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For most people, Avogadro 2 is the best free desktop starting point: it lets you build, edit, inspect and export molecules in three dimensions while handling many chemical file types. If you already have a compound record in PubChem, the PubChem PC3D Viewer is the fastest way to inspect a prepared 3D structure or compare conformers. For scripted views or an interactive viewer inside a web page, use Jmol or its HTML5-based JSmol.
The important distinction is that a 2D structural formula shows connectivity on a page, whereas a 3D viewer displays one chosen geometry from a file, database record or calculation. A polished rendering is useful evidence of how that geometry is represented; it is not, by itself, proof that the molecule has been experimentally measured in that exact shape.
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What a 2D formula and a 3D model actually tell you
A 2D structure diagram is primarily a map of chemical connectivity. Lines represent bonds, labels identify atoms, and stereochemical marks can indicate a spatial relationship that cannot be seen from a flat drawing alone. The diagram is compact and excellent for discussing reaction schemes, functional groups and bonding patterns.
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Use a viewer to answer questions such as:
- Are the atoms connected as intended?
- Is a stereocentre oriented correctly?
- How do two conformers differ after overlay?
- Does a substituent project above, below or alongside a ring?
- Will a figure communicate shape more clearly than a flat formula?
Do not present an unvalidated rendering as an experimental structure. A database conformer or imported coordinate set is a starting geometry for visualization and further work, not an automatic measurement.
Choose the free tool that matches 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, online retrieval and broad file support. |
| Quickly inspect a known PubChem compound | PubChem PC3D Viewer | Renders available three-dimensional structures, opens supported molecule files and overlays conformers. |
| Script views or embed a viewer in a web page | Jmol/JSmol | Jmol provides open-source scripting and export; JSmol supplies an HTML5 embeddable viewer. |
| Keep the most chemical metadata while editing | Avogadro native CJSON | Its native format can retain information that simpler interchange files may discard. |
Avogadro 2: the general-purpose desktop choice
Avogadro 2 is free and open source. Its project documentation describes it as a molecular editor and visualization tool for computational chemistry, molecular modeling, education, bioinformatics and materials science. It is designed to construct and view molecules and materials in 3D, retrieve molecules from online sources and read many chemical formats through Open Babel.
Choose it when you need to draw or modify a structure, inspect geometry interactively, add a publication-oriented view and save a working file for later editing. It is the most complete single application in this comparison because construction, editing, viewing, retrieval and export happen in one desktop workflow.
PubChem PC3D Viewer: the fastest route from a record to a picture
PC3D Viewer is convenient when the compound is already represented in PubChem. Its documentation describes rendering multiple 3D structures, opening supported molecule files, comparing structures with conformer overlays and producing high-resolution, publication-quality images. It is better suited to fast inspection than to a full editing workflow.
Jmol and JSmol: scripting and browser delivery
Jmol is a free, open-source Java viewer for chemical structures in 3D. It supports a broad range of molecular formats, has a scripting language and can export images, documents, 3D files and web-oriented output. JSmol is its HTML5 modality for embedding an interactive viewer in a web page. Select this family when reproducible scripted scenes, a teaching page or a browser-based presentation matters more than desktop editing.
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Get a reliable starting structure
Begin with the best source available instead of drawing a complicated molecule from memory.
When you know the compound name or identifier
- Find the compound’s record in PubChem.
- Use the record’s downloadable structure files to obtain a coordinate-containing file when one is available. PC3D Viewer documentation specifically describes opening molecule files and points to downloadable compound files.
- Keep the original downloaded file unchanged as your reference copy.
If all you have is a SMILES string, use it to locate the matching compound record and then download a structure file. This avoids treating a text string as if it already contained a measured 3D arrangement: SMILES encodes connectivity and stereochemical notation, while coordinates must come from a generated or stored conformer.
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Common inputs include MOL, SDF, XYZ, PDB and CML, along with other formats handled through Open Babel. Check the file extension and, where possible, its accompanying metadata before importing. A coordinate file may contain positions but little chemical annotation; another file may preserve bond orders, charges or crystallographic information.
Keep an information-rich master
Save a native or otherwise information-rich copy before exporting images or simplified interchange files. Avogadro’s CJSON format can retain atoms, bond orders, formal charges, unit-cell and space-group data, surfaces, orbitals, vibrations and spectra. Avogadro also warns that some exports lose information, so treat XYZ, PDB, SDF or another interchange file as a delivery copy unless you have checked what it preserves for your project.
Step-by-step: build and inspect a molecule in Avogadro 2
1. Open, retrieve or construct the structure
Open the downloaded MOL, SDF, XYZ, PDB or CML file in Avogadro, or use its construction tools to place atoms and bonds. Avogadro can also retrieve molecules from online sources. For a small molecule, verify the element labels and the number of hydrogen atoms before changing the camera or style; a visually attractive model with a missing atom is still the wrong model.
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2. Check connectivity and stereochemistry
Rotate the model until every ring and substituent is visible. Compare each bond to the 2D formula or source record. Pay particular attention to stereocentres, double-bond geometry and ring junctions. If the imported file contains an unexpected charge or bond order, correct the structure in the editor or return to the source record rather than silently accepting a misleading rendering.
3. Choose a representation for the question
- Wireframe: gives the least visual obstruction and is useful for tracing connectivity in a crowded structure.
- Stick: keeps bonds prominent while using less space than spheres.
- Ball-and-stick: balances atom identity, bond direction and overall readability for teaching and general figures.
- Space-filling: emphasizes approximate van der Waals occupancy and steric crowding, but can hide bonds and labels.
These are visual conventions, not independent measurements. Atom radii, colors, lighting and perspective can change how large or close atoms appear without changing the coordinate set.
4. Rotate, zoom and inspect conformational details
Use several viewing angles rather than judging a structure from the first orientation. Look along rotatable bonds, across ring planes and around stereocentres. If two files represent different conformations, inspect them separately first so that a camera angle does not make a real torsional difference look like a connectivity error.
5. Save the editable source
Save the project in CJSON before making export copies. This gives you a recoverable file with the chemical information Avogadro can store, including optional surfaces, orbitals, vibrations and spectra. Name exported files with the compound identifier and representation so a later reader can distinguish the structure source from a rendered image.
Compare conformers and records with PubChem PC3D Viewer
PC3D Viewer is most useful when the question concerns a known PubChem record rather than manual construction.
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- Open the compound record or a supported molecule file.
- Display the available three-dimensional structure.
- Use the conformer-overlay capability when you need to compare alternative conformations from the record.
- Rotate and zoom the overlay, checking which atoms or bonds move relative to the others.
- Export a high-resolution image when the result is intended for a report, lesson or publication figure.
An overlay shows geometric differences between the structures supplied to the viewer. It does not establish which conformer dominates in a particular solvent, temperature or experimental condition unless that information comes from an independent, validated study.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.Use Jmol or JSmol for repeatable views and the web
Jmol on the desktop
Jmol’s scripting model is useful when you need the same orientation, selection, coloring or display style repeatedly. It supports many molecular formats and can export JPG, PNG, GIF and PDF images, as well as document, 3D and web-oriented outputs. Keep the script with the source structure so another person can reproduce the scene instead of relying on a screenshot whose settings are unknown.
JSmol in a browser
JSmol provides an HTML5 route to an interactive molecular view. It is appropriate for course material, documentation or a project page where readers should rotate the model without installing desktop software. Test the page with the actual structure files and browsers you intend to support, and provide a 2D or static image fallback for readers who cannot run the interactive view.
Create a publication-quality molecular image
Start by deciding what the figure must communicate. A connectivity-focused figure usually benefits from wireframe or stick rendering; a shape or steric-occupancy figure may need space-filling; a general explanatory image often works best with ball-and-stick.
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- Choose a consistent representation. Do not mix styles between panels unless the caption explains the difference.
- Preserve atom and bond readability. Excessive perspective, large labels or opaque space-filling spheres can hide the feature the figure is meant to show.
- Export at a high resolution. PC3D Viewer documents high-resolution, publication-quality image output; Jmol documents JPG, PNG, GIF and PDF export.
- Keep the source beside the image. Archive the CJSON, downloaded structure file or Jmol script with the rendered figure.
- Write a precise caption. Identify the source of the coordinates and state that the image is a visualization of that geometry when it has not been experimentally validated.
File formats and what can be lost
No single interchange format carries every kind of molecular information equally well. XYZ is convenient for Cartesian coordinates but may provide little information about bond orders or formal charges. PDB is common for biological structures, while MOL and SDF can carry connection tables and associated fields. CML is an XML-based chemical representation. The exact contents depend on the file and the exporter.
Avogadro’s native CJSON is the safer working format when you need to preserve richer project data. Open Babel support gives Avogadro access to more than 100 chemical file formats, but broad import support does not mean that every format can represent every feature. After conversion, reopen the exported file and verify atom count, bond orders, charges, coordinates and any unit-cell information that your analysis requires.
Common problems and practical fixes
The model looks flat or distorted
First check whether the source contains real 3D coordinates. A file that stores only connectivity may open in a default or generated arrangement. Reopen the source, confirm that a 3D conformer was downloaded, and avoid presenting the result as a measured geometry merely because the viewer displays it in three dimensions.
Bonds or charges changed after export
Compare the exported file with the CJSON or original source. If bond orders, formal charges or other metadata disappeared, return to the information-rich file and choose a format that supports the required fields. Never overwrite the master with a lossy export.
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A stereocentre appears reversed
Rotate the molecule and compare it with the source notation from multiple angles. A camera flip can make a correct arrangement look different, while a wrong atom order or missing stereochemical flag can produce a genuinely incorrect structure. Check the source record and the imported connectivity before editing coordinates.
Two conformers seem identical
Use an overlay or view the structures side by side, then inspect torsion angles and flexible substituents. A different camera orientation can conceal a conformational change. PC3D Viewer’s overlay function is designed for this comparison.
The image is attractive but chemically ambiguous
Switch temporarily to wireframe or stick view, verify the connectivity and stereochemistry, then return to the style needed for the final figure. Add a caption identifying the coordinate source and representation so viewers do not mistake rendering choices for experimental evidence.
A simple decision checklist
- Choose Avogadro 2 when you need to draw, edit, inspect and export on a desktop.
- Choose PubChem PC3D Viewer when a PubChem record is already your starting point and you need rapid 3D inspection, conformer overlays or a high-resolution image.
- Choose Jmol when scripted control and broad format support are central.
- Choose JSmol when the final viewer must run inside an HTML5 web page.
- Keep a CJSON or other information-rich master before creating simplified exports.
- Label every figure with the coordinate source and distinguish visualization from experimentally validated structure determination.
For a free, end-to-end desktop workflow, download or retrieve the structure, open it in Avogadro, verify connectivity and stereochemistry, select the representation that answers your question, save CJSON, and export only the formats or images your audience needs. Add PC3D Viewer for quick record-based conformer comparison and Jmol/JSmol when automation or browser delivery becomes the priority.
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