Explore 3D Molecular Visualization Tools and Techniques

Sources of molecular models

Free searchable database of protein compounds: PDB Database.

This resource also serves carbohydrate, lipid and nucleic acids and has multiple configurations and morphologies for some molecules. For example, a crystal structure derived arrangment, or a tightly wound single strand version of a virus. Mol* 3D Viewer is provided as a browser-based visualizer and file converter. It can be used to convert uploaded files or to convert files stored on their database before downloading. It also offers various display styles that will change the model filesize and geometry. It is not as performant and sophisticated as Chimera for this purpose.

Heavily overlapping PDB is NIH 3D, which provides models created with 3D printing in mind. STL files can easily be converted to other formats used for animation. It also provides WebXR links for Meta headset browser to display.

Another source is The National Library of Medicine which also links out to external sources and PubMed. Not all entries in this resource resolve to 3D models. However, it does link out to more specialized collections such as BacDive, which contains the world’s largest database of bacteria information.

Depending on the visualization style desired, it may be necessary to open the exported model in a visualization tool such as Chimera X. These tools can be used to combine common molecular modeling display styles which affect geometry, such as cartoon, ribbon, “blob” and ligands. These are specialty forms that generalist 3D packages will not normally handle internally. PDB has online viewers and export settings as well.

Chimera X does a very good job of providing tools to combine multiple display styles. The .glb format preserves the visual material formats and their associations within a data tree Blender and Maya can support. One thing it does not do is make changes to the model hierarchy: if you need to export a model with selectable chains a workaround is required. I plan to detail the process for this soon as I faced this challenge recently.

Final modeling and texturing is best performed in a 3D animation tool such as Blender or Maya to allow for optimisation of geometry and textures.

Molecular Display Models

• Ai assisted list of Molecular display styles
• There are variations on the display models in both what they are called and how they are built if you use different molecular software. There isn’t an authoritative naming and style standard that I have found.

Hybrid Molecular Display Models and when/why you might use them

• Cartoon + Surface Model: A molecule’s biological function is intrinsically linked to its precise 3D shape and spatial orientation. Combining representations, such as cartoon for overall structure and a surface model for interaction sites, helps show how different aspects of a molecule contribute to its function.
• Modeling Complex Interactions: Biological processes involve complex interactions between numerous molecules (e.g., a drug binding to a protein). Integrated models can reveal specific atomic interactions using a more detailed display style at a binding site. A more simplified representation (with translucent appearance) can be used to provide context of the rest of a large molecule without obscuring the binding.
• Enhanced Visualization and Education: Physical 3D printed models and computer-generated interactive visualizations (including extended reality) allow information to be perceived through an expanded range of human senses, including touch and direct stereoscopic vision. This tangibility and interactivity facilitate new insights, improve teaching, and enhance scientific communication.
• When displaying molecules in a rendered environment such as Virtual Reality Specialty Molecular Software lets you decide what display model you want to view a molecule with. This is possible because they contain specialized algorithms written to render molecules. Virtual Reality and other forms of visualization display relatively static geometry that is completed and optimized in modelling software. This might force some choices to be made to balance effective visualizations while respecting the technical limitations of the playback hardware and software available.

The role of lighting and focus in visualization

One aspect of molecular visualization that I find both fun and intimidating is that nobody has actually seen many of the structures described with their own eyes. At such small scales indirect techniques must be used to detect the arrangement of atoms, bonds, and event which elements are present. This leaves room for artistic interpretation to bring clarity to what is otherwise a fairly abstract and obscure world.

The initimidating aspect is that advances in imaging are gradually revealing more and smaller details over time. There is a real risk that honest interpretation won’t age well. That interpretation could imply structural and bio mechanical relationships that are revealed to be incorrect or based on subjectivity that goes beyond describing what is known. The other indimidating aspect is that viewers who are used to tuning the vizualization in a specialized tool may not agree with the visualization I choose to set up.

As a designer, I favor following conventions where they are useful and automatic, such as element coloring, single and double-bond sticks and so forth. Where there is a need for emphasis on a certain ligand or interaction the display that most clearly shows a mechanism, reaction or interaction takes precedence over “beauty”. That said, lighting, materials, textures and depth of field can make ball and stick models look amazing while being efective.

The relative scale of microscopic things and how they translate to human scale.

When creating experiences for consumption by “lay-people” it is important to provide context regarding the relative scale of structures and the time-scale of what is shown. This is similar to how a navigation map provides a scale which also maps to the time required to travel a unit of distance.

If a Hydrogen atom is up to 100,000 times smaller than a single human skin cell, an analogy in human scale would be single pea vs a large single-family home.

The scale of molecular biology subjects exist along a range that can oustrip human-viewable object relationships. Human DNA is only 20 times wider than a hydrogen atom, but is 2 meters long when unwound (6 feet). It is difficult to provide an analogy because the difference is 1:100,000,000. Comparing the width of a human hair to a distance of 10 kilometers, (6.2 miles).

How to convey meaning by dilating time and physical characteristics for affect.

Levels of abstraction in physical display: mechanical, chemical, morphological, structural, assembly, transformational, electric/nervous, fluid, porosity, domain-based and more.

Dramatic moments, Mechanism of action, comparisons, before/after,

Development Process: Bottom-up: define the finite variables. How variables might influence each other. Filter the data to isolate just what is needed and relevant to visualize the process. Map that data to visualizations to establish a spatial layout to contain everything. From that concept a storyboard can be developed to represent a time-slice of the process as a visualization.

Molecular Databases with 3D models:

https://www.rcsb.org/structure/6WTT

https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1HHO&bu=1

Basic ball and stick models: https://www.biotopics.co.uk/jsmol/RNAbases.html

AlphaFold Uniprot uses Ai to predict structures based on a molecule’s amino acid sequence. It is often more accurate than experimental data results. Only available for non-commercial work.