7 Best Free Online Molecule Viewer Websites

Here is a list of best free online molecule viewer websites. A molecule or molecular file contains data about atoms, residues, segment names, occupancy, beta factor, coordinate sets, etc., of a molecular structure. There are many types of molecule files such as PDB, SDF, CDX, CDXML, and more. If you want to view and analyze the molecular structure present in a molecule file, then check out these online molecule viewer websites. All of these websites are completely free to use. Plus, users can access them from anywhere without much hassle.

On these websites, users can load one molecule file to view the molecular structure. To show molecular structure, most websites employes 3D or three-dimensional approach. Although a few websites still use the 2D approach to show molecular structure. All the basic interaction tools are present in all these websites through which users can rotate, move, and zoom in on a molecule structure. Besides this, users can also find advanced tools like Anaglyph Stereo, Data Viewer, Show Symmetry, etc., tools to view a molecular structure. Through some websites, users can also change the molecular structure type, background color, highlight specific atom types, and more. After viewing a molecule structure, users can export them in PDB, FBX, MDL, SMD, etc., formats.

These websites also come with additional tools that may come in handy. Using additional tools, users can measure molecular structure, take screenshots, render stricture, and more. Go through the list to know more about these websites.

My Favorite Online Molecule Viewer Website:

webmo.net is my favorite website as it supports molecule files of multiple formats. Plus, it also offers all the essential tools to view and analyze a molecule structure.

You can also check out lists of best free Online Stock Chart, Online PDF Page Remover, and Online Phylogenetic Tree Maker websites.

webmo.net

webmo.net is a free online molecular viewer website. Using this website, users can easily view molecular designs present in PDB and SDF file formats. It also offers multiple engines to calculate and show molecular design such as Gaussian, Molpro, Molpac, Tinker, QChem, etc. Plus, a dedicated Molecule Viewer section is also present in it. Now, check out the primary features of this website.

Main Features:

Molecule Viewer: It is the primary viewer of this website in which users can view the molecule structure present in the molecule file. It also offers tools to move structure and zoom in on the molecule.
Show Symmetry Elements: Use it to view the symmetry elements of a molecule structure.
Calculate: Using this tool, users can calculate molecular orbitals, electron density, electrostatic potential, and more.
Data Viewer: It is another handy tool that allows users to view all the data associated with a molecule file.

Additional Feature:

Preferences: It contains multiple options through which users can orbital colors, molecule colors, isosurface value, and more.
Cleanup: It offers advanced tools through which users can generate bonds, optimize structure mechanics, add hydrogens, etc.

Final Thoughts:

It is one of the best free online molecule websites in which users can easily view and analyze molecular structures.

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Jena3D Viewer

Jena3D Viewer is another free online molecule viewer website. As the name of this website suggests, it shows molecule structure in 3D format. I also like its ability to support molecule files of various formats such as PDB, mmCif, CIF, CML, MOL, XYZ, and more. Now, check out the main features of this website.

Main Features:

3D Viewer: After loading a molecule file, a 3D viewer will open up showing the molecular structure in multiple colors. users can easily interact with the 3D viewer to rotate the structure and zoom in on the structure.
Rendering: Use it to change the rendering type of the structure from various available ones such as Cartoon, Ribbon, Strands, backbone, Trace, etc.
Atom Selection: It is a handy tool through which users can highlight specific atoms of a molecule structure such as Protein, Nucleic, Backbone, Sidechain, Solvent, etc.
Graphic Window: use it to manually change the size of the 3D viewer window.

Additional Features:

This website offers multiple additional features like script support, background coloring, molecule coloring, and more.

Final Thoughts:

It is another capable online molecule viewer website through which users can easily highlight atoms of different types.

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molsoft.com

molsoft.com is a free online molecule viewer website. Using this website, users can load any molecule file in the form of a PDB file format. After loading a PDB, file, users can closely analyze the molecular structure. Now, check out the main features of this website.

Main Features:

3D Molecular Structure: On this website, users can view the 3-dimensional molecular structure of a molecule file. Plus, it also shows different elements of a molecule in distinct colors.
Interact and Zoom: This website also lets users interact with molecular structure through the mouse. Besides this, it also lets users zoom in on molecules for closer inspection.
Anaglyph Stereo: This feature creates a copy of the existing molecular structure.
Rocking: Once enabled, this feature automatically rocks or moves the direction of molecular structure.
Display: Use it to view molecular structure in multiple ways like Wire Mode, CPK Mode, Ball & Stick Mode, etc.
Labels: It adds atomic labels over the molecular structure.

Additional Features:

This website offers multiple additional features through which users can change background color, measure molecular structure, capture molecules in the form of an image, and more.

Final Thoughts:

It is a feature-rich online molecule viewer website through which users can easily view and analyze molecular structures.

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Miew

Miew is a free open source online molecular viewer website. This website shows molecular data in beautiful 3D format. Although, it only supports molecule files of the PDB format. It comes with multiple display modes and displays color modes that users can easily toggle. Plus, essential rotate and zoom features are also present in it. Now, check out the main features.

Main Features:

3D Molecular View: This website shows molecule structure in three-dimensional form.
Model Interaction: This website also lets users interact with molecule structures. Plus, it also lets users select a part of the molecule structure to view the number of atoms present in the selected part and the type of part selected.
Display Modes: This website offers multiple display modes to view a molecular structure such as Lines, Balls, Trace, Tube, Text, and more.
Display Color Presets: It comes with many display color presets to view a structure like a Sequence, Chain, Uniform, Temperature, Occupance, and more.
Export: Use it to export the molecule file in FBX file format.

Additional Feature:

This website offers many additional features like screenshot, get URL, save settings, render settings, and more.

Final Thoughts:

It is another good online molecular viewer website through which users can easily view and analyze molecules and molecular structures.

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rcsb.org

rcsb.org is another free online molecular viewer website. Through this website, users can view molecular structures present in molecular files of various formats like SDF, PDB, MRC, MAP, and more. Now, check out the main features of this website.

Main Features:

3D View: This website shows a 3D view of molecular structure.
Interaction and Analysis: This website lets users interact with molecular structure and closely analyze it using the zoom feature.
Components: Using it, users can select a part of the structure and view all its components.
Export: Use it to export the molecule structure in compressed zip format.

Additional Features:

Measurement: This section carries tools to measure and distance between molecular structures.
Export Animation: This feature create a basic movement animation and lets users export it in the MP4 video format.

Final Thoughts:

It is another good online molecular website in which users can easily view and analyze molecule files.

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PubChem Sketcher

PubChem Sketcher is yet another free online molecule viewer website. This website shows the molecular structure in 2D format. It also shows molecule and atom names with the molecule structure. Besides this, it can also be used to edit the existing molecular models. Now, take a look at the primary features of this website.

Main Features:

Various Molecule File Support: This website supports molecule files of various formats like PDB, SDF, MDL, CDX, and more.
Molecule Viewer: It is the main viewer in which users can view the molecular structure contained in a molecule file in 2D file format along with added molecule information.
Editing: To edit the existing molecule structure, it offers various molecule bonds, molecule shapes, elements, etc., tools.
Export: After viewing and editing a molecule structure, users can export it in various formats like MDL, INCHL, SMD, JME, PNG, etc., file formats.

Final Thoughts:

It is another good online molecule viewer website that not only lets users view but also modifies the molecule structure.

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EzMol

EzMol is the last free online molecule viewer website. On this website, users can easily view molecule files of PDB and EZM format. After loading a molecule file, just press the Submit button to view the molecular structure. Now, check out the primary features of this website.

Main Features:

On-screen model interaction tools: This website offers multiple on-screen tools to rotate, move, enlarge, roll, and rock the molecule model.
Side Chains: Use it to highlight the side chains of a molecular structure in various colors.
Style: Through this tool, users can change the structure backbone type from various available ones like Cartoon, Stick, Hide, etc.
Surfaces: Use it to manually adjust the molecular structure surface type, color, and transparency.

Additional Features:

Through the additional tools of this website, users can render the structure, change the color of individual residues, change the structure background color, and more.