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Exploring PDB structures in 3D with Mol* (MolStar)

Introduction to Mol* Video Tutorial Series

The tutorial series below is an introductory guide to visualizing PDB structures and creating graphics and animations with the Mol* Viewer. To access the individual sections, click on the links under each tutorial and hit “Play” on the video. The video will start playing at the indicated time.

Creating Images in the Molecule of the Month Style

If you would like to create molecular images in the style of the Molecule of the Month illustrations using Mol*, access the tutorial available on the the Mol* documentation website.

Mol* tutorial for creating images in the Molecule of the Month style

Mol* Documentation

Detailed Mol* documentation is available on RCSB.org.


Tutorial 1 – Introduction to Visualization with Mol*


  • What is PDB ID? – 00:05

  • Accessing the Structure Summary Page using PDB ID – 00:52

  • Identifying the structure components on the Structure Summary page – 01:08

  • Accessing the 3D Viewer Mol* and basic overview of the interface – 01:46

  • Removing residual water molecules – 02:44

  • Mouse operations in the 3D Viewport – 03:00

  • Adding and removing molecular representations for each component type – 03:21

  • Focusing on individual elements and showing non-covalent interactions – 04:03

  • Adjusting which non-covalent interactions to show – 05:23

  • Adjusting color theme for components: data driven color themes – 05:39

  • Adjusting color themes for components: illustrative color theme – 06:14

  • Creating selections and changing colors for selected elements – 07:01

  • Deleting selected elements – 08:10

  • Creating new components from selections – 08:55

  • Stylizing and saving images – 09:42


Tutorial 2 – Creating Animations with Mol*


  • Introduction to the structure and to Mol* animation – 00:00

  • Setting up a Camera Spin animation with default parameters – 00:20

  • Adjusting the resolution of the viewing window – 00:44

  • Rendering, downloading, and viewing the animation – 01:14

  • Creating a Camera Spin animation with custom parameters – 01:36

  • Designing a Camera Spin animation for the active site – 02:41

  • Creating a Spin Structure animation – 04:05