Nanome suits chemistry and biology topics taught at the molecular or atomic scale, from VSEPR shapes to an enzyme's active site, and a class activity in it is a workspace the instructor builds and steps through with the class. Nanome ships no premade lesson modules, and the academic page lists the tools for building one instead. A lesson is a set of structures loaded by PDB ID or from a file, cut into guided steps with the Scenes Panel, which students move through like slides in a browser or a headset.
Students follow along as Viewers, or each group works hands-on in its own duplicate of the lesson workspace.
How a lesson is put together
A workspace holds structures, their representations, scenes and permissions, as the session guide lays out. Each scene keeps the representations and visibility as they stood when it was made, and Set Scene POV lands every user in the same framing.
The guide's own pattern reads like a lecture outline: duplicate the scene, change one thing, and each step shows a little more than the last. Previous and Next arrows move between scenes, and a workspace holds up to 50 of them since v2.6.
Viewers can explore, spotlight, follow and move through scenes, but they can't edit representations or arrange structures, which suits a lecture. A separate workspace per group means one group's changes stop at that group.
The scene menu guide walks through the controls, and a walkthrough of modern molecular presentations covers building a sequence that holds a room.
Which course topics fit
| Topic | Fit | How it gets into Nanome, or where it belongs instead |
|---|---|---|
| Protein structure | Fits | Load by PDB ID, then cartoon colored by secondary structure (representations) |
| Ligand binding | Fits | An automatic pocket view for any structure with a ligand, plus interaction types from hydrogen bonds to metal coordination |
| VSEPR and isomerism | Fits | Builder geometries up to tetrahedral, with distance, angle and dihedral measurement; larger shapes load as files |
| Conformers | Fits | The Torsion Tool (beta), with strain shown as a bond turns |
| Crystallography and solid-state defects | Partly | XYZ supercells exported from crystallography software; .cif is documented only as mmCIF/PDBx |
| Polymers | Fits | PDB, SDF or XYZ files from the course's modeling software, or MOL2 through a MARA tool in the web app |
| MD trajectories | Fits | GRO on its own, or XTC, TRR and DCD attached to a loaded model (supported formats) |
| Pathway and cycle diagrams | Doesn't fit | A 2D figure on a slide; the enzymes in the pathway load one structure at a time |
| Process engineering (Aspen Plus, COMSOL, Ansys Fluent) and CFD | Doesn't fit | Flowsheets and fluid fields have no atoms to show, so they stay in their own tools |
Lesson 1: VSEPR shapes and isomers in the builder
The Builder Tool places atoms with 3 geometry options, Linear, Trigonal and Tetrahedral, which set how many open bonds each new atom carries. A tetrahedral carbon starts methane, a trigonal one starts formaldehyde, and a linear one starts ethyne.
Minimize relaxes each structure with MMFF94, MMFF94s or UFF and reports the energy in kJ/mol. The Measurement Tool then reads distances in ångströms and angles in degrees, so students set each H-C-H angle against their textbook.
Butane and isobutane built side by side make a structural-isomer pair from the same 4 carbons. The Torsion Tool, still a beta feature, turns butane's central bond, and since v2.5 it colors the atoms by strain: green for low, yellow outside standard ranges, red for high. Staggered and eclipsed conformers then come from one bond turning in a student's hand, with a dihedral measurement on the same 4 carbons.
Two limits shape the lesson plan. None of the representations in the docs draws lone pairs, so water shows its bent shape and students supply the 2 pairs that explain it. The builder's elements are H, C, N, O, F, P, S and Cl, and its geometries stop at tetrahedral, so trigonal bipyramidal and octahedral shapes come in as files with the geometry already set: an SDF or XYZ dragged into the web app.
Lesson 2: a ligand in its pocket, edited and fitted back
Lesson 2 runs on 1IEP, the c-Abl kinase domain bound to imatinib (STI-571). The entry holds 2 copies of the complex, chains A and B, and the class works on one.
- Loading the complex. The structure loads by ID from the RCSB, and Nanome builds a pocket view automatically for any structure carrying a ligand. The pocket component is the 5 Å sphere around the ligand.
- Reading the interactions. Create interaction components, under Structure Actions, computes interactions in Polymer-Ligand mode, and the Chemical Interactions panel then lists every interaction found, with clash detection as a toggle (sample workflows). Students measure 2 or 3 of the hydrogen bonds and write the distances down, and how to analyze protein-ligand interactions explains what each type means.
- Editing a copy. The pencil icon in the Ligands tab opens the ligand in the Builder, where Replace atom, Draw by group and Delete change it (main panel). Minimize settles the new geometry on the ligand by itself, since the v2.4 notes list minimizing inside the pocket as a later update. Save as new ligand keeps the crystal pose beside the edited one.
- Fitting it back. Position Molecules moves structures independently, so the edited ligand first gets an entry of its own through Extract to entry or Duplicate to entry, both named in the 2.6.1 release notes. With Position Molecules on, it then moves by hand while the chemical interactions update in real time. Ligand alignment is the other way to set it over the crystal ligand, and since 2.6.1 it holds through a substitution or a bond-order change. Position Molecules goes off afterwards, because the tips page says spotlight misbehaves with it switched on, and Reset position returns a structure to where it loaded.
- Comparing. The Ligands tab shows RDKit properties such as HbondA, HbondD and LogP for both ligands, and the class remeasures the same contacts on the new pose.
The Builder's documented steps end at minimize and save, with nothing that scores a pose, so the class judges the fit by setting the step 2 distances against the new ones. A docking score is a job for MARA, which runs Smina and DiffDock-L, and the best molecular modeling software sets that next to Nanome's build-and-minimize loop and the desktop builders.
Lesson 3: an enzyme active site, taught as a scene sequence
4CHA, α-chymotrypsin, carries the textbook catalytic triad: His57, Asp102 and Ser195. The entry holds 2 copies of the enzyme, chains A to C and E to G, and a lecture on the first copy fits in 5 scenes:
- The enzyme as a cartoon, colored by secondary structure, with the second copy hidden.
- A Semi surface over it, showing where the active site sits.
- The surface off, the triad as sticks, and everything else hidden.
- Distance measurements along the triad's hydrogen-bond network.
- The view colored by chain, which shows the triad spread across 2 of the chains left behind when chymotrypsinogen is cut.
The session guide suggests naming each scene for what it shows, so scene 3 becomes "Catalytic triad" rather than "Scene 3". It also suggests hiding what a scene doesn't need, since atoms behind an opaque surface still render, and it rates a Quest Comfortable at about 2,500 shown atoms. One copy of 4CHA, about 1,800 atoms with its waters, sits under that line, and both copies together pass it. During the lecture, Spotlight Me makes the instructor's view the shared one, and colored dots on each scene show who has wandered ahead.
Scene Recording in v2.6 captures the full walkthrough with text and audio annotations, and playback runs in Nanome Web. The lecture can then be replayed from a browser the week before the exam.
Lesson 4: crystals and defects as XYZ supercells
A crystallographic CIF holds a crystal's unit-cell dimensions, its space-group symmetry and the atom positions in the asymmetric unit. Nanome's import list files .cif only under mmCIF/PDBx, the Protein Data Bank's macromolecular format, and the docs describe no unit-cell or symmetry expansion. The lesson therefore runs on XYZ, which the list does include.
The course's crystallography software expands a cell from a source such as the Crystallography Open Database into a supercell and exports it as XYZ. A second supercell with a vacancy or an interstitial loads beside the perfect one, and students find the defect by comparing the two.
Who does what: headsets and browsers
Since v2.5, web and XR users share one live session, and a browser user can follow a headset user's view.
- Lesson 1: headset students build and minimize; browser students follow and keep the table of angles and energies.
- Lesson 2: a headset student drives the edit and the fit; browser students edit ligands in the web app's sketch tool and propose the next change.
- Lesson 3: the instructor spotlights, and everyone follows from either device.
- Lesson 4: browser students turn the supercells on their own screens; headset students scale them up and look down the lattice planes.
Running a class where some students have no headset, plus comfort and accessibility, is covered in teaching students without VR headsets. The classroom license guide sizes the seat count.
More material
- nanome.ai/edu: the academic license and the features it includes.
- help.nanome.ai: the docs, including the session guide for planning, permissions and comfort.
- youtube.com/nanome: video walkthroughs of the same tools.
FAQ
Is there a Krebs cycle module?
No. Nanome ships no premade modules, and the cycle itself is a 2D diagram that works best on a slide. The enzymes in it do fit: citrate synthase (1CSC) loads by PDB ID, and a scene per enzyme turns the cycle into a sequence of real structures.
Does Nanome suit IB chemistry, chemical engineering or materials science?
It suits the molecular parts of each. IB bonding and molecular geometry map onto Lesson 1, and materials courses use the XYZ supercell route in Lesson 4. Where a chemical engineering course works at the scale of flowsheets or fluid flow, Aspen Plus, COMSOL and Fluent stay the right tools.
Is there a library of teaching molecules?
No. Structures come from the RCSB PDB by ID, from PubChem as downloaded SDF files, from SMILES strings that MARA turns into 3D structures, or from the Builder.
Can each student group work on its own copy?
Yes. The session guide gives each group its own workspace when they need to change things, and the prepared workspace stays at Viewer, so the original stays as it was built.