Athanor by arbastro
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Help center

Athanor help center

Step-by-step guides with pictures for every part of Athanor, from your first structure to plugins and the MCP server.

Getting startedDraw your first structureSwitching from ChemDrawSwitching from ChemDraw to AthanorNMR and spectraHow to predict a 1H NMR spectrumDrawing basicsHow to insert a structure by name, SMILES or CAS numberFiles and formatsHow to export a figure or structure filePluginsBuild your first pluginMCP serverConnect your AI assistant

Every section

Getting startedOpen Athanor, draw your first structure, find your way round the window and learn where your work is kept. No account needed.10 pagesSwitching from ChemDrawOpen your CDX and CDXML files, find ChemDraw's commands under their Athanor names, keep your journal style sheets and paste into Office.8 pagesDrawing basicsBonds, chains, atoms, rings, erasing, cleaning up, inserting by name, drawing with a pen and moving around the canvas.13 pagesAtoms, bonds and ringsCharges and lone pairs, abbreviations, stereochemistry, projections, aromatic rings, organometallic bonds and the other details of a structure.19 pagesText and labelsCaptions, atom labels, chemistry formatting as you type, equations, compound numbers and text that turns into structures.7 pagesSelection and arrangingSelect, move, flip, align, group, hide, lock and find things on the page, and the Layers panel.12 pagesStyles and journal formatsFormat structures for ACS, RSC, Wiley, Nature and other journals, set bond length and fonts, name document colors and use a brand kit.5 pagesReactions and arrowsReaction arrows, tidy schemes, balanced equations, stoichiometry tables, atom mapping, catalytic cycles and reaction review tools.12 pagesMechanismsCurved arrows and lone pairs, Build mechanism, the Timeline and its advanced mode, energy diagrams, and exporting a mechanism as video.7 pagesPrediction and planningPredicted products as you draw, retrosynthesis routes back to buyable starting materials, hazards and stock, and how safety screening works.3 pagesNMR and spectraPredicted 1H and 13C NMR with journal text, imported spectra, peak picking and integration, and comparing a measured spectrum with the prediction.10 pagesNames, properties and checksName structures, calculate properties, check valence and stereo, copy identifiers and score synthetic accessibility.6 pagesResearch and lab recordsCompound and SAR tables, R-group enumeration, notebook entries, compound registration, literature search, procedures and Python scripts.7 pagesCompound info and the LibraryAbout 1,200 curated compounds, templates, guides, icons and community uploads, plus Compound info for what you drew.7 pages3D and orbitalsTurn a drawing into 3D, measure it, show orbitals, Hückel and MO diagrams, view proteins and export 3D files.8 pagesBiochemistryBuild DNA, RNA and peptides from a sequence, FASTA or HELM, work with monomers, transform sequences, align them and draw plasmid maps.5 pagesFigures, diagrams and documentsShapes and the pen, brackets and frames, glassware and safety labels, tables, charts, flowcharts, physics diagrams, pictures and document pages.16 pagesSlides and presentingTurn frames into slides, present full screen with a pen, run live polls and record a walkthrough.3 pagesFiles and formatsOpen ChemDraw, MOL, SDF and SMILES; export figures for papers; copy into Office; the .athanor format; backups.13 pagesAI assistant (arbastro Intelligence)Ask in plain words and the assistant draws, converts, animates and checks on the canvas. What it can do, what is sent, credits and your own key.6 pagesTeachingInteractive problem sets with automatic grading, a version per student, classes, labs, flashcards and LMS connections.10 pagesCollaboration and sharingInvite people with roles, share links with passwords and expiry, publish to the web, comment, suggest, branch, review and see version history.4 pagesAccounts, plans and billingSign in with your arbastro account, compare Free and the Suite plans, AI credits and storage, student verification and organizations.2 pagesWorkspace and settingsArrange panels, the Properties panel, Settings, light and dark themes, distraction-free drawing, accessibility and the desktop app.8 pagesPluginsInstall plugins that add commands, panels, formats and checks, build your own with the plugin API, and publish them to the directory.33 pagesSend to other appsSend a scheme to Google Slides or Notion with your own account; Athanor never sees your password.1 pageMCP serverUse Athanor's chemistry engine from Claude, ChatGPT, Cursor and other assistants. Free, no account.12 pagesCommand lineConvert, name, check and screen structures from a terminal with the same engine as the app. Offline.3 pagesEmbed the editorPut the Athanor editor on your own page and drive it from code. A drop-in path for Marvin JS and Ketcher pages.6 pagesKeyboard shortcutsPress ? in a document for the Controls cheat sheet, or Ctrl+K and search for a command to see its shortcut. Every shortcut can be changed in Settings › Shortcuts. On a Mac, Ctrl is Cmd.2 pagesTroubleshooting and FAQAnswers to common questions and fixes for problems with drawing, files, sync, AI, plugins and the desktop app.8 pagesGlossaryA glossary of the terms used in Athanor and its help center, each with a one-line definition and a link to the page that explains it.1 page

Still stuck?

Read the frequently asked questions, or use Help › Report a problem in the app, which attaches your version and platform. You can also email support.