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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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