ChimeraX: Next Generation Molecular Graphics

Advisory Committee
March 25, 2015

What is ChimeraX?

New Technologies and Capabilities in ChimeraX

Advanced graphics using GPU programming

Ambient occlusion lighting. GPU programming allows interactive speed with 100 cast shadows.

Virus capsomere
PDB 1m4x
PDB 1aon
70S ribosome
PDB 4v63
Bacteriophage T7
EMD 6035
Chimera 1
ambient shadows
Fast selection outlines.
Fast silhouette edges.
Fast molecule copies.
20,000 molecule HIV model.

High performance handling large models or hundreds of models

HIV capsid, 2.4 million atoms, 3j3q.cif 106 PDB models matching fibronectin sequence P02751

Reliable algorithms for large models: surface and area calculations

Human ribosome 4v6x. Graph of all contact areas between 87 molecular components takes 8 seconds.

Unique Capabilities

Some examples:

Density Map Time Series

Movie of cell motion. Collagen only near cell path. 3-D printed cell.
Measure motion
Cell centroids (orange dots),
size and axes (blue ellipsoid).
Plot cell speed and size changes. Visualize filament motion
(green and red prickles).

Immersive Visualization

  • Oculus Rift goggles give 360 degree view.
  • More for inspiration than analysis.
  • View inside the a network of collagen filaments. Demo at lunch.
  • Collaborator Dyche Mullins: "Now I know what it feels like to be the cell!"

New user interface toolkit: Qt Widgets


Web browser apps based on WebGL

Example: Map series web application

Example: Protein sculpture design web app

Alpha helix at
Linus Pauling house.
Hemoglobin Sculpture design Web app.

Community plugin development

Tool shed distribution system

ChimeraX Status