NGL Viewer for molecule representation #3601
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Thanks @anuprulez! |
bgruening
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area/visualizations
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guerler
reviewed
Feb 13, 2017
| initialize: function( options ) { | ||
| var dataset = options.dataset, | ||
| settings = options.chart.settings, | ||
| url = window.location.protocol + '//' + window.location.host + "/datasets/" + dataset.dataset_id + |
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I think this should be url = dataset.download_url. Then it will also work if the instance url is prefixed.
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I repacked the scripts with |
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Looks good to me. |
dannon
reviewed
Feb 15, 2017
| color: settings.get( 'colorscheme' ), | ||
| opacity: settings.get( 'opacity' ) | ||
| }; | ||
| stage_parameters = { ext: dataset.extension, name: dataset.name, defaultRepresentation: true }; |
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Is dataset.name escaped at this point? Is there any risk here of unsanitized names being displayed in the viz?
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The name option does not seem to be used anywhere nor its documented as option for loadFile. Thanks for pointing it out.
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Cool, good to know. Since it's unused (and not required), let's cut that out, and then I'm +1 and will merge?
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Thanks for the contribution, this looks great! |
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Introduction:
This Pull Request includes the NGL viewer for visualizing molecular structures like PDB. It uses WebGL to exhibit 2D/3D molecular structures and offers an array of intriguing representations. It is available as charts in the Galaxy.
Here are some representations of PDB molecules using NGL viewer:
Display modes:
There are multiple display modes like representation with axes (Axes), secondary structure abstraction (Cartoon), bonds and atoms shown as cylinders and spheres respectively (Ball+Stick), lines for bonds (Line) and many more. More information can be read here.
Other features:
There is a list of rich color schemes like Uniform, Random, Polymer, Hydrophobicity and so on to display a representation in multiple shades.
The background color of the viewer can be chosen as either light or dark. The radius of a representation can be chosen using a slider. Moreover, any representation can be rotated on an axis by turning on the spin feature.
WebGL support:
To run the NGL viewer, it requires a browser to support WebGL (which is accessible in current browser versions. More information about WebGL support in browsers can be found out here).
Courtesy:
The source code of this library is at here.
AS Rose, AR Bradley, Y Valasatava, JM Duarte, A Prlić and PW Rose. Web-based molecular graphics for large complexes. ACM Proceedings of the 21st International Conference on Web3D Technology (Web3D '16): 185-186, 2016. doi: link
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: link
Credits:
Thanks a lot to @bgruening and @guerler for their suggestions and reviews.
Note:
The "Surface" display mode takes a few seconds to generate. It is under development as per the official documentation.
The visualizations in Galaxy can be enabled by adding a path in
galaxy.inifilevisualization_plugins_directory = config/plugins/visualizationsThe text was updated successfully, but these errors were encountered: