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Mol* Tutorial

Note

This cheat sheet, with edits, is from the complete Mol* documentation.

General Interface

Mol* Interface

Mol* Interface

Action How to
Rotate Left mouse button + drag, or Shift + left mouse button + drag
Zoom Mouse wheel. On touchpad: two-finger drag. On touchscreen: pinch two fingers
Move Right mouse button + drag, or Ctrl + left mouse button + drag. On touchscreen: two-finger drag
Center and zoom Right mouse button click on the part of the structure you wish to see
Change clipping planes Shift + mouse wheel. On touchpad: Shift + two-finger drag

Toggle Menu

Mol* Interface

Mol* has two modes that change the behavior of a click. Switch between them using the Selection Mode icon (shaped like a cursor) in the Toggle Menu.

Default Mode: A click on a residue focuses on it. The focused residue and its surroundings are displayed in ball & stick representation with all local non-covalent interactions shown. Click again to hide surroundings.

Selection Mode: A click on a residue selects it. Selected parts appear with a bright green tint in the 3D canvas and Sequence Panel. Holding Shift while clicking extends the selection along the polymer from the last clicked residue.

How To...

Select

  1. Open Selection Mode (cursor symbol in Toggle Menu)
  2. Change the Picking Level if needed (residue/chain/etc)
  3. Then either:
    • 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

Note

Components are located in the Control Panel. If you want to set coloring for separate entities, create a component for each entity.

Color scheme Path
N→C terminus (rainbow) Components → Polymer → Set Coloring → Residue Property → Sequence Id
pLDDT Components → Polymer → Set Coloring → Validation → pLDDT
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 rcsb.org/3D-view.

  • By chains — Select 2 or more polymer chains/residues → Superposition → By Chains → Superpose (RMSD-based or TM-align)
  • By atoms — Select 1 or more atoms → Superposition → By Atoms → Superpose

Make Measurements

  • Distance — Make 2+ selections → Measurements → Add → Distance
  • Angle — Make 3+ selections → Measurements → Add → Angle
  • Dihedral — Make 4+ selections → Measurements → Add → Dihedral

Upload Structures

Go to the Home main menu. Options include:

  • Download from PDB — paste a PDB ID
  • Open Files — upload from your laptop

Mol* Interface

Exercise 1 (together)

Upload from PDB the crystal structure of human myoglobin (PDB ID: 1MBO) and hemoglobin (PDB ID: 4HHB).

Myoglobin is a monomer and hemoglobin is a tetramer. Select one chain of hemoglobin and one of myoglobin and superpose them using TM-align. Then hide all chains of hemoglobin that were not superposed with myoglobin.

Exercise 2

Upload the best model for the PIGU protein from Exercise 1 of the ColabFold tutorial to Mol and color it by pLDDT*.

PIGU protein (UniProt ID: Q9H490) is part of the human glycosylphosphatidylinositol (GPI) transamidase complex.

Download from PDB the structure of GPIT (PDB ID: 7W72) and superpose the modeled PIGU protein with PIGU in the complex.

  • Analyze the TM-score and RMSD scores
  • What can you say about the structural alignment?
  • Hide all chains that were not superposed with PIGU