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For most desktop users, start with Avogadro 2. It is a free, open-source editor that lets you build molecules, view them in three dimensions, retrieve structures, change representations, and export common chemical files. If you already have a compound record in PubChem, its PC3D Viewer is usually the fastest way to inspect a 3D conformer or compare conformers. Choose Jmol or its HTML5 version, JSmol, when scripting, automated image creation, or embedding an interactive viewer in a web page is the priority.
This guide explains how to move from a 2D formula, SMILES string, or structure file to a useful 3D visualization, how to choose a rendering style, how to export without silently losing chemical information, and how to avoid treating a picture as proof of an experimentally validated geometry.
What a 2D structure shows—and what a 3D viewer adds
A 2D structural formula is a diagram of chemical connectivity. Lines indicate bonds, labels identify atoms, and wedge or dash notation can communicate stereochemistry. The drawing is intentionally arranged for readability; it is not a literal photograph of the molecule in space.
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This distinction matters when you present a molecule in teaching material or a paper. A viewer can reveal a malformed bond, an inverted stereocenter, or a surprising conformation, but it does not by itself establish that the geometry is the lowest-energy structure or that it matches a measured crystal or spectroscopic structure.
Which free tool fits your task?
| Need | Best starting point | Why it fits |
|---|---|---|
| Build or edit a small molecule on a desktop | Avogadro 2 | Combines a 3D editor, visualization, structure retrieval, and broad file support. |
| Quickly inspect a known PubChem compound | PubChem PC3D Viewer | Renders 3D structures, opens supported molecule files, and supports conformer overlays. |
| Script views or embed an interactive viewer in a web page | Jmol/JSmol | Provides open-source scripting; JSmol supplies an HTML5 embeddable modality. |
| Keep the richest chemical metadata while editing | Avogadro native CJSON | Preserves extensive information that simpler interchange formats may omit. |
Avogadro 2: the general-purpose desktop choice
Avogadro 2 is a free, open-source molecular editor and visualization application used in computational chemistry, molecular modeling, education, bioinformatics, and materials science. It is designed to construct and view molecules and materials in 3D. You can draw atoms and bonds, modify an existing structure, retrieve molecules from online sources, inspect coordinates, and export several chemical formats.
It is the most complete starting point when your workflow includes editing rather than merely viewing. You can begin with an empty canvas, a downloaded structure, or a record retrieved from an online database, then use the same application to examine geometry and prepare an image.
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PubChem PC3D Viewer: the fastest route from a compound record
PC3D Viewer is useful when the compound is already identified in PubChem. Its documented workflow can render multiple three-dimensional structures, open supported molecule files, overlay conformers, and create high-resolution, publication-quality images. It minimizes setup: find the compound record, open the 3D view, and inspect the available conformers.
Use this route for a quick check of a known compound or for a record-based comparison. If you need to change atom positions, add a fragment, or build an unregistered molecule, move the structure into an editor such as Avogadro.
Jmol and JSmol: scripting and browser delivery
Jmol is a free, open-source Java viewer with broad chemical-format support and a scripting language for controlling selections, colors, representations, orientations, and exports. JSmol is its HTML5 modality for embedding an interactive viewer in a web page. This combination is better suited to repeatable views, demonstrations, web-based teaching material, and automated image generation than to hand-building a molecule from scratch.
What you need before opening a viewer
Prepare one of these starting points:
- A compound record in PubChem, if you want a database-provided structure and conformers.
- A SMILES string, when the molecule is available as line notation but not yet as a coordinate file.
- A MOL or SDF file for a small molecule, an XYZ coordinate file, a PDB file for a protein or other biomolecule, a CML file, or another supported chemical format.
- A clear 2D drawing from which you can manually construct the connectivity and stereochemistry in Avogadro.
Keep the original file untouched. Make a working copy before editing, and record where the coordinates came from. A file downloaded from a database, a geometry generated by software, and a manually sketched structure have different evidentiary status even if they look identical on screen.
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Workflow: turn a compound record or file into a 3D visualization
1. Obtain a structure file or record
- Search PubChem for the compound by name, identifier, or other known record information.
- Use the record’s download controls to obtain a supported structure file when you want a local copy. PubChem documentation describes downloadable compound files and a PC3D workflow for opening molecule files.
- If you already have a MOL, SDF, XYZ, PDB, CML, or related file, verify that it opens as text or in a chemical editor and note whether it contains coordinates, bond orders, formal charges, hydrogens, or only connectivity.
A SMILES string is connectivity notation, not a complete 3D model. It may encode stereochemistry, but it does not inherently provide a unique set of Cartesian coordinates. To visualize it in 3D, import it into a tool that can generate coordinates or build the molecule atom by atom.
2. Open or construct the molecule in Avogadro
- Launch Avogadro 2 and open the downloaded file through its file-open command, or use its structure-retrieval features when starting from an online record.
- For a SMILES string or a 2D formula, use the molecule-building tools to create the atoms and bonds. Confirm element labels, formal charges, aromatic bonds, and any wedge or dash stereochemistry before generating or adjusting 3D coordinates.
- If the file opens without visible hydrogens, check whether hydrogens are implicit or absent. Add them only when chemically appropriate; a missing hydrogen can change valence and apparent geometry.
- Save an editable working copy in Avogadro’s native CJSON format before making substantial changes.
Avogadro is intended for constructing and viewing molecules in 3D, but a freshly constructed model may need geometry optimization or another validation step for a chemically sensible arrangement. A visually tidy structure is not necessarily an energy-minimized one.
3. Select a representation that answers your question
- Wireframe: Shows connectivity with minimal visual clutter. It is useful for large structures and for checking which atoms are connected.
- Stick: Gives bonds a visible thickness while keeping atoms relatively unobtrusive. It works well for inspecting bond paths and ring systems.
- Ball-and-stick: Balances atom identity and connectivity and is usually the clearest default for teaching or general explanation.
- Space-filling: Scales atoms to approximate van der Waals occupancy. It helps communicate steric crowding and surface coverage, but it can hide bonds and make distant atoms appear merged.
Representations are visual conventions. The apparent size of an atom, the color palette, and the perspective can change what a reader notices without changing the underlying coordinates.
4. Rotate, zoom, and inspect the model
- Rotate the structure through several angles instead of accepting the initial orientation.
- Zoom into stereocenters, double bonds, rings, and functional groups where a hidden overlap could obscure the connectivity.
- Check that the element labels and formal charges match the intended compound.
- Compare the 3D arrangement with the original 2D formula, paying particular attention to wedge and dash bonds and to E/Z or cis/trans relationships.
- Look for implausible valences, overlapping atoms, disconnected fragments, or an unexpectedly protonated or deprotonated group.
When a database supplies several conformers, inspect more than one. A conformer overlay can show which parts of the molecule remain similar and which flexible groups move. PC3D Viewer specifically supports conformer overlays for record-based comparisons.
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5. Export an image only after checking the model
Set the orientation, representation, atom labels, background, and lighting before exporting. For a publication figure, choose a high enough resolution that bonds and labels remain legible at the final printed or displayed size. PC3D Viewer documents high-resolution, publication-quality image output. Jmol documents image exports including JPG, PNG, GIF, and PDF.
Save the view settings or a reproducible script when possible. A second person should be able to recreate the orientation and style rather than relying on a screenshot whose camera position was never recorded.
Converting SMILES and 2D drawings into 3D
Why a SMILES string needs another step
SMILES describes atoms, bonds, branches, ring closures, and optionally stereochemistry in a compact line. It does not, by itself, specify the three-dimensional position of every atom. Software must generate an initial geometry, and that geometry may represent one of several possible conformers.
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After importing a SMILES string into a 3D editor, inspect stereochemical markers and verify the resulting structure against the source notation. If the original SMILES omitted stereochemistry, the generated model cannot recover information that was never supplied.
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Building from a 2D formula
In Avogadro, select an element, place atoms, and draw bonds to reproduce the formula. Set bond orders deliberately for double, triple, aromatic, and coordinate-bond cases. Add formal charges and stereochemical indicators before adjusting the 3D arrangement. Then rotate the model and compare every stereocenter and ring junction with the 2D source.
For an educational illustration, this may be sufficient. For computational work, record how coordinates were generated and apply an appropriate optimization or calculation outside the viewer when a defensible geometry is required.
Opening common molecular file types
| Format | Typical content | Practical caution |
|---|---|---|
| MOL | Small-molecule atoms, coordinates, and bonds | Check bond orders, charges, and hydrogen treatment after import. |
| SDF | One or more MOL-style records, often with attached data fields | Confirm which record is displayed when the file contains a collection. |
| XYZ | Element symbols and Cartesian coordinates | Connectivity and bond orders may need to be inferred or supplied separately. |
| PDB | Coordinates and records commonly used for proteins and other biomolecules | Alternate locations, residue records, missing atoms, and connectivity conventions can affect the view. |
| CML | XML-based chemical structure information | Review how the importing application maps metadata and coordinates. |
| CJSON | Avogadro’s native JSON-based chemical representation | Prefer it as the editable master when you need to retain rich metadata. |
Avogadro uses Open Babel support for more than 100 chemical file formats. That breadth is valuable for interchange, but every conversion is a possible information boundary. Keep the original and the native working file even when the final deliverable must be XYZ, PDB, or SDF.
Preserve information when exporting
Avogadro’s native CJSON format can retain atoms, bond orders, formal charges, unit-cell and space-group data, surfaces, orbitals, vibrations, and spectra. Simpler exports do not necessarily carry all of those objects. Avogadro’s documentation warns that some exports can lose information.
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- Save the original downloaded or generated file unchanged.
- Save the edited model as CJSON while all available metadata is still present.
- Export a copy in the format required by the next application.
- Reopen the exported copy and compare atom count, connectivity, bond orders, charges, coordinates, and any required annotations with the CJSON master.
- Label the export with its format and purpose so a future user does not mistake a reduced interchange file for the authoritative working model.
For example, XYZ can carry coordinates and element identities but may not preserve the full bond model. A PDB export may be appropriate for a biomolecular viewer while omitting application-specific surfaces or spectra. The right format is the one that preserves the information your next step actually needs.
Using PubChem PC3D Viewer for conformer inspection
PC3D Viewer is especially efficient when the question is, “What does this PubChem compound look like in 3D?” Open the compound record, enter its 3D view, and inspect the available structures. If more than one conformer is provided, use the overlay feature to compare them rather than judging each orientation independently.
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Overlays are most informative when you keep the same atom correspondence and choose a consistent viewpoint. Flexible side chains may diverge while a rigid ring system remains aligned. That visual difference indicates conformational variability in the supplied models; it does not establish which conformer dominates under every solvent, temperature, or chemical environment.
Automating views with Jmol and JSmol
When scripting is worthwhile
Use Jmol when you need repeatable camera positions, selections, colors, representations, or batch exports. A script can apply the same style to a series of structures and reduce accidental differences between figures. Jmol supports many chemical formats and exports to image, document, 3D, and web-oriented outputs.
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Choose JSmol when readers need to rotate a molecule directly in a web page. Because it is the HTML5 modality, it can deliver an interactive viewer without requiring the older Java-based desktop approach. Test the embedded page in the browsers and screen sizes your audience uses, and provide a static image or text description for readers who cannot run the interactive view.
Keep scripted output reproducible
- Store the structure file beside the script and record its provenance.
- Set the representation, background, orientation, and export dimensions explicitly.
- Use stable atom selections rather than relying only on screen position.
- Render a test image and inspect labels, clipping, and overlapping atoms before publishing.
Making a publication-quality molecular image
Choose the message before the style
Use ball-and-stick when readers must see both atom identity and bonds. Use space-filling to emphasize steric shape or approximate surface occupancy. Use wireframe or sticks for a crowded biomolecule where a filled model would hide the internal structure.
Make orientation and labels readable
Place the camera so the feature under discussion faces the reader. Avoid an angle that hides a stereocenter behind a larger atom. Add labels only where they answer a question; labeling every atom can turn a clear model into an unreadable thicket. Use a high-contrast background and check the image at its actual publication size.
Document what the image represents
Caption the source of the coordinates and identify whether the image shows a database conformer, an imported experimental structure, a manually built model, or a geometry produced by a calculation. State the software and representation when that information affects interpretation. This prevents a decorative rendering from being mistaken for a measured structure.
Common problems and practical fixes
The molecule opens flat or has no useful 3D shape
A file may contain 2D coordinates only, or an XYZ file may contain coordinates without inferred connectivity. Generate or adjust 3D coordinates in the editor, then inspect valence and stereochemistry. Do not assume that an automatic layout has selected the chemically preferred conformer.
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Bonds or charges look wrong after conversion
Reopen the original and compare bond orders, aromaticity, formal charges, and hydrogen counts. If the target format cannot represent a feature, return to the CJSON master and export a format that can. Never repair a conversion by eye without checking the underlying atom and bond data.
A stereocenter appears inverted
Rotate the model rather than judging from one projection. Compare the 3D arrangement with the wedge/dash notation or stereochemical SMILES. If the source did not encode stereochemistry, mark the result as unspecified instead of claiming a definite configuration.
Atoms overlap or a ring looks distorted
Check whether the coordinates came from a rough construction, a low-quality conversion, or a conformer that has not been optimized. Rebuild suspect bonds, regenerate coordinates, or perform a suitable geometry optimization in a computational-chemistry workflow. A viewer can expose the problem but does not automatically solve it.
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Increase the export resolution, set the final aspect ratio before rendering, and leave margin around the outermost atoms. Reopen the exported image at its intended display size and check small labels and bond lines.
Visualization versus molecular modeling
Free viewers and editors answer visual questions: What atoms are connected? How are the supplied coordinates arranged? How do two conformers differ? They do not, by themselves, calculate binding energies, predict reaction outcomes, establish a crystal structure, or prove that one conformer is experimentally dominant.
For a defensible scientific claim, identify the origin of the coordinates and use an appropriate calculation or measurement for the claim. Use the viewer to inspect, communicate, and export the result of that work. This separation keeps a clear image from carrying more certainty than the underlying model deserves.
Quick Recap
A practical decision guide
- Need to draw and edit a molecule locally: Use Avogadro 2, save CJSON, then export a copy for other software.
- Have a PubChem record and need a quick 3D check: Use PC3D Viewer and inspect its conformers or overlays.
- Need a repeatable set of figures: Use Jmol scripting and retain the script with the source structures.
- Need an interactive page for students or readers: Use JSmol, with a static fallback image and explanatory caption.
- Need to preserve the most metadata: Keep Avogadro CJSON as the master and treat simplified exports as derivatives.
Final checklist before you publish or share
- Is the structure source identified and preserved?
- Do atom count, connectivity, bond orders, charges, and stereochemistry match the intended molecule?
- Did you inspect more than one orientation?
- Is the representation appropriate to the point you are making?
- Were coordinates generated, measured, retrieved, or manually constructed?
- Did you save a rich native file before exporting?
- Can another person reproduce the orientation or script?
- Does the final image remain legible at its actual size?
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