The interactive visualization of very large macromolecular complexes on the web is becoming a challenging problem as experimental techniques advance at an unprecedented rate and deliver structures of increasing size. We have tackled this problem by introducing the binary and compressed MacroMolecular Transmission Format (MMTF) to reduce network transfer and parsing time, and by developing NGL,a highly memoryefficient and scalable WebGL-based viewer. NGL renders molecular complexes with millions of atoms interactively on desktop computers and smartphones alike, making it a tool of choice for web-based molecular visualization in research and education.
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Poster: Scalable 3D molecular graphics on the web @ 3Dsig and Web3D 2016
1. Scalable 3D molecular graphics on the web
PDB a billion atom archive
Steps 1 + 2: Speeding-up download & parsing
Funding and acknowledgements
Step 4: Molecular representations geometry
Step 3: Efficient storage & access
Steps to display a structure
Growth of the PDB archive
Step 5: Rendering without plugins
Does it scale?
> 1 Billion atoms in the asymmetric units
Instancing: Create geometry once,
send to GPU once, then transform
position & render multiple times.
• Green surface is reused 59 times for
highly symmetric virus capsid
Impostors: For each pixel GPU tests
intersection of sphere and camera
ray to reduce triangle count.
• Quality resolution independent
as more pixels are tested
• Impostors also used for cylinders.
• Java Applets have provided fast execution and GPU access
• Removed from Google Chrome in version 45 (Sep 2015)
• Oracle to deprecate Java plugin in upcoming JDK 9
• Browsers don’t need plugins anymore
• JavaScript approaches native speed
• WebGL offers plugin-free access to the graphics card
HIV-1 capsid at three scales:
216 hexameric and
12 pentameric subunits,
~2.4M unique atoms
Faustovirus major capsid:
2760 instances of
14478 unique atoms,
~40M overall atoms
Alexander S. Rose, Anthony R. Bradley, Yana Valasatava,
Jose M. Duarte, Andreas Prlić, Peter W. Rose
• Largest structure: HIV-1 Capsid (PDB ID 3J3Q)
• ~2.4M unique atoms
• gzipped mmCIF file: 48.7MB
• 68 of the 100 largest structures deposited in past 3 years
• Advances in experimental techniques fuel the growth
Download File
Decompress & Parse
Populate Data Model
Create Geometry
Render
BD2K Grant: U01 CA198942 RCSB PDB Team
• MMTF
• Libraries & Specification: http://mmtf.rcsb.org
• NGL Viewer
• Supports MMTF, uses columnar stores & WebGL
• Openly developed: https://github.com/arose/ngl
AS Rose & PW Hildebrand.
NGL Viewer: a web application for molecular visualization.
Nucl. Acids Res. (1 July 2015) 43 (W1). doi:10.1093/nar/gkv402
• The PDB archive is growing: structures are getting larger and more complex
• Here we present approaches for scalable 3D molecular graphics on the web
• The MMTF format provides highly compressed structure files
• The NGL Viewer efficiently stores & renders millions of atoms
• Even the largest structures can be rapidly downloaded & displayed in about
1 second to 1 minute depending on device and connection speed
NGL Viewer
• MacroMolecular Transmission Format (MMTF)
• New file format, optimized for transmission of macromolecules
• Binary - for fast parsing
• MessagePack “binary JSON" as an extensible container
• Bespoke compression strategies - for small file size
• Comparison with mmCIF (whole PDB archive, gzipped)
• Size reduced by a factor of >4 (30GB to 7GB)
• Parsing time reduced by a factor of ~12 (205 min to 17 min)
using JavaScript libraries
MMTF
• Columnar stores
• Single TypedArray per property
• Parsed data can be copied in blocks
• Convenient access via proxy objects
Software availability
PDB ID 1RB8
PDB ID 3J3Q
PDB ID 5J7V
Impostor Geometry
2 Triangles
Normal Geometry
320 Triangles
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