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Visualizing PDB Structures with UCSF Chimera

This tutorial series will enable viewers to become proficient in using UCSF Chimera (Version 1.17)1 an extensible molecular modeling software. Topics covered range from foundational selections and actions to more complex subjects like structure analysis and animation.

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.

Tutorial 1 – Getting Started with Chimera


  • Introduction to UCSF Chimera – 00:00

  • Understanding macromolecule data from rcsb.org – 00:12

  • Chimera software download and orientation – 01:09

  • Opening and importing structure files – 01:47

  • Mouse controls for structure manipulation – 02:23

  • Saving an image from the graphics window – 03:10

  • Saving, restoring, and ending a session in Chimera – 04:13

  • Biological assembly vs. Asymmetric unit – 04:36


Tutorial 2 – Menu Selections & Basic Actions


  • Overview of Select Menu capabilities – 00:00

  • Selecting by element and by protein chain – 00:19

  • Inverting a selection and changing the selection mode – 01:03

  • Understanding small molecule data from rcsb.org – 01:36

  • Selecting a specific ligand through intersection – 02:40

  • Resetting the selection mode and clearing a selection – 03:12

  • Coloring ribbons and atoms/bonds – 03:21

  • Designing the depiction of atoms/bonds – 04:02

  • Hiding/showing and deleting selected parts of the structure – 05:07


Tutorial 3 – Advanced Selection Methods


  • Selecting a residue atom interactively – 00:00

  • Arrow key commands for modifying selections – 00:32

  • Selecting multiple atoms interactively – 00:49

  • Selecting and deselecting a protein region interactively – 00:58

  • Accessing the command line – 01:22

  • Selecting a residue sequence using the command line – 01:42

  • Selecting a specific residue using the command line – 02:14

  • Accessing the amino acid sequence of a protein chain – 02:38

  • Identifying and selecting a residue by sequence – 03:07

  • Displaying the side chain and focusing on it – 03:27

  • Labeling the residue and changing the color of the label – 03:40


Tutorial 4 – Further Depiction Options


  • Modifying nucleic acid depiction – 00:00

  • Designing biologically–relevant color schemes – 00:46

  • Exploring advanced effects (ribbon edging, silhouettes, etc.) – 01:46

  • Emulating the Molecule of the Month rendering style – 02:59

  • Coloring atoms/bonds in the CPK color convention – 04:07


Tutorial 5 – Structure Analysis & Comparison


  • Overview of structure analysis capabilities – 00:00

  • Selecting residues in the vicinity of a ligand – 00:17

  • Measuring and displaying the distance between two atoms – 01:16

  • Finding all the hydrogen bonds in a protein structure – 01:50

  • Finding hydrogen bonds involving a specific structural component – 02:11

  • Introduction to structure comparison – 02:42

  • Comparing two protein structures via chain alignment – 02:58

  • Analyzing the two superposed protein chains – 03:35


Tutorial 6 – Creating an Animation


  • Overview of animation capabilities – 00:00

  • Sizing the graphics window – 00:22

  • Introduction to the animation interface – 01:05

  • Creating and updating animation keyframes – 01:40

  • Arranging keyframes in the timeline and optimizing transition lengths – 02:54

  • Adding a rotation to the animation and optimizing its length – 03:58

  • Exporting the finished animation to create a video file – 04:18

  • Viewing the exported animation – 04:47


Tutorial 7 – Workarounds for the Lack of Undos


  • Introduction to the need for workarounds – 00:00

  • Saving and resetting structure positions using the command line – 00:18

  • Creating an "artificial undo" by frequently saving the session – 01:44

  • Using animation snapshots to store structure depiction states – 03:06


1. Note, UCSF Chimera has reached end-of-life and is no longer being developed or supported. By contrast, a new software called ChimeraX is under active development. Many features discussed in this tutorial are available in ChimeraX, though the interface might be different. Learn more about UCSF Chimera vs. ChimeraX.