BiostructureViewer

BiostructureViewer is a package for the Datagrok platform that enables visualization of biological structures.

Supported Formats

The following file formats are supported:

• Molecular structures (mmCIF, PDB, PQR, GRO, MMTF)
• Density volumes (MRC/MAP/CCP4, DX/DXBIN, CUBE, BRIX/DSN6, XPLOR/CNS)

Note: The Chem package opens formats 'mol2', 'sdf', 'mol' for small molecules.

Semantic Types

The BiostructureViewer package enables detection and handling of the Molecule3D semantic type.

Cell Renderers

Grid cells of columns with the Molecule3D semantic type are drawn using a designated NGL-based cell renderer. Clicking on a cell opens a BiostructureViewer to explore the structure details.

Viewers

Both BiostructureViewer and NglViewer use the same method to obtain a structural data into the viewer from different sources (in order of priority) controlled by properties of the 'Data' category:

1. A PDB string value of the 'pdb' property.
2. A PDB string value of the data frame tag named of 'pdbTag' property.
3. A PDB string value of the data frame '.pdb' tag in case 'pdbTag' property is not specified.

NglViewer

NglViewer is a Datagrok DG.JsViewer derived component based on the NGL Viewer nglviewer.org library developed by Alexander Rose.

BiostructureViewer

BiostructureViewer is a Datagrok DG.JsViewer derived component based on the RCSB PDB implementation of Mol*. Documentation for the Mol project can be found here.

The 'Style' category properties allow customization of the viewer appearance representation as cartoon, backbone, ball+stick, licorice, hyperball, and surface.

References

1. David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: Mol Viewer: modern web app for 3D visualization and analysis of large biomolecular structures, Nucleic Acids Research, 2021; doi.org/10.1093/nar/gkab314.

File previews and File handlers

Files with handled extensions are previewed and opened with the BiostructureViewer.

This package implements file viewers for supported file types. This is how it looks in action:

See also:

• NGL Viewer
• Scripting
• Files
• File Shares
• RCSB PDB implementation

Versions

@rcsb/rcsb-molstar v1.8.7 is the last version dependent on rxjs of version 6.x.x, and it has a dependency on "molstar": "^2.4.1".