A new version of the 3D molecular visualisation software, Mol* (), is now being used at PDBe and PDBe-KB pages, bringing a host of improvements and new features. These include export of superimposed coordinates from the PDBe-KB aggregated views of proteins, speed and rendering improvements, and the addition of UniProt numbering for amino acids.
Mol* v3
The Mol* () viewer is used at the PDBe and PDBe-KB pages to display various macromolecular structure data directly in the browser. A recent major update of the Mol* software has now been integrated into the pages at PDBe and PDBe-KB, to provide a host of improvements and new functionalities.
Export of coordinates
One significant improvement of the new Mol* version allows the export of coordinates from the viewer, in either CIF or binary CIF format. In the PDBe-KB aggregated views, there are a number of superimpositions generated to highlight different structural clusters or display superposed ligands. These superimposition views can be displayed in Mol* and now the superimposed model coordinates can also be downloaded, using the ‘Export models� option. The video below is a screen capture highlighting how to export models from Mol* at PDBe-KB pages.
This feature is also available on the PDBe search and entry pages, allowing the easy export of structures from the browser viewer for further analysis elsewhere. Furthermore, on the PDB pages, there is also the option to export geometry files for use in 3D printing or rendering, with common export options available, along with the associated materials files to retain colouring of the structures. There is also the option to export animations from Mol* at PDBe, allowing users to quickly and easily create videos depicting the structure from all angles.
Rendered image of PDB entry 4CCZ, exported directly from Mol* at PDBe and rendered using the Cycles engine in Blender 3.1.2.
UniProt integration
The vast majority of proteins in the PDB archive are mapped to UniProt entries, with the SIFTS (Structure integration with function, taxonomy and sequence) process at PDBe-KB further standardising sequence information and expanding functional annotations. With the update to the Mol* viewer, we have added additional information about the UniProt mapping and numbering when hovering over amino acids in the viewer at PDBe and PDBe-KB pages. This update is in line with our recent changes to the updated mmCIF files at PDBe, which now contain direct UniProt mapping within the model coordinates. As the numbering of proteins in PDB entries is not standardised, this additional information will help users easily view the structure in the context of standard UniProt numbering.
Further visualisation improvements
In addition to the new functionalities discussed above, the new version of the Mol* viewer has a number of general improvements to speed and rendering quality, hopefully making visualisation of structures at PDBe and PDBe-KB quicker and easier. Part of these improvements includes the addition of new ‘quick styles� options, providing three different visualisation options: ‘default�, ‘stylized� and ‘illustrative� (see image below). ‘Default� displays the standard Mol* visuals, while ‘stylized� gives a more cartoon-like interpretation of the structure, and ‘illustrative� displays an artistic spacefill representation, akin to the work of David Goodsell.
Visualisation of PDB entry 7apu in Mol* at PDBe, viewed using the different ‘quick styles�: default (left), stylized (center), illustrative (right).
If you have any comments or suggestions about the new version of the Mol* viewer at PDBe and PDBe-KB, you can contact us using the ‘feedback� option on any of our pages.
