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Large Structure Visualization with NGL/MMTF

08/23

Scalable Molecular Visualization

Fast, interactive display of molecular complexes containing millions of atoms is now possible, without plug-ins, on both desktop computers and smartphones. Our new molecular visualization tool, the NGL Viewer, enables easy visualization of even the largest structures for everyone in research and education. In addition, we have developed the new binary compressed Macromolecular Transmission Format (MMTF) to massively reduce network transfer and parsing times. With these advances, we are prepared for upcoming advances in experimental techniques that are already delivering structures of rapidly increasing size and complexity.

Launching & Using the NGL Viewer

The NGL Viewer can be launched from the image display box on each structure summary page (e.g., 4HHB). For large structures comprising more than 10,000 residues in either the asymmetric unit or the biological assembly, the NGL Viewer is now the only supported tool (e.g., 4V99). For structures with a large asymmetric unit, a backbone-only structure is displayed by default to improve loading time. Display style and quality are optimized so that the viewer will run smoothly on both mobile and desktop systems, but can be customized for more powerful systems or for the generation of high resolution images.

Feature Overview

  • Assembly support (Asymmetric Unit, Bioassemblies, Crystallographic Cells)
  • Model support (NMR & multi-model X-ray structures)
  • Basic Symmetry support (Local & global symmetry axes)
  • Protein/RNA/DNA Styles (Backbone, Surface, Cartoon, Spacefill, Licorice)
  • Ligand Styles (Ball+Stick, Spacefill)
  • Color schemes (By Chain, Rainbow (default), Element, B-Factor, Secondary Structure, Hydrophobicity)
  • Rendering Quality (Automatic, Low, Medium, High)
  • Optional Display (Water, Hydrogens, Ions)
  • Viewer options (Spin, Center, Fullscreen, Screenshot)
RCSB PDB News ImageNGL Viewer user interface and surface rendering of "The Crystallographic Structure of Panicum Mosaic Virus" (4V99)

Crystallographic Cells

For X-ray structures, crystallographic unit cells can be displayed, as well as “supercells” comprising a set of adjacent unit cells.

RCSB PDB News ImageUnitcell representation of the "Crystal structure of Metarhodopsin II in complex with a C-terminal peptide derived from the Galpha subunit of transducin" (3PQR)
RCSB PDB News ImageSupercell representation of the "Crystal structure of Metarhodopsin II in complex with a C-terminal peptide derived from the Galpha subunit of transducin" (3PQR)

Reference Links

  • Macromolecular Transmission Format (MMTF) - http://mmtf.rcsb.org/
  • Web-based molecular graphics for large complexes. AS Rose, AR Bradley, Y Valasatava, JM Duarte, A Prlic and PW Rose. 2016. In Proceedings of the 21st International Conference on Web3D Technology (Web3D '16). ACM, New York, NY, USA, 185-186. DOI: 10.1145/2945292.2945324


2016 New Features News Index