Selection → Color → Apply Theme
To Compare Structures
First upload two or more structures at rcsb.org/3D-view
By chains - Select 2 or more polymer chains/residues → Superposition → By Chains → Superpose
By atoms - Select 1 or more atoms → Superposition → By Atoms→ Superpose
To Make Measurements
Distance - Make 2 or more selections → Measurements → Add → Distance (for first 2 selections)
Angle - Make 3 or more selections → Measurements → Add → Angle (for first 3 selections)
Dihedral - Make 4 or more selections → Measurements → Add → Dihedral (for first 4 selections)
Based on the RCSB PDB mol* documentation thanks to the generosity of RCSB PDB and Dr. Shuchismita Dutta.