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.

Contents

in progress

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 NGL viewer: 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.

1CGD collagen.

More features - on Your request.
To add model controls "by hand" on the Oculus Quest 2? (in a while :)
test

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. See Intrinsically Disordered Proteins (Wiki) and IDP (Proteopedia).

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 (fixed conformers). See Thermal motion of peptide (Proteopedia.org) and foldit.fandom.com/wiki/Rotamer.

Animation of 2MSK "thermal fluctuations" 25 conformers structures with the lowest energy (fixed conformers).

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." Alexeii Finkelstein

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.

Protein molecules "Zoo"


Protein Folds

Concepts

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) and uses pure JavaScript + WebGL + WebXR (~50kb yet). The main features:

MiniMol features

VR biomolecule viewers:
github.com/SBUtltmedia/aframe-glmol-component
durrantlab.com/pvr/.
VRmol.net.

Links
Proteopedia
Ramachandran principle
Molecules in web augmented reality

Hydrogen in macromolecular models.

GLmol surface
surfaceTest


WebXR samples     updated 15 Oct 2020   twitter/EvgenyDemidov   "demidov at ipm.sci-nnov.ru"