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README.md

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NGL Viewer is a web application for molecular visualization. WebGL is employed to display molecules like proteins and DNA/RNA with a variety of representations.

See it in action:

Documentation:

Features

  • Molecular structures (mmCIF, PDB, PQR, GRO, SDF, MOL2, MMTF)
  • Density volumes (MRC/MAP/CCP4, DX/DXBIN, CUBE, BRIX/DSN6, XPLOR/CNS)
  • User interaction (mouse picking, selection language, animation, image export)
  • Coordinate trajectories (DCD & PSF, NCTRAJ & PRMTOP, TRR/XTC & TOP, remote access via MDSrv)
  • Embeddable (single file, API)

Usage

Since the NGL Viewer is a set of static files to be viewed in a web-browser there is not much of an installation needed. For development purposes it will be helpful to clone this repository and serve it locally (see below). When embedding the NGL Viewer as a library it is sufficient to include the self contained build dist/ngl.js. A full web application including a GUI can be found in the examples directory.

To install the current release from npm do npm install ngl. To install a development release from npm do npm install ngl@next or npm install ngl@ts2.

Acknowledgments

This project would not be possible without many fine open-source projects. Especially the three.js project provides a great foundation.

Funding sources:

  • RCSB PDB funding by a grant [DBI-1338415; PI: SK Burley] from the NSF, the NIH, and the US DoE
  • NCI/NIH award number U01 CA198942
  • DFG Projekt HI 1502

Cite

When using NGL please cite:

  • AS Rose, AR Bradley, Y Valasatava, JM Duarte, A Prlić and PW Rose. NGL viewer: web-based molecular graphics for large complexes. Bioinformatics: bty419, 2018. doi:10.1093/bioinformatics/bty419
  • AS Rose and PW Hildebrand. NGL Viewer: a web application for molecular visualization. Nucl Acids Res (1 July 2015) 43 (W1): W576-W579 first published online April 29, 2015. doi:10.1093/nar/gkv402