# Athanor documentation > How to use and build on Athanor, the chemistry editor by arbastro. Every page is also plain Markdown at its own path plus .md. The full text of every page is at /docs/llms-full.txt. ## Getting started - [How to open Athanor](https://athanor.arbastro.com/docs/get-started/open-athanor.md): Start Athanor at athanor.arbastro.com/app or install the Windows app, then draw your first structure in a couple of minutes. No account needed. - [How to install Athanor on Windows](https://athanor.arbastro.com/docs/get-started/install-on-windows.md): Download and install Athanor for Windows 10 and 11. It updates itself, opens .athanor, CDX and CDXML files by double-click, and works offline. - [Draw your first structure](https://athanor.arbastro.com/docs/get-started/draw-your-first-structure.md): A two-minute tutorial: draw ethanol with the Bond tool, change an atom to oxygen, add a benzene ring, clean it up and export a picture. - [The Athanor window](https://athanor.arbastro.com/docs/get-started/the-window.md): Where everything is in Athanor: the toolbar, the contextual bar, the panels, the tab bar, the Main menu, the issues badge and Search everything. - [How to start a new document from Home](https://athanor.arbastro.com/docs/get-started/start-from-home.md): Home lists your documents and every way to start one: a blank drawing, document pages, a template, an animation, a problem set or practice. - [How to find any command with Search everything](https://athanor.arbastro.com/docs/get-started/search-everything.md): Press Ctrl+K to search every command, tool and compound, see each shortcut, and ask the assistant. The Main menu lists the same commands. - [How to find out what a button does](https://athanor.arbastro.com/docs/get-started/what-is-this-button.md): Hold Alt and point at any control in Athanor to see what it does, its shortcut and where it is in the menus. Or use Help › What is this button? - [How to take the tour with Athy](https://athanor.arbastro.com/docs/get-started/take-the-tour.md): Athy, the Athanor guide, walks you through the window step by step while you try each part. Start any time from Help › Take the tour with Athy. - [How to work with tabs](https://athanor.arbastro.com/docs/get-started/tabs.md): Each Athanor document opens in its own tab. New tab Ctrl+T, close Ctrl+W, reopen the last one Ctrl+Alt+T, and switch with Ctrl+Tab. - [Where your work is saved](https://athanor.arbastro.com/docs/get-started/where-your-work-is-saved.md): Athanor has no save button. Every change is kept as you make it, on this device and, when you are signed in, in your arbastro account. ## Switching from ChemDraw - [Switching from ChemDraw to Athanor](https://athanor.arbastro.com/docs/switch-from-chemdraw/overview.md): Everything a ChemDraw user needs on day one: open CDX and CDXML, the same tools under new letters, journal styles, and what works differently. - [How to open CDX and CDXML files](https://athanor.arbastro.com/docs/switch-from-chemdraw/open-chemdraw-files.md): Open .cdx and .cdxml files in Athanor, in your browser or on Windows. Structures, arrows and text stay editable, not pictures. - [ChemDraw commands and their Athanor names](https://athanor.arbastro.com/docs/switch-from-chemdraw/chemdraw-menu-names.md): Where ChemDraw's Clean Up Structure, Check Structure, Convert Name to Structure and other commands are in Athanor, with their shortcuts. - [Keyboard shortcuts for ChemDraw users](https://athanor.arbastro.com/docs/switch-from-chemdraw/chemdraw-shortcuts.md): Element letters, tool keys and editing shortcuts in Athanor compared with ChemDraw hotkeys, and how to turn on the ChemDraw classic set. - [How to use your ChemDraw style sheets](https://athanor.arbastro.com/docs/switch-from-chemdraw/chemdraw-style-sheets.md): Apply ACS Document 1996 and the other ChemDraw journal styles in Athanor, and save your document type as a ChemDraw style sheet (.cds). - [How to import your ChemDraw templates and libraries](https://athanor.arbastro.com/docs/switch-from-chemdraw/import-chemdraw-libraries.md): Bring ChemDraw templates (.ctp), documents (.cdx), style sheets (.cds), SVG and SDF files into your Athanor library so they are one drag away. - [How to send a file to someone using ChemDraw](https://athanor.arbastro.com/docs/switch-from-chemdraw/send-files-to-chemdraw-users.md): Export your drawing as ChemDraw CDXML or CDX, or copy it as CDXML, so a ChemDraw user can open it and keep editing. - [What works differently from ChemDraw](https://athanor.arbastro.com/docs/switch-from-chemdraw/what-is-different.md): No save button, problems flagged rather than silently fixed, actions beside your selection, tabs, and live collaboration. What to expect. ## Drawing basics - [How to draw bonds and chains](https://athanor.arbastro.com/docs/drawing/draw-bonds-and-chains.md): Use the Bond tool (D) to click out bonds one at a time, and the chain variant (G) to drag out a zigzag carbon chain of any length, counted as you go. - [How to make a double or triple bond](https://athanor.arbastro.com/docs/drawing/change-bond-order.md): Change a single bond to a double or triple bond in Athanor: click it with the Bond tool to raise its order, or point at it and press 2 or 3. - [How to draw wedge and hash bonds](https://athanor.arbastro.com/docs/drawing/wedge-and-hash-bonds.md): Draw wedge (U), hash (H), wavy (Y) and the other stereo bonds in Athanor, and watch the R or S label change as you draw. - [How to change an atom to another element](https://athanor.arbastro.com/docs/drawing/change-atoms.md): Point at an atom and press its letter, press Enter to type any label, or pick an element for the selected atoms from the Periodic table. - [How to add rings](https://athanor.arbastro.com/docs/drawing/add-rings.md): Press R for rings: J for benzene, 3 to 8 for cycloalkanes, and Insert › Ring size for any size from 3 to 30. Click a bond to fuse a ring. - [How to erase atoms, bonds and objects](https://athanor.arbastro.com/docs/drawing/erase.md): Remove atoms, bonds, arrows and shapes in Athanor with the Erase tool (E), the Delete key on a selection, or a quick scribble with a pen. - [How to undo, redo and replay a drawing](https://athanor.arbastro.com/docs/drawing/undo-and-replay.md): Undo with Ctrl+Z, redo with Ctrl+Shift+Z, step back through every edit in Version history, and replay a drawing stroke by stroke. - [How to clean up a structure](https://athanor.arbastro.com/docs/drawing/clean-up-structure.md): Clean up structure (Ctrl+Shift+K) redraws bond lengths and angles evenly without changing the chemistry, like ChemDraw's Clean Up Structure. - [How to insert a structure by name, SMILES or CAS number](https://athanor.arbastro.com/docs/drawing/quick-insert.md): Press / in Athanor and type a name, SMILES string or CAS number. Quick insert places the structure on the canvas, drawn and ready to edit. - [How to paste SMILES as a structure](https://athanor.arbastro.com/docs/drawing/paste-smiles.md): Use Edit › Paste SMILES… or paste a SMILES string into Quick insert to get a drawn, editable structure in Athanor. - [How to draw chemistry with a pen or stylus](https://athanor.arbastro.com/docs/drawing/draw-with-a-pen.md): Draw with a stylus in Athanor and your strokes become bonds, chains and rings. A scribble erases, and Pen only stops your palm from drawing. - [How to zoom and move around the canvas](https://athanor.arbastro.com/docs/drawing/zoom-and-pan.md): Zoom in with Ctrl+=, out with Ctrl+-, fit everything with Shift+1, fit the selection with Shift+2, 100% with Ctrl+0, and use the minimap on big drawings. - [How to use grids, paper and guides](https://athanor.arbastro.com/docs/drawing/grids-paper-and-guides.md): Show a grid, pick grid, dot, lined, isometric or hex paper, drag guides from the rulers, and snap to angles and smart guides, all from the View menu. ## Atoms, bonds and rings - [How to add charges, radicals and lone pairs](https://athanor.arbastro.com/docs/structures/charges-radicals-lone-pairs.md): The Charges tool (Q) adds plus and minus, circled charges, lone pairs, radicals, diradicals and partial charges to any atom in Athanor. - [How to use abbreviations like OMe, Boc and Ph](https://athanor.arbastro.com/docs/structures/abbreviations.md): Type a group label such as OMe or Ph on an atom, draw it out with Expand labels, contract atoms back to a label, and define an abbreviation of your own. - [How to show R and S, E and Z labels](https://athanor.arbastro.com/docs/structures/stereochemistry-labels.md): View › Show stereochemistry labels every stereocenter R or S and every stereo double bond E or Z in Athanor, worked out by the CIP priority rules. - [How to draw chair, Newman, Haworth and Fischer projections](https://athanor.arbastro.com/docs/structures/projections.md): The Ring tool in Athanor draws cyclohexane chairs (with or without hydrogens), Newman projections, Haworth sugars and Fischer projections. - [How to list every stereoisomer of a structure](https://athanor.arbastro.com/docs/structures/stereoisomers.md): Object › Chemistry › Stereoisomers lists every stereoisomer of the selected structure with its R/S labels, meso forms counted once, ready to place. - [How to list the tautomers of a structure](https://athanor.arbastro.com/docs/structures/tautomers.md): Object › Chemistry › Tautomers lists the forms one proton shift apart and further, ordered by rule of thumb, and places the ones you pick. - [How to choose undefined stereocenters](https://athanor.arbastro.com/docs/structures/choose-undefined-stereocenters.md): Choose undefined stereocenters proposes wedges for every stereocenter you have not drawn; reject them and hashes are proposed instead. - [How to mark stereo groups (AND, OR, absolute)](https://athanor.arbastro.com/docs/structures/stereo-groups.md): Mark drawn stereocenters as absolute, AND (a racemic mixture) or OR (one of the two, unknown which) from the Object menu, with a label on each center. - [How to convert between Lewis structures and bond-line](https://athanor.arbastro.com/docs/structures/lewis-and-bond-line.md): Convert to Lewis structure draws every atom, hydrogen and lone pair; Convert to bond-line puts the skeletal drawing back. - [How to tilt a ring into perspective](https://athanor.arbastro.com/docs/structures/perspective-tilt.md): Tilt into perspective draws a ring as if seen from the side, for Haworth projections and chair-like views. Flatten to face-on undoes it. - [How to draw a mixture](https://athanor.arbastro.com/docs/structures/mixtures.md): Make mixture puts the selected structures in one bracket with their proportions, molar or by mass, and shows the mole and weight percent of each. - [How to turn a structure in space with the Perspective tool](https://athanor.arbastro.com/docs/structures/perspective-tool.md): The Perspective tool turns a drawn structure in space by dragging, like ChemDraw's Structure Perspective. Every stereocenter keeps its R or S at any angle. - [How to highlight functional groups](https://athanor.arbastro.com/docs/structures/functional-groups.md): View › Show functional groups colors each functional group on the page and names it in a legend under the drawing. - [How to draw aromatic rings with circles](https://athanor.arbastro.com/docs/structures/aromatic-rings.md): Show aromatic rings as circles for the whole page from the View menu, or per structure in Properties, without changing the chemistry. - [How to show terminal carbons and atom numbers](https://athanor.arbastro.com/docs/structures/display-carbons-and-atom-numbers.md): Show the CH3 at chain ends and number every atom, for the whole page from the View menu or for one structure under Display in Properties. - [Atom properties](https://athanor.arbastro.com/docs/structures/atom-properties.md): Select one atom to set its label and charge, make it a query atom for searches, and read its VSEPR shape: steric number, AXE, geometry and hybridization. - [How to draw haptic bonds](https://athanor.arbastro.com/docs/structures/haptic-bonds.md): Haptic bond joins a metal to a ring or double bond with one bond from its center, such as an η6 benzene complex or the two rings of ferrocene. - [How to draw repeating units](https://athanor.arbastro.com/docs/structures/repeating-units.md): Compress repeating units draws a run of identical units once, in brackets, with its count; Expand repeating units draws it out in full again. - [How to label an isotope (deuterium, carbon-13)](https://athanor.arbastro.com/docs/structures/isotopes.md): Set an atom's isotope by typing D, T or 13C on it, or in Properties › Isotope. The label, formula, masses, SMILES and MOL files all carry it. ## Text and labels - [How to add text and captions](https://athanor.arbastro.com/docs/text/add-text.md): The Text tool (T) adds captions and notes in Athanor. Bold Ctrl+B, italic Ctrl+I, and align left, center or right with Ctrl+Shift+L, C or R. - [How to type atom labels like CO2Et or NHBoc](https://athanor.arbastro.com/docs/text/atom-labels.md): Click an atom with the Text tool, or point at it and press Enter, and type a label such as CO2Et, NHBoc or Cl. Labels Athanor knows count as real atoms. - [How to turn a name or SMILES in text into a structure](https://athanor.arbastro.com/docs/text/text-to-structure.md): Select a text block holding a name or SMILES and press Ctrl+Shift+N. Convert text to a structure replaces the text with the drawn structure. - [How to insert an equation](https://athanor.arbastro.com/docs/text/equations.md): Insert › Equation… (Alt+=) typesets an equation from LaTeX or the palettes, with a live preview, and can copy it as LaTeX or MathML. - [How to format chemistry as you type](https://athanor.arbastro.com/docs/text/format-chemistry-as-you-type.md): Format chemistry as you type turns H2SO4 into H₂SO₄ and Fe3+ into Fe³⁺ in text as you type it. It is on to start; turn it off from Edit › Text. - [How to write the formula as a caption](https://athanor.arbastro.com/docs/text/formula-caption.md): Write the formula as a caption puts the molecular formula of the selected structure under it as text you can move and edit. - [How to number compounds](https://athanor.arbastro.com/docs/text/number-compounds.md): Edit › Number compounds puts a bold number under each structure in reading order, left to right and top to bottom. ## Selection and arranging - [How to select atoms, structures and objects](https://athanor.arbastro.com/docs/arrange/select.md): The Select tool (V) in Athanor: a click takes a whole structure, Marquee (M) only the atoms it covers, and Lasso (L) whatever you draw around. - [How to select every atom or object of the same kind](https://athanor.arbastro.com/docs/arrange/select-same.md): Select same widens the selection to every atom of the same element, every bond of the same type, or every object of the same kind and color. - [How to align and space structures evenly](https://athanor.arbastro.com/docs/arrange/align-and-distribute.md): Align left edges, right edges, tops, bottoms or centers, and space structures evenly across or down, with Object › Align and space or Ctrl+Shift+Alt keys. - [How to find a structure on the page](https://athanor.arbastro.com/docs/arrange/find-and-replace.md): Find and replace (Ctrl+F) searches the page for a structure given as SMILES, as a substructure or an exact match, and steps through or selects every hit. - [The Layers panel](https://athanor.arbastro.com/docs/arrange/layers-panel.md): Layers lists everything on the page in Athanor. Click to select, double-click to name, search, hide, lock and group structures, arrows, text and shapes. - [How to move, rotate and flip](https://athanor.arbastro.com/docs/arrange/move-rotate-and-flip.md): Drag to move, rotate by 90° or 180° from the selection bar, and flip horizontally or vertically from the Object menu. - [How to group and ungroup](https://athanor.arbastro.com/docs/arrange/group-and-ungroup.md): Group (Ctrl+G) keeps several objects together so they move and select as one; Ungroup (Ctrl+Shift+G) splits them again. - [How to bring to front or send to back](https://athanor.arbastro.com/docs/arrange/drawing-order.md): Bring to front and Send to back, with the ] and [ keys, change which object draws on top when objects overlap on the page. - [How to duplicate, copy and paste](https://athanor.arbastro.com/docs/arrange/duplicate-copy-and-paste.md): Duplicate (Ctrl+Shift+D), copy and paste, paste in place (Ctrl+Shift+V), and Copy as for SMILES, InChI, InChIKey, chemfig, mhchem, molfile and CDXML. - [How to copy and paste style](https://athanor.arbastro.com/docs/arrange/copy-and-paste-style.md): Copy style takes the colors, line widths and text style of the selection; Paste style puts them on another selection without changing its content. - [How to hide and lock objects](https://athanor.arbastro.com/docs/arrange/hide-and-lock.md): Hide selection (Ctrl+Shift+H) takes objects out of view and Lock or unlock stops them being moved; View › Show everything hidden brings them back. - [How to combine shapes](https://athanor.arbastro.com/docs/arrange/combine-shapes.md): Combine shapes joins two or more closed shapes into one: Union, Subtract, Intersect or Exclude, from the Object menu or with Alt+Shift shortcuts. ## Styles and journal formats - [How to pick a journal style](https://athanor.arbastro.com/docs/styles/journal-presets.md): Document type in Properties sets the drawing standard of the whole document, such as ACS Document 1996: bond length, line widths, fonts and spacing. - [Document settings](https://athanor.arbastro.com/docs/styles/document-settings.md): With nothing selected, Properties shows the document settings: document type, bond length, layout and measurements. - [How to use document colors](https://athanor.arbastro.com/docs/styles/document-colors.md): A document color has a value for print and one for the projector. Shapes that use it change with the mode, so one document works on paper and on slides. - [How to make and apply a brand kit](https://athanor.arbastro.com/docs/styles/brand-kit.md): A brand kit carries document colors, text styles, the drawing standard and a logo. Make one from a document, apply it to another, or import a kit file. - [How to preview for color vision deficiency](https://athanor.arbastro.com/docs/styles/color-vision-previews.md): View › Color vision previews the page as seen with protanopia, deuteranopia, tritanopia or achromatopsia, to check a figure still reads. ## Reactions and arrows - [How to draw a reaction scheme](https://athanor.arbastro.com/docs/reactions/draw-a-reaction.md): Draw reactants, a reaction arrow (W) and conditions above it, then the products, or insert a whole reaction as reaction SMILES with Quick insert. - [Reaction arrow types](https://athanor.arbastro.com/docs/reactions/arrow-types.md): Every reaction arrow in Athanor and what it means: forward, equilibrium, resonance, retrosynthetic, curly, fishhook, no reaction, dashed and plain. - [Product prediction and planning](https://athanor.arbastro.com/docs/reactions/predict-and-plan.md): Signed in, Athanor predicts the products of the reaction you draw and plans routes back to buyable starting materials, every route screened. - [How to tidy a reaction scheme](https://athanor.arbastro.com/docs/reactions/clean-up-reaction.md): Clean up reaction (Ctrl+Shift+X) lines up the reactants, the arrow and the products of a reaction scheme and evens out the spacing between them. - [How to draw a catalytic cycle](https://athanor.arbastro.com/docs/reactions/catalytic-cycles.md): Make catalytic cycle (Ctrl+Alt+Y) puts the selected intermediates on a circle with arrows. Name steps, make them reversible, tidy or reverse it. - [How to make a stoichiometry table](https://athanor.arbastro.com/docs/reactions/stoichiometry-table.md): The stoichiometry table lists each reactant and product with MW, equivalents, mmol and mass, and gives the theoretical yield from the limiting reagent. - [How to balance a chemical equation](https://athanor.arbastro.com/docs/reactions/balance-an-equation.md): Balance a typed equation finds the coefficients, in acidic or basic solution, and names what is oxidized and reduced. Insert puts it on the page. - [How to map reaction atoms](https://athanor.arbastro.com/docs/reactions/atom-mapping.md): Map reaction atoms automatically numbers each reactant atom and the product atom it becomes, and marks the bonds that form. Pairs can be mapped by hand. - [How to review a reaction for green chemistry](https://athanor.arbastro.com/docs/reactions/green-chemistry.md): Green chemistry reports the atom economy of each step and flags solvents by the CHEM21 guide and hazards in what is written, step by step. - [How to review a route for scale-up](https://athanor.arbastro.com/docs/reactions/scale-up-review.md): Scale-up review flags steps worth a second look at scale, such as energetic groups, alkylating agents and residual metals, from the conditions as written. - [How to predict where substitution goes on a ring](https://athanor.arbastro.com/docs/reactions/where-substitution-goes.md): Where substitution goes marks the expected and minor positions for electrophilic aromatic substitution on a benzene ring, from the directing rules. - [How to sprout a reaction from a structure](https://athanor.arbastro.com/docs/reactions/sprout-a-reaction.md): Sprout reaction adds an arrow and a copy of the selected structure to its right, ready to edit into the product. ## Mechanisms - [How to draw curved arrows for a mechanism](https://athanor.arbastro.com/docs/mechanisms/draw-curved-arrows.md): Draw electron-pushing curly arrows and single-electron fishhooks in Athanor, from lone pairs and bonds to the atoms and bonds the electrons go to. - [How to animate a reaction mechanism](https://athanor.arbastro.com/docs/mechanisms/animate-a-mechanism.md): Draw the curved arrows and press Animate my arrows: Athanor builds the next steps and plays them as a film, bonds breaking and forming along each arrow. - [How to use the Timeline's advanced mode](https://athanor.arbastro.com/docs/mechanisms/timeline-advanced-mode.md): The Timeline's advanced mode shows each step's timing and easing, and a Keyframes view with a track for every structure that changes. - [How to add an energy diagram that follows the animation](https://athanor.arbastro.com/docs/mechanisms/energy-diagram.md): Add an energy profile beside an animated mechanism in Athanor; a marker follows the playhead through the transition state and each step. - [Mechanism problem templates (SN1, SN2, E1, E2)](https://athanor.arbastro.com/docs/mechanisms/mechanism-presets.md): Problem sets have mechanism templates for SN1, SN2, E1 and E2, carbocation shifts, proton transfer, cyanohydrin and hydride addition, graded on the arrows. - [How to export a mechanism as a video, GIF or slides](https://athanor.arbastro.com/docs/mechanisms/export-an-animation.md): Export an Athanor animation as MP4, GIF, a PowerPoint deck, animated SVG or Lottie, at 720p, 1080p or 4K, with a transparent, white or black background. - [How to present a mechanism step by step in a lecture](https://athanor.arbastro.com/docs/mechanisms/present-a-mechanism.md): Present plays a mechanism one step at a time, full screen, with a laser pointer, pen, captions and the energy diagram. No account needed. ## Prediction and planning - [How Athanor screens structures and routes for safety](https://athanor.arbastro.com/docs/prediction/safety-screening.md): Generated structures and routes are checked against the Chemical Weapons Convention schedules and the Australia Group list, in the app and on the server. - [How to export or delete your prediction feedback](https://athanor.arbastro.com/docs/prediction/prediction-feedback.md): Your approvals, rejections and edits on predictions can be exported, or deleted from this computer, from Help › Prediction feedback. - [How Athanor's chemistry predictions work](https://athanor.arbastro.com/docs/prediction/how-predictions-work.md): The arbastro chemistry models behind product prediction, routes, mechanisms, handwriting, pictures and NMR, where they run, and how confidence is shown. ## NMR and spectra - [How to predict a 1H NMR spectrum](https://athanor.arbastro.com/docs/nmr/predict-1h-nmr.md): Select a structure and choose Predict 1H NMR. Athanor predicts each proton shift with its range, multiplicity, J and integral, as a spectrum and a table. - [How to predict a 13C NMR spectrum](https://athanor.arbastro.com/docs/nmr/predict-13c-nmr.md): Select a structure and choose Predict 13C NMR. Athanor predicts each carbon shift with its range and its CH3, CH2, CH or C type, as a spectrum and a table. - [The NMR window](https://athanor.arbastro.com/docs/nmr/nmr-window.md): Everything in the Predicted NMR window: the 1H and 13C tabs, field strength, solvent, integrals, zoom, the table and the buttons under it. - [How to copy NMR data as journal text](https://athanor.arbastro.com/docs/nmr/copy-nmr-journal-text.md): Copy as journal text writes the predicted 1H or 13C NMR data in the line format journals use, marked as predicted, ready to paste into a paper or report. - [How to label a structure with its chemical shifts](https://athanor.arbastro.com/docs/nmr/show-shifts-on-the-structure.md): Show shifts on the structure writes each predicted 1H or 13C shift next to its atom on the drawing. Undo removes them all at once. - [How to put a predicted spectrum on the page and export it](https://athanor.arbastro.com/docs/nmr/insert-a-predicted-spectrum.md): Insert spectrum puts the predicted NMR spectrum on the page as a figure you can export. CSV saves the peak table; JCAMP-DX saves the spectrum itself. - [How to import an NMR, IR or mass spectrum](https://athanor.arbastro.com/docs/nmr/import-a-spectrum.md): Insert › Import spectrum places an NMR, IR, mass or UV-Vis spectrum on the page from a JCAMP-DX file or a zipped Bruker dataset, ready to analyze. - [How to pick peaks and integrate a spectrum](https://athanor.arbastro.com/docs/nmr/analyze-a-spectrum.md): Analyze spectrum picks peaks, integrates, reads multiplets and writes the report line for an imported spectrum, ready to copy or add to the page. - [Diastereotopic protons in a predicted spectrum](https://athanor.arbastro.com/docs/nmr/diastereotopic-signals.md): How Athanor shows diastereotopic CH2 protons in a predicted 1H spectrum: one row each, flagged, with one shift because the difference is not predicted. - [How accurate predicted NMR shifts are](https://athanor.arbastro.com/docs/nmr/nmr-accuracy.md): Athanor's predicted 1H shifts have a typical error of 0.08 ppm and 13C shifts 0.7 ppm on held-out data. What the 90% range means and what is not predicted. ## Names, properties and checks - [How to get the IUPAC name of a structure](https://athanor.arbastro.com/docs/chemistry-tools/name-a-structure.md): Structure to name (Ctrl+Alt+N) copies the IUPAC name of the selected structure and offers to insert it as text under the structure. - [How to calculate molecular weight, logP and other properties](https://athanor.arbastro.com/docs/chemistry-tools/calculate-properties.md): Calculate properties lists formula, exact mass, TPSA, hydrogen bond donors and acceptors, rotatable bonds and Lipinski checks for the selected structure. - [How to check a structure for errors](https://athanor.arbastro.com/docs/chemistry-tools/check-structure.md): Check structure (Shift+K) lists valence and other problems in the selected structure, atom by atom, with a suggestion for each. - [How to copy a structure as SMILES, InChI or a molfile](https://athanor.arbastro.com/docs/chemistry-tools/copy-as-identifiers.md): Edit › Copy as copies the selected structure as SMILES (Ctrl+Alt+C), InChI, InChIKey, a molfile, CDXML, chemfig or an mhchem formula. - [How to name every structure and rename them](https://athanor.arbastro.com/docs/chemistry-tools/name-every-structure.md): Name every structure gives each structure its IUPAC name. Rename structures… numbers them to a pattern such as Compound #, left to right. - [How to score synthetic accessibility](https://athanor.arbastro.com/docs/chemistry-tools/synthetic-accessibility.md): The SA score rates how easy a structure is to make, from 1 (easy) to 10 (hard), using the Ertl and Schuffenhauer method. It is an estimate, not a route. ## Research and lab records - [How to make a compound table](https://athanor.arbastro.com/docs/research/compound-table.md): View › Compound table lists every structure on the page with formula, MW, H-bond donors and acceptors, rotatable bonds, rings, TPSA, Fsp3 and Ro5, as CSV. - [How to make an SAR table](https://athanor.arbastro.com/docs/research/sar-table.md): The SAR table lines up compounds against a core drawn with R1, R2 labels, with activity values from a pasted table, and copies as CSV. - [How to register a compound and its batches](https://athanor.arbastro.com/docs/research/register-a-compound.md): Register compound gives a compound an ID such as ATH-000001 and the drawing a batch number, with its amount, purity, supplier and notes. - [How to search the literature](https://athanor.arbastro.com/docs/research/search-the-literature.md): Search the literature asks OpenAlex, an open index of scholarly papers, in plain words, with most cited and open access filters and an optional AI summary. - [How to turn a procedure into steps](https://athanor.arbastro.com/docs/research/procedure-to-steps.md): Procedure to steps reads an experimental paragraph into numbered steps with reagents, amounts and conditions, and places them as a timeline or flowchart. - [How to run Python scripts with RDKit](https://athanor.arbastro.com/docs/research/python-scripts.md): Run a Python script runs Python with an RDKit subset on this device, with no network. It reads the open document and changes it as one undo step. - [How to enumerate a compound library](https://athanor.arbastro.com/docs/research/enumerate-a-library.md): Enumerate a library applies a reaction to every combination of its building blocks with RDKit, in one or more steps, up to 2,000 combinations. ## Compound info and the Library - [The Library](https://athanor.arbastro.com/docs/library/library.md): Athanor's Library: about a thousand curated compounds, reaction templates, guides and icons to drag onto the page, searchable by name or by structure. - [The Library panel](https://athanor.arbastro.com/docs/library/library-panel.md): The Library panel searches compounds by name, CAS or code, browses categories, and keeps your favorites and recent compounds. Drag one onto the canvas. - [How to search the library](https://athanor.arbastro.com/docs/library/search-the-library.md): Type a name, CAS number, code or SMILES in the Library panel to find compounds; official entries carry the Athanor mark. Drag one onto the canvas. - [The Compound info panel](https://athanor.arbastro.com/docs/library/compound-info-panel.md): Compound info (I) identifies the selected structure: common and systematic names, CAS number, PubChem link, InChI and SMILES, and calculated properties. - [How to start from a template](https://athanor.arbastro.com/docs/library/templates.md): The Templates tab of the Library holds page templates, such as a reaction scheme, two-step synthesis, equilibrium and retrosynthesis, and parts. - [How to use the guides in the Library](https://athanor.arbastro.com/docs/library/guides.md): The Guides tab of the Library holds one-page references you can open beside your work, such as drawing shortcuts, orbitals and how to read an MO diagram. - [How to add icons and illustrations](https://athanor.arbastro.com/docs/library/icons-and-illustrations.md): The Icons tab of the Library has colored, shaded and outlined science art: brushes such as lipid bilayers and DNA strands, glassware and more. ## 3D and orbitals - [How to view a structure in 3D](https://athanor.arbastro.com/docs/3d/3d-view.md): View › 3D view (Shift+D) shows the drawn structure in 3D. Drag to turn it, shift-drag to pan and scroll to zoom; 2D goes back. - [How to label and measure in 3D](https://athanor.arbastro.com/docs/3d/measure-in-3d.md): The 3D view switches the style and shows hydrogens, labels, lone pairs, orbitals, bond angles and symmetry elements, each with a one-key shortcut. - [How to draw orbitals on a structure](https://athanor.arbastro.com/docs/3d/visualize-orbitals.md): Visualize orbitals draws the p orbitals and hybrid lobes on a structure, in two phases, as shapes you can edit. - [How to calculate Hückel π orbitals](https://athanor.arbastro.com/docs/3d/huckel-orbitals.md): Hückel π orbitals solves simple Hückel theory for a structure: each π orbital, its energy in α and β, and the HOMO, LUMO and gap. - [How to insert an MO energy diagram](https://athanor.arbastro.com/docs/3d/mo-diagram.md): Insert MO energy diagram places a schematic molecular orbital diagram with filled levels, the bond order and whether the molecule is paramagnetic. - [How to save a 3D picture, video or model](https://athanor.arbastro.com/docs/3d/export-3d-files.md): From the 3D view, save a PNG of the view, a video of one revolution, the conformer as PDB, or a model for 3D printing (STL, 3MF) and AR (GLB). - [How to view a protein from the PDB or AlphaFold](https://athanor.arbastro.com/docs/3d/protein-structures.md): Open a protein by its PDB id or UniProt accession and see it as a 3D ribbon, colored by structure, with surfaces and a one-press citation. - [How to draw orbitals on a structure](https://athanor.arbastro.com/docs/3d/orbitals-in-2d.md): The Orbitals tool (O) places p, sp3, sp2 and sp orbitals, hybrid sets, pi bonds, s, d and f orbitals on atoms, with their phases shown. ## Biochemistry - [How to build a peptide, DNA or RNA from its sequence](https://athanor.arbastro.com/docs/biochemistry/build-from-a-sequence.md): Build from sequence turns one-letter codes into a peptide, DNA or RNA, drawn as residues or as the full structure, with its formula and molar mass. - [How to open a HELM string](https://athanor.arbastro.com/docs/biochemistry/helm.md): Paste a HELM string into Quick insert and choose Build from HELM. The sequence builder reads back the residues, formula and mass, and inserts it. - [How to browse and add monomers](https://athanor.arbastro.com/docs/biochemistry/monomers.md): Monomers lists the peptide, nucleotide and chemical building blocks Athanor knows, by name or structure, and lets you add your own with attachment points. - [How to align two sequences](https://athanor.arbastro.com/docs/biochemistry/align-two-sequences.md): Align two sequences gives a global alignment of two DNA, RNA or protein sequences, with the identity, the gaps, the score and the aligned pair to copy. - [How to draw a plasmid map](https://athanor.arbastro.com/docs/biochemistry/plasmid-maps.md): Plasmid map… draws a circular or linear map from a sequence, FASTA or GenBank, with the features from the file, restriction sites and primers. ## Figures, diagrams and documents - [How to draw with the pen and shapes](https://athanor.arbastro.com/docs/figures/shapes-and-pen.md): The Annotate tool draws freehand with the pen, smooth paths, and shapes, with a pen color and thickness, and can upload a picture. - [How to draw brackets and frames](https://athanor.arbastro.com/docs/figures/brackets-and-shapes.md): The Brackets tool (S) draws brackets, parentheses, boxes, frames and ellipses around structures, and offers lab glassware. - [How to draw lab glassware](https://athanor.arbastro.com/docs/figures/lab-glassware.md): The Library has 58 pieces of lab glassware, from round-bottom flasks and condensers to burettes and separatory funnels, to drag onto the page. - [How to add NFPA and GHS safety labels](https://athanor.arbastro.com/docs/figures/safety-labels.md): Insert an NFPA 704 diamond or a GHS label from the Insert menu, then fill in the hazards, pictograms and statements in Properties. - [How to insert a table](https://athanor.arbastro.com/docs/figures/tables.md): Insert › Insert table places a blank table on the page, ready for your values, beside your structures and charts. - [How to insert a chart](https://athanor.arbastro.com/docs/figures/charts.md): Insert chart plots pasted or loaded data as a scatter, line, linear fit, titration, dose-response or chromatogram, with the fit equation and R². - [How to draw a flowchart from text](https://athanor.arbastro.com/docs/figures/flowcharts.md): Insert flowchart from text draws a flowchart from Mermaid flowchart text: a direction, then one step or arrow per line. - [How to insert compounds from a list](https://athanor.arbastro.com/docs/figures/compounds-from-a-list.md): Insert compounds from a list turns a list of names, one per line, into structures on the page, each with its name under it. - [How to link shapes to data](https://athanor.arbastro.com/docs/figures/link-shapes-to-data.md): Link shapes to data keeps tables in the document that shapes and text can follow. Paste a table, give it a name, and linked objects update when it changes. - [How to add sticky notes](https://athanor.arbastro.com/docs/figures/sticky-notes.md): The sticky tool on the pen row drops a note where you click, ready to type, in nine paper colors. Text wraps and shrinks to fit; Alt-drag duplicates. - [How to insert an optics bench or P-V diagram](https://athanor.arbastro.com/docs/figures/physics-diagrams.md): Insert an optics bench, with the ray diagram worked out for a lens, or a P-V diagram with the work, heat and internal energy of the process. - [How to record audio with your writing](https://athanor.arbastro.com/docs/figures/record-audio-with-writing.md): Record what you say while you write with the pen. Each stroke keeps its moment, so a stroke plays back what you were saying as you drew it. - [How to work on pages](https://athanor.arbastro.com/docs/figures/document-pages.md): View › Show page frame turns the canvas into pages, with a page size such as Letter, a header and footer, page numbers and a layout grid in Properties. - [How to add a picture or file to the page](https://athanor.arbastro.com/docs/figures/upload-a-file.md): Insert › Upload a file places a picture on the page, listed in Layers by its file name. Right-click it to trace it, take its background off, or convert it. - [How to trace a picture to lines](https://athanor.arbastro.com/docs/figures/trace-a-picture.md): Trace picture to lines turns a picture into filled vector outlines, with threshold, detail and speck settings, and a mode for chalk on a blackboard. - [How to take the background off a photo](https://athanor.arbastro.com/docs/figures/remove-a-photo-background.md): Take the background off a photo removes it by flooding in from the edges, with tolerance and soften settings, and trims the picture to what is left. ## Slides and presenting - [How to make slides](https://athanor.arbastro.com/docs/present/slides.md): Every frame on the canvas is a slide. View › Slides… orders them, sets transitions and skips, and starts the show with Present. - [How to present slides](https://athanor.arbastro.com/docs/present/present-slides.md): View › Present slides shows your slides one at a time, with Back and Next, a laser, a pen, a black screen, and Poll, Camera, Captions and Presenter view. - [How to record a walkthrough](https://athanor.arbastro.com/docs/present/record-a-walkthrough.md): Record a walkthrough captures what you do on the canvas, with your voice if the microphone is on, and saves it as an MP4 named after the document. ## Files and formats - [How to open structure files](https://athanor.arbastro.com/docs/files/open-files.md): Press Ctrl+O to open a structure file, such as an SDF with several compounds, a MOL, a SMILES file or a ChemDraw CDX or CDXML file. - [References](https://athanor.arbastro.com/docs/files/references.md): The References panel in Athanor keeps the document's numbered reference list in one citation style, ready to copy into a paper, a slide or a report. - [Supported file formats](https://athanor.arbastro.com/docs/files/supported-formats.md): Athanor exports images (PNG, SVG, PDF, TIFF, EMF, EPS), ChemDraw CDXML and CDX, MOL, SDF, SMILES, InChI, CML, Marvin, RXN and 3D formats. - [How to export a figure or structure file](https://athanor.arbastro.com/docs/files/export.md): Export (Ctrl+Shift+E) saves pictures, structure files, 3D models and animations from Athanor. Ctrl-click to pick several formats; Ctrl+Alt+E exports again. - [How to bring in a Word document](https://athanor.arbastro.com/docs/files/open-word-documents.md): Open or drop a .docx file: its text comes in editable, each ChemDraw drawing in it as an editable structure, plus its pictures and tables, in one group. - [How to export a figure for a journal paper](https://athanor.arbastro.com/docs/files/export-for-a-paper.md): Apply the journal's document type in Athanor, then export SVG, PDF, EPS or EMF, or a high-resolution PNG or TIFF at the dpi the journal asks for. - [How to bring in a PowerPoint deck](https://athanor.arbastro.com/docs/files/open-powerpoint.md): Drop a .pptx file on the canvas and every slide becomes an Athanor slide with its text, shapes, pictures and tables, ready to edit and present. - [How to write alt text for an exported figure](https://athanor.arbastro.com/docs/files/alt-text.md): The Export window writes alt text from the name, formula and SMILES, and checks accessibility. Edit it to say what matters before you export. - [ChemDraw CDX and CDXML files](https://athanor.arbastro.com/docs/files/cdx-and-cdxml.md): How Athanor reads and writes ChemDraw CDX and CDXML, what the 6,492-molecule round-trip suite checks, and what to watch for. - [How to save and open MOL and SDF files](https://athanor.arbastro.com/docs/files/mol-and-sdf.md): Export MOL V2000 or V3000 and SDF, copy a molfile to the clipboard, and open SD files with every record on the page, each named. - [How to use structures in LaTeX (chemfig and mhchem)](https://athanor.arbastro.com/docs/files/latex-chemfig-and-mhchem.md): Copy as chemfig gives LaTeX chemfig code for a drawn structure, for your thesis or Overleaf. Copy as mhchem formula gives the \ce{} formula. - [How to back up and restore your documents](https://athanor.arbastro.com/docs/files/backups.md): Storage & backups sets an automatic backup folder, exports every document at once and restores from files. It also shows how much this device holds. - [The .athanor file format](https://athanor.arbastro.com/docs/files/athanor-file-format.md): An .athanor file is a ZIP with one MOL V3000 file per structure, a document.json and a thumbnail, so anyone can unzip it and recover every structure. ## AI assistant (arbastro Intelligence) - [The AI assistant](https://athanor.arbastro.com/docs/ai/assistant.md): The AI assistant in Athanor works in the editor. Ask in plain words and it draws, edits and explains, showing its plan. What it can do and sends. - [How to choose the AI model or use your own API key](https://athanor.arbastro.com/docs/ai/ai-settings-and-your-own-key.md): Settings › AI picks the provider and model the assistant uses, or your own key for Anthropic, OpenAI, Google, xAI, Meta or Alibaba on arbastro Suite plans. - [AI credits](https://athanor.arbastro.com/docs/ai/ai-credits.md): Hosted AI uses monthly credits: 150 on Free, 300 on Suite Lite, 1,000 on Suite Plus and 2,500 on Suite Ultra. Bigger models use credits faster. - [What the AI assistant sends, and where](https://athanor.arbastro.com/docs/ai/what-is-sent.md): Your question, the conversation and a description of the page go to the provider shown under the box. Signed out, nothing is sent to any AI provider. - [How to use agents](https://athanor.arbastro.com/docs/ai/agents.md): Agents do a job across the whole document, such as naming or numbering every structure, and hand you the result as suggestions to accept or reject. - [How to save and manage assistant skills](https://athanor.arbastro.com/docs/ai/assistant-skills.md): Save a request you made to the assistant as a skill, to run again later, and manage your skills from Help › Prediction feedback › Manage assistant skills. ## Teaching - [Teaching with Athanor](https://athanor.arbastro.com/docs/teaching/overview.md): Problem sets graded automatically, from open textbooks, templates or your own; labs with pre-lab, data and calculations; flashcards, games and simulations. - [How to create a problem set](https://athanor.arbastro.com/docs/teaching/create-a-problem-set.md): File › New problem set starts a set from your textbook, templates or a blank problem, graded automatically, or a practice run for yourself. - [Textbook problem banks](https://athanor.arbastro.com/docs/teaching/textbook-problem-banks.md): From your textbook generates graded problems for sections of open textbooks such as OpenStax Chemistry 2e, Organic Chemistry and Biology 2e. - [Question types](https://athanor.arbastro.com/docs/teaching/question-types.md): The 21 answer types a problem can use, from drawn structures and mechanism arrows to Punnett squares and spectra, and how drawn answers are graded. - [How to give each student different numbers](https://athanor.arbastro.com/docs/teaching/versions-per-student.md): Variables give each student their own version of a problem: a number in a range, a word or structure from a list, R groups, or a row of linked values. - [How to run a lab with Athanor](https://athanor.arbastro.com/docs/teaching/labs.md): New lab sets up a lab as a problem set: pre-lab questions, data entry with each student's own numbers, and calculations graded from them. - [How to study with flashcards](https://athanor.arbastro.com/docs/teaching/flashcards.md): Study flashcards has ready-made decks for reactions and name to structure, a deck from your document, your own decks, and four or two grades. - [How to play the practice games](https://athanor.arbastro.com/docs/teaching/practice-games.md): Practice games drill naming, structures, functional groups and counting rings and H-bond donors, in a 60-second sprint or a calm round of 10. - [How to use the virtual lab and simulations](https://athanor.arbastro.com/docs/teaching/virtual-lab-and-simulations.md): Simulations covers gas laws, the pH scale, equilibrium and building a molecule, and a virtual lab bench with a stockroom of solutions and glassware. - [How to connect Athanor to your LMS (LTI 1.3)](https://athanor.arbastro.com/docs/teaching/lms-and-lti.md): The LTI 1.3 URLs and Canvas configuration a school's LMS admin needs to add Athanor problem sets to Canvas, Moodle, Blackboard or Brightspace. ## Collaboration and sharing - [Version history](https://athanor.arbastro.com/docs/editor/version-history.md): Version history in Athanor: every edit of the session as pictures you can step back to, and the named versions kept with your account across devices. - [How to comment on a document](https://athanor.arbastro.com/docs/collaboration/comments.md): Comment mode (Shift+C) opens the Comments panel. Comment on the whole document or on a region, attach a file, and filter Open, Resolved and All. - [How to use version history](https://athanor.arbastro.com/docs/collaboration/version-history.md): Version history (Shift+H) shows every step of this session with a thumbnail, automatic versions of the page, and a sign-off that records who approved it. - [How to branch a document and request review](https://athanor.arbastro.com/docs/collaboration/branches-and-merge-requests.md): Create a branch makes your own copy of a document that remembers its origin. Request review sends your changes back, to be accepted or rejected one by one. ## Accounts, plans and billing - [How to sign in to Athanor](https://athanor.arbastro.com/docs/account/sign-in.md): Athanor uses your arbastro account, the same one as arbastro.com. Sign in with Google, a passkey, or your email and password. - [Plans](https://athanor.arbastro.com/docs/account/plans.md): Free and the three arbastro Suite plans compared: cloud storage, monthly AI credits, AI models and your own key. Collaboration is in every plan. ## Workspace and settings - [Properties](https://athanor.arbastro.com/docs/editor/properties.md): Athanor's Properties panel changes whatever is selected: atoms, bonds, text, arrows and shapes, plus the document's style, bond length and page size. - [How to open, arrange and reset panels](https://athanor.arbastro.com/docs/workspace/panels.md): View › Panels opens Properties, Layers, Library, Compound info, Version history, References, AI assistant, 3D preview and Export, and resets the layout. - [The Properties panel](https://athanor.arbastro.com/docs/workspace/properties-panel.md): Properties shows the settings of whatever is selected: the document with nothing selected, a structure, one atom, a shape or a picture. - [Settings](https://athanor.arbastro.com/docs/workspace/settings.md): Settings › General sets the theme, the language, how new documents start, the scroll wheel and your abbreviations, and moves your preferences. - [Accessibility settings](https://athanor.arbastro.com/docs/workspace/accessibility.md): Settings › Accessibility turns on reduced motion, larger targets and high-contrast selection. Structures can be explored with the keyboard. - [How to change the language](https://athanor.arbastro.com/docs/workspace/language.md): Athanor is available in English and Spanish. Switch the language in Settings › General; it is saved on this device, and on your account when signed in. - [How to switch theme and hide the chrome](https://athanor.arbastro.com/docs/workspace/theme-and-focus.md): View › Switch theme flips between dark and light; Settings › General sets System, Dark or Light. View › Hide all chrome (Tab) leaves only the canvas. - [The desktop app and the web app](https://athanor.arbastro.com/docs/workspace/desktop-and-web.md): The Windows app and the web app are the same editor. The desktop app adds file double-click, the full Office clipboard and starting with Windows. ## Plugins - [Plugins overview](https://athanor.arbastro.com/docs/plugins/overview.md): What Athanor plugins are, what they can add to the editor, how the sandbox and permissions keep your work safe, and where to go next. - [The Plugins button](https://athanor.arbastro.com/docs/plugins/plugins-button.md): The Plugins button in Athanor's top bar lists every installed plugin's windows and commands, then Browse plugins and Manage plugins. - [How to browse and install plugins](https://athanor.arbastro.com/docs/plugins/browse-and-install.md): The Plugins window lists plugins with filters and a detail column. Pick one, read what it adds and what it can do, and install it. - [Plugin permissions](https://athanor.arbastro.com/docs/plugins/permissions.md): What a plugin may do is listed before you install it. Change it afterwards from the Installed tab, with one switch per permission. - [How to start a plugin and find where it lives](https://athanor.arbastro.com/docs/plugins/try-it-and-where-to-find-it.md): Each plugin's detail column says where to find it, and the button under it starts the plugin, so you know where it lives from then on. - [How to move, dock and close plugin windows](https://athanor.arbastro.com/docs/plugins/floating-windows.md): A plugin's window floats over the canvas with its own title bar. Drag it anywhere, dock it beside the canvas, or close it from its title bar. - [How to turn off or uninstall a plugin](https://athanor.arbastro.com/docs/plugins/turn-off-and-uninstall.md): Switch a plugin off from the Installed tab to stop it without removing it, or uninstall it from the menu on its row. - [Using plugins](https://athanor.arbastro.com/docs/plugins/using-plugins.md): Find, install, run, configure, update, turn off and uninstall Athanor plugins, read the permission sheet, and rate, review or report a plugin. - [Official plugins](https://athanor.arbastro.com/docs/plugins/official-plugins.md): The four official plugins that come installed with Athanor: Periodic table, Solution and buffer calculator, Formula finder and Solvent selector. - [The Periodic table plugin](https://athanor.arbastro.com/docs/plugins/official-periodic-table.md): The official Periodic table plugin shows every element in a window. Pick an element to change the selected atoms, or to insert it. - [The Solution and buffer calculator plugin](https://athanor.arbastro.com/docs/plugins/official-solution-and-buffer-calculator.md): Work out how much to weigh for a solution, a dilution or a buffer from the selected structure's molar mass, and put the recipe on the page. - [The Formula finder plugin](https://athanor.arbastro.com/docs/plugins/official-formula-finder.md): Formula finder lists molecular formulas that match an HRMS m/z within a ppm window, for the ion and the elements you choose. - [The Solvent selector plugin](https://athanor.arbastro.com/docs/plugins/official-solvent-selector.md): Solvent selector lists solvents ranked by the CHEM21 solvent selection guide, with their boiling point and kind, filtered to what you need. - [Build your first plugin](https://athanor.arbastro.com/docs/plugins/quickstart.md): Turn on developer mode, create a plugin from the Command template, run it, edit it with hot reload, and inspect it in the plugin console. - [How to turn on plugin developer mode](https://athanor.arbastro.com/docs/plugins/developer-mode.md): Plugin developer mode adds the New plugin templates, Import plugin from folder, Hot reload plugins and the plugin console to the Plugins menu. - [Plugin templates](https://athanor.arbastro.com/docs/plugins/templates.md): Seven templates start a working plugin: Window, Command, Exporter, Analysis check, Input source, and two full examples. - [The plugin console and hot reload](https://athanor.arbastro.com/docs/plugins/console-and-hot-reload.md): Hot reload restarts your plugin when its files change, and the plugin console shows its log output and errors while you build it. - [Commands](https://athanor.arbastro.com/docs/plugins/guide-commands.md): Add commands to Athanor's Plugins menu, the canvas right-click menu and Ctrl+K, handle them in main.js, and act on the current selection. - [Panels and windows](https://athanor.arbastro.com/docs/plugins/guide-panels.md): Give an Athanor plugin a window with ui.html, open it as a panel or from a command, and pass messages between the window and main.js. - [Changes, undo and previews](https://athanor.arbastro.com/docs/plugins/guide-changes.md): How an Athanor plugin edits the page by sending a change, which ops a change can carry, how undo and the safety screen work, and how to propose edits. - [Importers and exporters](https://athanor.arbastro.com/docs/plugins/guide-formats.md): Add a file format to Athanor's Export window with a plugin exporter, return text or binary files, and use 3D coordinates. Importers are reserved. - [Analysis checks](https://athanor.arbastro.com/docs/plugins/guide-checks.md): Add a check to Athanor's issues badge with a plugin: return findings for atoms on the page, keep within the time budget, and pick a severity. - [Input sources](https://athanor.arbastro.com/docs/plugins/guide-input-sources.md): Add a search source to Athanor's Quick insert with a plugin, so people can type a name and insert structures your plugin offers. - [Settings](https://athanor.arbastro.com/docs/plugins/guide-settings.md): Declare settings in an Athanor plugin's manifest, let Athanor draw the form, read the values with athanor.settings.get(), and react to changes. - [Network access](https://athanor.arbastro.com/docs/plugins/guide-network.md): Let an Athanor plugin reach the internet: the network permission, allowedDomains and reasoning, where requests can be made from, and the publishing rules. - [Theming with Athanor's tokens](https://athanor.arbastro.com/docs/plugins/guide-theming.md): Make an Athanor plugin window match the app in light and dark: the built-in styles for plain HTML, and the design tokens as CSS variables. - [API reference](https://athanor.arbastro.com/docs/plugins/api-reference.md): Every member of the athanor object an Athanor plugin can call in API version 1, with signatures, return values, permissions and the shapes they use. - [Manifest reference](https://athanor.arbastro.com/docs/plugins/manifest-reference.md): Every field of an Athanor plugin's manifest.json in API version 1: types, limits and examples, the permissions list, contributes and network rules. - [Plugin API changelog](https://athanor.arbastro.com/docs/plugins/changelog.md): Changes to the Athanor plugin API by version. API version 1 shipped with Athanor 0.3.31 on November 11, 2026, with plugins on for everyone. - [Publishing a plugin](https://athanor.arbastro.com/docs/plugins/publishing.md): Publish an Athanor plugin to the directory: who may publish, the four Publish steps, automatic screening, human review, updates and Ed25519 signing. - [Plugin review guidelines](https://athanor.arbastro.com/docs/plugins/review-guidelines.md): What is checked before an Athanor plugin is published: the automatic screen, then quality, trust and safety, chemistry safety, business and legal. - [Plugin developer terms](https://athanor.arbastro.com/docs/plugins/developer-terms.md): The Plugin Developer Terms you agree to when you publish an Athanor plugin: who may publish, the license, user data, review and removal, and fees. - [Security model](https://athanor.arbastro.com/docs/plugins/security-model.md): How Athanor runs plugins safely: the QuickJS sandbox in a worker, time and memory limits, the sandboxed window and its CSP, network rules and signing. ## Send to other apps - [Send to other apps (coming soon)](https://athanor.arbastro.com/docs/send-to/overview.md): Send to will put a scheme straight into Google Slides, Notion and other apps with your own account. It is not available yet; this page says what is coming. ## MCP server - [Athanor MCP server](https://athanor.arbastro.com/docs/mcp/overview.md): Use Athanor's chemistry engine from Claude, ChatGPT, Cursor and other AI assistants through MCP: structures, and whole documents. Free, no account. - [Connect your AI assistant](https://athanor.arbastro.com/docs/mcp/setup.md): Add Athanor's MCP server to ChatGPT, Claude, Claude Code, Codex, Cursor, VS Code or Gemini CLI in about a minute. - [How to use Athanor in ChatGPT](https://athanor.arbastro.com/docs/mcp/chatgpt.md): Add Athanor as a ChatGPT connector in developer mode: name, URL, no authentication. Then ask ChatGPT to name or check a structure. - [How to use Athanor in Claude](https://athanor.arbastro.com/docs/mcp/claude.md): Add Athanor as a custom connector in claude.ai or the Claude desktop app with one URL, then turn it on in a chat. - [How to use Athanor in Claude Code](https://athanor.arbastro.com/docs/mcp/claude-code.md): One command adds Athanor's chemistry tools to Claude Code, per project or for every project, or add them in .mcp.json. Free, no account. - [How to use Athanor in Codex CLI](https://athanor.arbastro.com/docs/mcp/codex.md): Two lines in ~/.codex/config.toml give Codex CLI Athanor's chemistry tools. Restart Codex and ask it to name a structure. - [How to use Athanor in Gemini CLI](https://athanor.arbastro.com/docs/mcp/gemini-cli.md): One command or a settings.json entry gives Gemini CLI Athanor's chemistry tools. Trust the folder so the server loads. - [How to use Athanor in Cursor](https://athanor.arbastro.com/docs/mcp/cursor.md): Add Athanor to ~/.cursor/mcp.json, or a project's .cursor/mcp.json, for chemistry tools in Cursor's agent. Free, no account, no key. - [How to use Athanor in VS Code](https://athanor.arbastro.com/docs/mcp/vscode.md): Add Athanor as an HTTP MCP server for GitHub Copilot in VS Code, from the Command Palette or a .vscode/mcp.json file. - [Tools](https://athanor.arbastro.com/docs/mcp/tools.md): Every tool Athanor's MCP server offers, 8 engine tools and 12 document tools, with inputs, an example call and the real result. - [MCP troubleshooting](https://athanor.arbastro.com/docs/mcp/troubleshooting.md): The assistant does not list Athanor's tools, too many requests, or a structure is refused: what each means and what to do. - [How to run Athanor's MCP server on your own computer](https://athanor.arbastro.com/docs/mcp/local-mcp-server.md): athanor mcp runs the engine's convert, name, properties, check and screen tools over stdio on your own computer, with no network at all. ## Command line - [How to install the athanor command line](https://athanor.arbastro.com/docs/cli/install.md): Download athanor.exe, the command-line tool with the same chemistry engine as the app, check its version, and see every command. Windows, offline. - [athanor command reference](https://athanor.arbastro.com/docs/cli/commands.md): Every athanor command with its options, the formats it reads and writes, exit codes, and real output from version 0.1.0. - [How to convert a folder of structures at once](https://athanor.arbastro.com/docs/cli/batch-convert.md): athanor batch converts every structure file in a folder to CDXML, MOL or another format, and prints ok or failed with the reason for each file. ## Embed the editor - [Embed the Athanor editor](https://athanor.arbastro.com/docs/embed/overview.md): Add athanor-embed.js, create an editor, set and read structures as SMILES, molfile, SVG or PNG, and listen for changes. A drop-in path from Marvin JS. - [The athanor-editor element](https://athanor.arbastro.com/docs/embed/element.md): Use the athanor-editor element with smiles, tools, readonly, theme, label and stereo attributes, the editor methods, and ready and change events. - [Embed options and URL parameters](https://athanor.arbastro.com/docs/embed/options.md): Every embed option: smiles, molfile, tools, readOnly, theme, label, stereo, origin, src, height and timeout, and the URL parameter each one maps to. - [The embed protocol (version 1)](https://athanor.arbastro.com/docs/embed/protocol.md): Requests, replies and events of the athanor-embed postMessage protocol, for driving the embedded editor without the helper script. - [Who may talk to an embedded editor](https://athanor.arbastro.com/docs/embed/security.md): Only the embedding page, only an allowed origin, nothing before the handshake, and no answer to strangers. What an embedded editor never stores or shows. - [How to move from Marvin JS or Ketcher to Athanor](https://athanor.arbastro.com/docs/embed/migrate-from-marvin-js.md): athanor-marvin.js gives Marvin JS pages the calls they already make, and Ketcher pages a Ketcher-shaped object. Marvin JS ends sale in December 2026. ## Keyboard shortcuts - [Keyboard shortcuts](https://athanor.arbastro.com/docs/shortcuts.md): Every default keyboard shortcut in Athanor: tools, bonds, rings, arrows, editing, selection, chemistry, view and panels. On a Mac, Ctrl is Cmd. - [How to change a keyboard shortcut](https://athanor.arbastro.com/docs/shortcuts/customize-shortcuts.md): Settings › Shortcuts lets you give any command a shortcut, change or remove one, and switch to the ChemDraw classic shortcut set. ## Troubleshooting and FAQ - [Frequently asked questions](https://athanor.arbastro.com/docs/troubleshooting/faq.md): Is Athanor free, does it work offline, can it open ChemDraw files, where is the save button, is my data used for training, and more answers. - [Why an atom is flagged](https://athanor.arbastro.com/docs/troubleshooting/valence-warnings.md): What the issues badge at the bottom left of the Athanor canvas means, why Athanor flags a problem instead of fixing it, and how to find and fix each one. - [A file will not open](https://athanor.arbastro.com/docs/troubleshooting/file-will-not-open.md): What each message means when a ChemDraw, MOL, SDF or other file does not open, or opens with parts missing, and what to try next. - [An export looks wrong](https://athanor.arbastro.com/docs/troubleshooting/export-looks-wrong.md): Fix blurry PNGs, a missing or wrong background, the wrong journal style, and cropped or missing parts in an exported figure. - [A plugin stopped working](https://athanor.arbastro.com/docs/troubleshooting/plugin-problems.md): What each plugin error in Athanor means, from "stopped responding" to "not signed by Athanor", and how to get the plugin running again. - [Desktop app updates](https://athanor.arbastro.com/docs/troubleshooting/desktop-app-updates.md): The Windows app downloads updates in the background and shows Restart to update. How long you can wait, Store installs, and what to do if no update comes. - [Storage is full](https://athanor.arbastro.com/docs/troubleshooting/storage-full.md): When your arbastro account or this device runs out of space, Athanor keeps your work and says so. What still works, and how to free space or get more. - [How to report a problem](https://athanor.arbastro.com/docs/troubleshooting/report-a-problem.md): Help › Report a problem writes a report of what happened for you to copy and send to arbastro. Nothing is sent from the app itself. ## Glossary - [Glossary](https://athanor.arbastro.com/docs/glossary.md): Short definitions of the terms used across the Athanor help center, from abbreviation and agent to SMILES and stereo group, each linking to its guide.