WebXR "MiniMol" molecule viewer
Google images search "RCSB server big bio molecules PDB"
shows, that complexity of bio-molecules exceeds imagination and
triangles budget of hardware (quickly enough in my Oculus Go).
We need not an artist to create complex VR scenes, Nature makes them easy :)
VR is tested in Oculus Go browser and new Firefox Reality 10.1.
VR samples work in Chrome on Android 10 too.
For tests on a desktop the "inline" webxr session is used (non-VR).
See also Hardware for VR.
Mini4 with simple ray-casted sphere impostors.
You can see 6vak or 6crv
(>20000 atoms) in the Oculus Go at ~72 FPS and
4cr2 (80139 atoms) at ~20 FPS.
C atoms are grey balls, N - blue, O - red, S - yellow, H - white, Fe - orange,
P - light orange, F - green.
For big molecules you can set colors corresponding to protein chains.
There are more accurate ray-casted impostors algorithms
(e.g. "GPU-Based Ray-Casting of Quadratic Surfaces" C.Sigg et al) and
web-based molecular graphics for large complexes library can be used for VR.
2m4j 40-residue beta-amyloid fibril derived from Alzheimer's disease brain.
More features - on Your request.
To add model controls "by hand" on the Oculus Quest 2? (in a while :)
VR models scaling
1CRN molecule maximum size is 27.4Å. You can compare
27.4cm and 27.4m 1CRN models.
Due to the parallax effect the small model looks more voluminous for me,
but you can get into large molecules.
With 6DoF HW you can walk around small molecules,
if touchpad controls do not work for you.
Animations of the protein conformers dynamics
Not all proteins have a rigid native structure.
Disordered Proteins (Wiki) and
2LJL and 1A5R
chaotic dynamics animations.
Animation of clipped 2MSK "thermal fluctuations".
The top of the protein is cropped to reveal the inside.
How do they study the structure of a protein if it fluctuates so much? :)
But the backbone is stable (the picture to the right from RCSB.org).
Animation of 2FXY "thermal fluctuations"
15 conformers structures with the lowest energy
motion of peptide (Proteopedia.org) and
Animation of 2MSK "thermal fluctuations"
25 conformers structures with the lowest energy
2hac helix morphing smooth animation.
Quadratic Bezier splines are used for
interpolation between 3 key-frames
2HAC a, 2HAC b and
2HAC c (made by hand in Avogadro).
Feedback transfer is used for point's transformation on GPU.
"Be careful with the animation!
Those samples that I saw (including yours) ignore disordered
Brownian movements (per 1 kinesin step taken, according to estimates,
~ 105 of "UNFINISHED" Brownian attempts), and therefore, despite
prettiness, often animations are more confusing than they help understanding."
My VR "movie" is to far from
How Enzymes Work :)
"Protein rendering modes" movie + audio
(mp3 EN/RU, 32 sec, 200 kb from ttsmp3.com). No TTS in Oculus.
To test the usefulness of VR for protein structure investigation
I'm making a tiny "MiniMol" viewer (open-sourced and based on GLMol).
It is intended for mobile chips (stand-alone Oculus or smartphones)
- One buffer (x,y,z coordinates + atom type) to render atoms and bonds.
- Instanced ray-casted impostors or low polygon spheres to render atoms
(only one call for all atoms).
- gl.drawElements(gl.LINES,...) to render bonds (one more call).
- Hetero atoms and protein interaction rendering mode (only a few important residues).
- Cartoon (ribbons) rendering mode.
- Feedback transfer is used for protein morphing on GPU. Multi-model PDB files,
spline interpolation of frames for smooth animations.
- 72Hz mode and Fixed Foveated Rendering are used on Oculus Go
- See also Design
and Architecture of GLmol.
VR biomolecule viewers:
Molecules in web augmented reality
in macromolecular models.
updated 15 Oct 2020
"demidov at ipm.sci-nnov.ru"