Mol* Cheat Sheet

Download and save Cheat Sheet.

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.

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

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

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

Compare Structures

First upload two or more structures at the stand-alone version of RCSB Mol* at rcsb.org/3D-view and superpose structures

  • By chains - Select 2 or more polymer chains/residues → Superposition → By Chains → Superpose
  • By atoms - Select 1 or more atoms → Superposition → By Atoms→ Superpose

Measurements

  • Distance - Select 2 or more atoms/residues → Measurements → Add → Distance (for first 2 selections)
  • Angle - Select 3 or more atoms/residues → Measurements → Add → Angle (for first 3 selections)
  • Dihedral - Select 4 or more atoms → Measurements → Add → Dihedral (for first 4 selections)


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Last updated: 6/23/2022