ChimeraX: Next Generation Molecular Graphics
March 25, 2015
What is ChimeraX?
- ChimeraX is our next generation molecular visualization software following Midas, MidasPlus and Chimera.
- Modernize user interface
- Emphasize performance
- Familiar user interface but not backwards compatible with Chimera
- Improve support for community plugin developers
- Original Chimera (henceforth "Chimera 1") initially released in year 2000. Since then:
- Increase in computer performance, CPU 50x, graphics 100x, disk space 200x, network 50x.
- Increase in data size and coverage: molecular structures, sequences, and density maps.
- Development effort during the past year
- 75% on ChimeraX
- 25% maintaining Chimera 1
New Technologies and Capabilities in ChimeraX
- Advanced graphics using GPU programming.
- High performance handling large models or hundreds of models.
- Unique capabilities.
- New user interface toolkit, rich html log output.
- Web browser apps using WebGL.
- Community plugin development, distribution system, stable programming interfaces and docs.
Advanced graphics using GPU programming
- Modern 3D graphics uses low level GPU programming that enables new rendering effects and maximum performance.
- Chimera 1 was based on older OpenGL using a limited library of functions.
- Many benefits:
- Ambient occlusion lighting for better depth perception
- Selection outlines 5x faster than Chimera 1
- Silhouette edges up to 100x faster than Chimera 1
- Several times faster rendering of large cellPACK models containing thousands of molecules.
Ambient occlusion lighting. GPU programming allows interactive speed with 100 cast shadows.
Fast selection outlines.|
Fast silhouette edges.|
Fast molecule copies.|
20,000 molecule HIV model.
High performance handling large models or hundreds of models
- Open and display molecules 10x faster than Chimera 1, e.g. HIV capsid model, 2.4 million atom, in 10 seconds.
- PDB provides single mmCIF file for entries over 100,000 atoms, no longer has multiple ids. December 2014.
- We worked with John Westbrook, mmCIF architect at RCSB, to optimize format.
- Fast display of hundreds of medium size models helps comparative modeling.
|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.
- Chimera 1 molecular surface and area calculations fail on many structure over 10000 atoms.
- Hundreds of users have reported this problem.
- ChimeraX has new solvent excluded surface calculation works for all structures, 30x faster.
- Surface and area calculation can use multiple cores.
- Demonstration: computing areas between all molecules in large complexes, RNA polymerase 1k83.
- Graphs and networks using Cytoscape and NetworkX.
- Visualization of density map time series
- Oculus Rift immersive visualization
Density Map Time Series
- Migrating neutrophil (hl60) cells demonstration in ChimeraX.
- Preprocessing makes multiresolution HDF5 file, removes jitter, compensates for photobleaching.
- Mask to show only collagen near cell.
- Quantify motion, centroid velocity, cell size, inertia axes, collagen deflections.
|Movie of cell motion.
||Collagen only near cell path.
||3-D printed cell.
|Cell centroids (orange dots),|
size and axes (blue ellipsoid).
|Plot cell speed and size changes.
||Visualize filament motion|
(green and red prickles).
- 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
- Dockable panels. Demonstrate.
- HTML for work log with images, sessions, links, movies.
- Chimera 1 toolkit Tk has only life support maintenance.
- Example problem: Dual display Tk crash reported 60 times by Chimera 1 users.
- Took 80 hours to diagnose and patch our code to avoid Tk bug.
Web browser apps based on WebGL
- Offer web browser applications derived from ChimeraX code.
- All major web browsers support WebGL 3-D graphics.
- Safari, Internet Explorer, and iPad/iPhone support added summer 2014.
- Allows same graphics performance in web browser as desktop apps.
Example: Map series web application
- 5 people in 3 labs at UCSF analyze Dyche Mullin's cell migration data.
- Data is on a server.
- Share placed marker and note annotations. Collaborative data analysis.
- No software installation.
Example: Protein sculpture design web app
- Box beam protein backbone sculptures made by sculptor Julian Vos-Andreae.
- Developed Chimera 1 extension to produce beam cutting instructions.
- Converted to web app to allow others to make sculptures.
- Collaboration with Daniel Gurnon at DePauw University and sculptor Julian Voss-Andreae.
Alpha helix at|
Linus Pauling house.
Sculpture design Web app.
Community plugin development
- Offer ChimeraX plugin distribution, version checking, and stable programming interfaces.
- Many Chimera 1 plugins created by outside developers, about 50 developed by 20 labs.
- Chimera 1 plugin difficulties:
- Hard for users to find useful plugins. Every developer distributes on their own web site.
- Plugins break after a few Chimera releases.
Tool shed distribution system
- ChimeraX user interface shows all available plugins from a central repository.
- Install with one click.
- Plugins that require other plugins automatically handled.
- Version compatibility checked.
- Stable and documented ChimeraX programming interfaces (APIs).
- Also get latest Chimera bug fixes with one click.
- Backend is working with primitive test user interface (image).
- Currently unreleased
- Target 0.x release in early 2017
- Will include demonstrated new features
- Will have a small subset of Chimera 1 functionality
- Handle molecule, sequence and density map data.
- Currently working on sequence code.
- Stable programming interfaces for developers in a later release.