Updated versions of 2D and 3D viewers now available on PDBe entry pages

New version of Mol* in PDBe pages gives enhanced visualisation options
17 March 2021

The Mol* viewer at PDBe has enabled our users to easily access the 3D visualisation of macromolecular structures within the browser. Now, Mol* improved even more, allowing you to easily create bespoke and stunning visualisations with more customisation, including display of interactions and measurements.

One of the significant benefits of Mol* at PDBe is the accessibility of this 3D structure viewer, working within your browser window and even on your mobile devices. Furthermore, the use of WebGL in Mol* allows for high-quality visualisations at lightning-fast speeds. We have built upon these benefits in the latest version of the viewer while retaining the speed and ease of use that makes Mol* so useful in browsing PDB structures online.

Visualisation at any scale

The size and complexity of macromolecular structures requires any 3D viewer to handle visualisation at multiple scales. Mol* now displays a light-weight surface representation upon loading for large macromolecular structures, reducing the rendering time and giving a clear overview representation of these structures. However, in many cases, you may want to see more details! A simple click (or tap) on the structure will ‘focus’ on that point, displaying the surrounding atoms in that region and highlighting non-covalent interactions. These varied visualisation scales help the users easily navigate the complexities of macromolecular structures at all dimensions.



Various visualisation scales of the Zika virus structure (PDB entry 5ire) are displayed above. When you first open the viewer, a low-detail surface representation is displayed by default (left). ‘Focusing’ on a region will switch to a ball-and-stick representation, along with non-covalent interactions (right).


High-Quality Rendering

As a WebGL-based molecular viewer, Mol* can generate high-quality visualisations in your browser. To make it even easier to create specific visualisation effects, these are now simply toggled via the settings menu. You can adjust the lighting effects to create specific renderings, including matte, glossy and even plastic! Furthermore, at the press of a button, you can display outlines and even generate ambient occlusion, heightening the realism of internal shadows. You can then simply click the screenshot button to create high quality rendered images at any resolution, and with the option of transparent backgrounds. All of this makes it straightforward to create great images of any structure in the PDB.



You can select different rendering options in Mol* (all with occlusion enabled), from left to right: flat, flat + outline, matte, glossy, plastic.


Customise your Mol* view

The introduction of a selection tool in Mol* now allows a level of customisation that was previously not possible in a browser-based viewer. Toggling on the selection mode will enable you to select specific regions of the structure at the granularity of atoms, chains and more. Such selections will allow you to create specific visualisations for each of these selections, using the ‘Add’ tool in the components section. In addition to defining representations, you can also use the selections to display specific labels and measurements on the structure, from labelling of key amino acids to measurements of bond angles. All this, from a viewer that loads in your browser!



Mol* visualisation of PDB entry 2dn2 with selection mode activated. The selection tools at the top of the window enable you to define different parts of the structure and apply labels and measurements. In this case, the HEM ligand and adjacent histidine residues are labelled, along with the distance from atom NE2 of His58 to the FE of HEM.


ProtVista on PDBe entry pages

In addition to the updates to the Mol* viewer, we have also introduced the ProtVista sequence feature viewer to the PDBe entry pages. ProtVista is a collaboration between PDBe, Uniprot and Interpro and allows easy visualisation of functional features on the protein sequence. Furthermore, on the macromolecules pages of PDBe, ProtVista is seamlessly integrated with the Mol* viewer. This integration allows you to use the sequence viewer to identify important functional features in the 3D structure. We have added more data to the sequence feature viewer on these pages, including sequence conservation and variant data, plus functional and biophysical annotations, such as predicted binding sites and backbone flexibility.

We hope you enjoy using these new visualisation features at PDBe and find them useful for your work. However, we are always keen to get your feedback (good or bad). If you want to get in touch, use the ‘feedback’ button on any PDBe page, or let us know at pdbehelp@ebi.ac.uk.