ChimeraX VR encapsulin ferritin demo

Tom Goddard
Feb 17, 2022
for NIH Virtual and Augmented Reality Scientific Interest Group

Show using ChimeraX virtual reality to look at molecular structures and electron microscopy maps. Look at encapsulin from Haliangium ochraceum which forms an icosahedral shell around encapsulated ferritins that convert Fe(II) to the less toxic Fe(III) oxidation state and store it.

There is a video of this demonstration.

    Pore dynamics and asymmetric cargo loading in an encapsulin nanocompartment.
    Ross J, McIver Z, Lambert T, Piergentili C, Bird JE, Gallagher KJ, Cruickshank FL, James P, ZarazĂșa-Arvizu E, Horsfall LE, Waldron KJ, Wilson MD, Mackay CL, BaslĂ© A, Clarke DJ, Marles-Wright J.
    Sci Adv. 2022 Jan 28;8(4):eabj4461. doi: 10.1126/sciadv.abj4461. Epub 2022 Jan 26. PMID: 35080974; PMCID: PMC8791618.

Data sets EMDB 12873, PDB 7oe2, PDB 5n5f.

Demonstration Steps

Do these steps in VR while screensharing RealSense D435 depth-sensing camera view showing person and room and models.

Asymmetric CryoEM Map of Encapsulin Nano-particle

Seeing Inside the Encapsulin Icosahedron

Clip Away Encapsulin Shell

Ferritin Complex Atomic Model

Ecapsulin Shell Atomic Model

Use AlphaFold Model to get Localization Signal Peptide

Connect Ferritin to Shell

Full Encapsulin Ferritin Atomic Model

Multi-Person VR