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Week 4 - Jmol

Jmol is an open source Java viewer for chemical structures in 3D. It allows users to visualize chemical structures like organic compounds, drugs, nucleic acids and proteins. Jmol has many options and tools to both analyze and modify structures.

This lab session is an introduction to:

  • Viewing protein structures
  • Analyzing structures with Jmol
  • Modifying a structure

First go to http://jmol.sourceforge.net/ and download Jmol.

Rotating and magnifying a protein

Example 1: View “epoxide hydrolase” (PDB ID: 3KOO) in Jmol

  1. Create a folder named pdb files on your Desktop.
  2. Download the PDB file of 3KOO in .txt format into the folder you created.
  3. Open the Jmol-14.32.47-binary folder and open the file jmol.bat.
  4. You should now see the Jmol window.
  5. Click File on the menu bar.
  6. Select Open.
  7. Choose the pdb files folder from the Look In box.
  8. Select 3KOO from the list displayed by double-clicking it.

Open a PDB file

Notes / alternatives:

  • Alternatively you can use File → Get PDB and search for the PDB ID directly from Jmol.

Manipulation:

  • Click and drag to rotate the protein.
  • Scroll forward to zoom out; backward to zoom in.
  • Alternatively:
  • Display → Zoom and choose 100%, 150%, 200%, 400%, 800%.
  • Hold Shift and click-drag back and forth.
  • To move (translate) the molecule:
  • Double click on the structure, then drag.

Visualization styles of proteins in Jmol

Jmol displays molecules in cartoon (ribbon) form by default, but other styles are available (ball-and-stick, spacefill, etc.).

Example 2: Display 3KOO in different styles

  1. Right-click on the screen.
  2. Select Style.
  3. Select Scheme.

  4. Click the following styles one by one and examine the structure:

  5. CPK Spacefill

  6. Ball and Stick
  7. Sticks
  8. Wireframe
  9. Cartoon
  10. Trace

Coloring atoms and residues

Example 3

  1. Open 3KOO in Sticks style.
  2. Right click → Color → Atoms → By Scheme → Amino Acid
  3. Each amino acid is colored.
  4. Colors are not assigned to a specific amino acid type (coloring is random).
  5. Right click → Color → Atoms → By Scheme → Element (CPK)
  6. Carbons: gray
  7. Oxygens: red
  8. Nitrogens: blue
  9. Sulfurs: yellow
  10. Right click → Color → Atoms → By Scheme → Secondary Structure
  11. Helices: pink
  12. Sheets: yellow
  13. Loops: white
  14. Right click → Color → Atoms → By Scheme → Temperature (Relative)

Coloring bonds

Example 4: Disulfide bonds and hydrogen bonds

  1. Open 3P3F and view it in Sticks style.
  2. Right click → Color → Disulfide Bonds → Cyan
  3. Positions of disulfide bonds can be displayed.

Alternative to improve visibility:

  1. Right click → Color → Bonds → Green
  2. Right click → Color → Disulfide Bonds → Cyan

Hydrogen bonds:

  • Right click → Style → Hydrogen Bonds → Calculate
  • You will see hydrogen bonds as red-blue lines.

Selecting

Example 5: Selecting ligands/residues/elements

Open 3NOJ (HMG/CHA aldolase).

Ligands:

  1. Right click → Select → Hetero → Ligand
  2. Right click → Select → Display Selected Only
  3. Right click → Select → Hetero → By HETATM → PG4 (or MG or PYR)
  4. Right click → Uncheck Display Selected Only
  5. Right click → Select → All

Residues:

  1. View the protein in Ball and Stick style.
  2. Right click → Select → Protein → By Residue Name → Ser (or any amino acid)
  3. Right click → Select → Selection Halos (check)
  4. Right click → Select → Protein → Backbone
  5. Halos show the peptide bond line.
  6. Side chains are not highlighted in backbone selection.
  7. To select side chains:
  8. Right click → Select → Protein → Side Chains

Elements:

  • Right click → Select → Element → S (sulfur)

Selecting a specific region

  1. Click on the cursor icon on the toolbar.

Selection tool

  1. Press Shift + Left click + Drag to select the longest tail-like α-helix region.

Labeling

Example 6

  1. Select and display only pyruvic acid.
  2. Right click → Style → Labels → With Element Name or Atom Name or Atom Number.
  3. Select and display only His residues and label them:
  4. With Atom Name
  5. Then with Atom Number
  6. To display the whole structure again:
  7. Right click → Select → All
  8. To remove labels:
  9. Right click → Style → Labels → None

Surface

Example 7: Display surfaces

Display the surface of HMG/CHA aldolase in different styles:

  • Right click → Surfaces → Dot Surface
  • Right click → Surfaces → van der Waals Surface
  • Right click → Surfaces → Solvent-Accessible Surface
  • Right click → Surfaces → Solvent Surface
  • Right click → Surfaces → Molecular Surface

Ligand surface:

  1. Select the ligand as you learned previously.
  2. Display the surface for the selected ligand.

Opacity and color:

  • Right click → Surfaces → Make Opaque / Make Translucent
  • Right click → Color → Surfaces → White

Spinning:

  • Right click → Spin → On
  • Right click → Spin → Off

Measurements

Example 8

Measuring a distance

  1. View the protein in Ball and Stick style.
  2. Click the ruler icon on the toolbar.

Ruler tool

  1. Zoom the molecule up to 400×.
  2. Double click on an atom, then double click on another atom to measure the distance.

Measuring an angle

  1. Right click → Measurements → Click for angle measurement
  2. Double click on three consecutive atoms on an amino acid to measure the angle.

Measuring torsion (dihedral) angles

  1. Right click → Measurements → Click for torsion (dihedral) measurement
  2. Measure:
  3. Four atoms on the side chain of a leucine
  4. Four atoms in a phenyl ring
  5. Compare and contrast the torsion angles.

You can list or delete measurements from the Right click → Measurements menu.

Model Kit

Example 9

  1. Click on the model kit icon on the toolbar.

Model kit tool

  1. Open 3NOJ in Ball and Stick style.

Replacing an atom with another

  1. Right click → bring the cursor on the spacefill-style molecule → check N for nitrogen.
  2. Click on an oxygen or carbon to replace it with nitrogen.

Jmol adds hydrogen atoms automatically to satisfy valence.

Deleting an atom

  1. Right click → bring the cursor on the spacefill-style molecule icon → check delete atom.
  2. Click on an atom to delete.

If an atom is not bonded to any other, the first click may add hydrogen and the second click deletes.

Dragging an atom

  1. Right click → bring the cursor on the spacefill-style molecule icon → check drag atom.
  2. Click an atom and drag it to a new position.

Track changes:

  • Measure the distance between two bonded atoms, then drag one while monitoring the distance.

Bond formation:

  • Right click → check drag to bond
  • Drag one atom onto another to form a bond.

Dragging a molecule:

  • Right click → check drag molecule (SHIFT TO ROTATE)
  • Click on PG4 and drag.
  • Hold Shift while dragging to rotate it independently.

Manipulating charges

  • Right click → check increase charge / decrease charge
  • Click an atom to change charge.

Manipulating bonds

  • Right click → (ball-and-stick tool) → check delete bond; click a bond to delete
  • Right click → check double; click a single bond to make it double
  • Right click → check single; click a double bond to make it single
  • Alternatively use increase order / decrease order

Rotating a bond

  1. Right click → (ball-and-stick tool) → check rotate bond.
  2. Click on a bond.
  3. Click an empty area and drag while holding Shift.

Adding hydrogens

  • Right click → ("..." icon) → Add Hydrogens

Saving a structure from Jmol

Example 10

  1. Go to the menu bar.
  2. File → Export → Export image
  3. Save a .jpg image of the structure.