Figure 4.

Practical demonstrations of Mol* Viewer visualization capabilities. We prepared several use cases that can be accessed from the Mol* web page (https://molstar.org). (A) Enveloped HIV capsid in blood serum. Originates from cellPACK and includes more than 13 million atoms. It is a simplified interactive version of Figure 1. (B) Superimposition of cytochromes P450. The superimposed structures are coloured according to a structure quality annotation based on wwPDB validation reports. (C) Villin un/folding simulation. A set of molecular dynamics trajectories for Markov state model analysis along villin headpiece folding and unfolding pathways. (D) SARS-CoV-2 Virion. The coarse-grained model composed of glycosylated S-proteins, M-proteins, E-proteins, and a lipid bilayer. (E) GAIN domain tethered agonist exposure simulation. Molecular dynamics trajectory. (F) Nuclear pore complex. Hybrid model originating from PDB-dev and including 238 288 unique residues. (G) Zika virus assembly including its Cryo-EM density. The original size of the data is about 1.6 GB. (H) Molecular orbitals and electron density of atorvastatin. Visualization of molecular orbitals and the electron density obtained using semiempirical GFN1-xTB method (34,35) (used at https://envision.entos.ai). (I) DNA binding protein assembly. A protein assembly is showcasing the RCSB PDB assembly symmetry annotation.