Mol* Help

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.


To Select

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

To Color

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)