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EzMol is web browser-based 'paint-box' for proteins. You can easily import structures from the Protein Database, and rotate, render, colour and label them in 3D.
A more detailled guide to EZMol is below:
The key feature of EzMol is that it is a step-by-step wizard-driven program. 
The home page of EzMol contains a submission form which gives the user a choice of whether to browse for a PDB file on their local storage to upload (limited to five megabytes in size), browse for a previously stored user-generate EZM file to upload, or enter a PDBID code and load the coordinates from the EzMol server. EZM files are the format that EzMol allows users to save their work in.They are designed to be human-readable, so that, if necessary, users can edit EZM files in their raw format. 
The first tab of the generated page contains a similar submission form to the home page to allow the user to upload subsequent files without having to return to the home page. The rendering script generates an interface that displays all the chains and residues and incudes the PDB structural data within the HTML of the generated page. From these data, 3Dmol.js is used to display the PDB data in a structural viewer preview pane which can be manipulated with the mouse. It indicates the movement controls, for translating, zooming and rotating the molecule object. Importantly, the user does not need first to find out and then recall mouse combinations for movement.


The user can color chains by individual residues. The display for the residues is controlled by an Amino Acid Grid Selector, and similar ones are used for sticks, surface coloring and labels. Accordions for each chain can be expanded to show boxes representing all the residues in the chain. InDNA chains, they display the nucleotides. Each box contains the PDB number (and insertion code where relevant) and the one-letter code for the amino acid or nucleotide. Colors are applied in real time as they are highlighted in the case of residues and side chains.

EzMol also contains “Show secondary structure on sequence below button,” which changes the single-letter amino acid codes on the grid to symbols representing secondary structure that the amino acid is part of (α for alpha helices, β for beta-sheets, · for coils). A second tab allows the user to apply a single color to all residues of a common secondary structure type.

“Render and download,” allows the user to save their work (as a readable file containing all commands applied in the EzMol session) or download the image in a resolution of 1280 pixels square in Portable Network Graphics format.

EzMol is intended to be a simple to use tool to allow the quick rendering and coloring of molecular structures. It provides limited functionality that is nevertheless sufficient for many biological purposes and does not require the user to download software. EzMol has applications in situations where the user has a short time to prepare images for an e-mail, presentation or lecture, or even using it dynamically to highlight areas of structures onscreen and visualize where they lie on the protein structure. 

EzMol also has potential for teaching, particularly for younger students who have not yet learned how to use a more complex molecular graphics program, and for the prototyping of macromolecule images.


Internal case number: 8156



Web server in software form for the rapid visualization and image production of protein molecules.

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