Explainers
Answers to common questions about molecular visualization, drug discovery software, XR, and AI copilots for chemistry, and where Nanome fits alongside the tools teams already use.
- How to set up Nanome on a class set of Quest headsetsOctober 13, 2026Setting up Nanome on classroom Quest headsets: install it through an MDM or the Meta Store, assign seats at home.nanome.ai, and sign students in by device code.
- How to get MARA, Nanome's AI copilot, and what it can and can't runOctober 13, 2026MARA runs in app.nanome.ai and comes with every Nanome seat, free Starter included. Credits per plan, docking and protein-prep limits, custom tools, private hosting.
- How much Nanome costs, from one academic seat to a full classroomOctober 13, 2026An academic Nanome seat is $250 a year, with 2 free seats for every 8 bought. Worked totals from 1 seat to a department, what a seat includes, and the terms.
- Nanome Classic and Nanome v2: what's different and where each feature livesOctober 13, 2026Nanome (v2) is the current app, Nanome Classic (v1.24) still runs, and both sign in to one Nanome account. A feature map, a naming guide and the Stacks fix.
- Per user or per headset: how many Nanome licenses a classroom needsOctober 13, 2026A Nanome seat is assigned to one person's account and works on any headset or browser they sign in from. Worked sizing examples for shared classroom headsets.
- Which file formats Nanome opens, and how it handles bonds, crystals and trajectoriesOctober 13, 2026Nanome opens PDB, mmCIF, SDF, XYZ and MD trajectories (GRO, XTC, TRR, DCD), and MOL2 via MARA. How it handles bonds, small-molecule CIFs, frames and size limits.
- Paying for Nanome by card or purchase order, and how renewals workOctober 13, 2026Self-serve seats go by card; departments and companies pay by quote and PO, invoiced in USD on 30-day terms. Supplier paperwork, renewals and cancelling.
- Is Nanome free? The free account, the 14-day trial and a first sessionOctober 13, 2026Yes. A free Nanome account opens the browser app on the Starter plan, and new accounts get a 14-day Full trial with no card or headset. What each tier includes.
- Nanome network requirements, data handling and security reviews for IT teamsOctober 13, 2026Nanome needs outbound HTTPS on port 443 to *.nanome.ai and *.nanome.com, and Classic adds collaboration and plugin ports. Student data, SSO and security reviews.
- Which VR headsets work with Nanome, and which to buy for a classroomOctober 13, 2026Nanome runs on Meta Quest 3 and 3S, Galaxy XR, Vision Pro (beta) and PCVR, and in a browser with no headset. A device matrix for Nanome and Nanome Classic.
- Teaching chemistry and biology in VR: what fits, and four lessons to build in NanomeOctober 13, 2026Nanome fits course topics at the molecular and atomic scale. Four lessons built from workspaces and scenes: VSEPR, ligand binding, an active site and crystals.
- Can students without a VR headset join a VR chemistry class?October 13, 2026Yes. Students in headsets and on laptops join one live Nanome session, and the browser suits anyone who would rather skip the headset. How to run a mixed class.
- Tools for protein structure analysisSeptember 24, 2026The best tools for protein structure analysis, from PyMOL and ChimeraX to Nanome's interactive 3D and XR inspection with MARA agents.
- VR tools for molecular modelingSeptember 24, 2026VR tools for molecular modeling let you build and study molecules in 3D. Nanome is the purpose-built VR/XR platform, with a web app too.
- The best tools for structure-based drug designSeptember 22, 2026The best tools for structure-based drug design, from Schrödinger and MOE to Nanome and MARA for collaborative visualization and AI-run docking.
- The best free molecular visualization softwareSeptember 22, 2026The best free molecular visualization software, from PyMOL and ChimeraX to Nanome's free browser seat for 3D structures.
- The best molecular visualization tools in 2026September 22, 2026The best molecular visualization tools in 2026, from PyMOL and ChimeraX to Nanome's collaborative XR and AI copilot.
- The best molecular modeling softwareSeptember 22, 2026The best molecular modeling software depends on your task. Nanome lets you build, edit, and minimize structures in 3D and XR.
- Running AlphaFold and Boltz-2 in a molecular workflowSeptember 17, 2026How to run AlphaFold in a workflow with Boltz-2 structure prediction, then assess confidence and visualize the result in 3D and XR with Nanome and MARA.
- The best AI tools for drug discoverySeptember 17, 2026The best AI tools for drug discovery, by category, plus how Nanome and MARA run them in plain English.
- The best cheminformatics tools for drug discovery teamsSeptember 17, 2026The best cheminformatics tools for drug discovery teams: RDKit, KNIME, CDD Vault, Schrodinger, and Nanome with MARA in plain English.
- Spatial computing for pharmaceutical researchSeptember 17, 2026Spatial computing for pharmaceutical research: Nanome runs immersive 3D structure review and MARA tools across headsets and the web.
- Natural language interfaces for molecular modelingSeptember 15, 2026Natural language molecular modeling with Nanome and MARA: type a plain-English request, watch the real tool run, and see results in 3D or XR.
- Software for visualizing molecular dynamics trajectoriesSeptember 15, 2026The best software for molecular dynamics trajectory visualization covers playback, RMSD, and per-frame analysis. Nanome does all 3 with MARA.
- How to share a 3D molecular structure with your teamSeptember 15, 2026Sharing a 3D molecular structure with a colleague: a workspace link carries the saved view, representations and labels, so nothing gets rebuilt.
- How to present computational results to an experimental teamSeptember 15, 2026How computational chemists get a docked pose, an MD trajectory or a packing difference across to a bench team, and when a plot is the better medium.
- Tools for visualizing protein-ligand interactionsSeptember 10, 2026The best protein-ligand interaction visualization tools, from PyMOL to Nanome's interactive 3D and XR inspection with MARA.
- How Nanome is different from VMDSeptember 10, 2026A fair VMD alternative guide: where VMD leads on MD trajectories and scripting, and where Nanome adds multiplayer, XR, and its MARA AI copilot.
- How to run an SAR meeting on a 3D structureSeptember 10, 2026An SAR meeting decides what to make next. How to run one on a live 3D structure: scenes as the agenda, a shared session, and a record that outlives the room.
- How Nanome is different from UCSF ChimeraXSeptember 10, 2026A fair look at Nanome as a ChimeraX alternative: real-time multiplayer, native XR, an AI copilot, and a web app that opens the same files.
- How Nanome is different from MOESeptember 8, 2026A fair MOE alternative guide: where the Molecular Operating Environment fits, and where Nanome adds multiplayer XR and the MARA AI copilot.
- How Nanome is different from BIOVIA Discovery StudioSeptember 8, 2026A Discovery Studio alternative for teams who want real-time multiplayer, native XR, and a plain-English AI copilot behind their firewall.
- How Nanome is different from PyMOLSeptember 8, 2026Nanome is a collaborative, XR-native alternative to PyMOL with an AI copilot that runs docking and structure tools from plain English.
- How Nanome is different from Schrödinger MaestroSeptember 8, 2026A Schrödinger Maestro alternative? Nanome is a collaborative, XR-native platform with an AI copilot, and it integrates with Schrödinger LiveDesign.
- MCP servers for cheminformatics and drug discoverySeptember 3, 2026MCP server for cheminformatics and drug discovery: Nanome exposes docking, structure prediction, and analysis to an LLM behind your firewall.
- An AI copilot for drug discovery workflowsSeptember 3, 2026MARA is Nanome's AI copilot for drug discovery workflows: plain-English orchestration of docking, co-folding, ADMET, and structure prediction.
- Agentic AI for computational chemistrySeptember 3, 2026Agentic AI for computational chemistry: how Nanome's MARA plans and runs real scientific tools from plain English, behind your firewall.
- Software for molecular docking visualizationSeptember 1, 2026The best software for molecular docking visualization lets you rank poses and inspect protein-ligand interactions in 3D. Nanome adds XR and team review.
- The best molecular visualization toolsSeptember 1, 2026The best molecular visualization tools, from PyMOL and ChimeraX to Nanome's collaborative XR and AI copilot.
- Software for computational antibody designSeptember 1, 2026The best antibody design software for CDR analysis, numbering, structure prediction, and de novo design, with Nanome and MARA agents.
- Drug discovery software for computational chemistrySeptember 1, 2026Top drug discovery software for computational chemistry, plus how Nanome and MARA tie your comp-chem stack together with AI.
- How to visualize proteins in VRAugust 31, 2026How to visualize proteins in VR with Nanome: pick a headset, load a PDB or SDF structure, choose representations, then collaborate or run MARA tools.
- How to view PDB files in 3D, and the tools that do it wellAugust 31, 2026The best software for viewing PDB files in 3D: PyMOL, ChimeraX, Mol*, and Nanome, which opens PDB and SDF in a browser or XR.
- Molecular visualization for structural biologistsAugust 31, 2026Molecular visualization for structural biology: how Nanome pairs with PyMOL, ChimeraX, and Coot for immersive 3D review of PDB and mmCIF structures.
- VR for medicinal chemistsAugust 31, 2026VR for medicinal chemistry, explained. How medicinal chemists use Nanome to review SAR, ligands, and pockets in immersive 3D.
- Collaborative drug discovery software for remote teamsAugust 31, 2026Collaborative drug discovery software for remote teams: Nanome runs real-time shared molecular sessions across web and XR, behind your firewall.
- The molecular PowerPoint: what a modern molecular presentation looks likeAugust 31, 2026A molecular presentation shows a 3D structure to the people who act on it. How Nanome builds one from scenes, and when a slide is still the right call.
- How to analyze protein-ligand interactionsAugust 31, 2026How to analyze protein-ligand interactions in Nanome: load a complex, show hydrogen bonds and contacts in 3D, and get a MARA report.