Molecule Portrait Maker

Create beautiful images in minutes

The Molecule Viewer is not currently available on mobile devices

Use your mouse to drag, rotate, and zoom in and out of the structure.

Create an Image

Choose a molecule

Upload a file
Search a database

Display Options

Select

Select chain

Select element

Select ligand or ion

Select secondary structure


Style

Choose a surface



Show hydrogens
Hydrogen bonds

Colour

Custom colour


Image Options

Material

Background

Molecule Portrait Maker – Controls

Rotate Left Click and Drag
Move up, down, left, right
(X,Y plane)
Shift + Left Double-Click and Drag
Middle Double-Click and Drag
Ctrl + Right Click and Drag
Reset and centre Shift + Left Double-Click
Middle Double-Click
*Double-click must be away from the molecule.
Rotate around Z axis Shift + Left Click and Drag Horizontally
Middle Click and Drag Horizontally
Shift + Right Click and Drag Horizontally
Zoom in / out Shift + Left Click and Drag Vertically
Middle Click and Drag Vertically
Use Mouse Wheel
Open JSmol menu Right Click
Ctrl + Left Click
Left Click on Logo

Molecule Portrait Maker – Tutorials

Click on a molecule to learn how to create the image with Molecule Portrait Maker.

The images are on ordered by the time it takes to make them, so 1. Indigo is the quickest to make and 10. Immunoglobulin takes the longest.

Molecule Viewer

The Molecule Viewer is on the left side of the page and comes already loaded with a molecule of indigo. What else would we choose!

Molecule Viewer - basic controls

Molecule Viewer – basic controls

Rotate Left Click and Drag
Move up, down, left, right
(X,Y plane)
Shift + Left Double-Click and Drag
Middle Double-Click and Drag
Ctrl + Right Click and Drag
Reset and centre Shift + Left Double-Click
Middle Double-Click
*Double-click must be away from the molecule.
Rotate around Z axis Shift + Left Click and Drag Horizontally
Middle Click and Drag Horizontally
Shift + Right Click and Drag Horizontally
Zoom in / out Shift + Left Click and Drag Vertically
Middle Click and Drag Vertically
Use Mouse Wheel
Open JSmol menu Right Click
Ctrl + Left Click
Left Click on Logo

Molecule Viewer and JSmol

Molecule Portrait Maker uses the JSmol molecule viewer. This is an extremely powerful package that allows visualization of small molecules, crystals, and biomolecules.

You don’t need to know how to use JSmol in order to create an image with Molecule Portrait Maker. The Create an Image panel lets you create visualizations of molecules easily, without having to spend time learning  how to use JSmol itself.

If you are already an experienced JSmol user then you can use all of the usual JSmol functionality available through the JSmol menu, console and scripts.

If you are not an experienced JSmol user, but would like to explore JSmol further, then the links below will get you started.

Useful links:

JSmol website

JSmol wiki

Jmol/JSmol mailing list

Jmol/JSmol interactive scripting documentation

Create an Image panel

On the right side of the page is the Create an Image panel. This is where you can create a molecular model  in the  Molecular Viewer.

The panel has three main parts:

Choose a molecule

If you click on this section you will be presented with a couple of options.

  • Click the Upload molecule button to upload molecule files (e.g. mol, pdb, cif, mol2, xyz).
  • Links to public databases of molecules can be found in the Search a database dropdown menu .

Display options

This is where you can change how your molecule looks. If you click on this section there are three parts to it.

  • The options under Select let you choose which part of the molecule you want to change. Choosing Chain, Element, Ligands and ions, or Secondary structure will present a second dropdown menu with some more detailed choices. Use the Hide and Show buttons to hide or display your selection.
  • The options under Style let you choose a representation style for your selection.
  • The options under Colour let you choose a colour for your selection.

Image options

This is where you choose how you want your image to look. If you click on this section there are two parts to it.

  • The options under Material let you choose if you want your molecule to be glossy, semi-matte or matte in the final image.
  • There is also a choice of backgrounds for your image under Backgrounds: black, white and transparent, but also two choices where the molecule is displayed as sitting on a surface in the final image. The low camera angle option views the molecule from close to the surface itself, while in the high camera angle option the view is from higher above the surface.

Buttons

At the bottom of the Create an Image panel are two buttons.

  • Click the orange Order free image button to order your image. The image is typically produced and available for download in 1-2 hours.
  • Click the blue Save session button in the middle to save your work, as a special .png file, so that you can work on it later or create more images in the future. The special .png file can be viewed as a standard .png file, and will show your molecule as it appeared in the Molecule Viewer, but it can also be uploaded to Molecule Portrait Maker just like any other molecule file and you can continue working on your model.

Molecule Portrait Maker – FAQs

Why is it free?

Molecule Portrait Maker is currently a Beta version and so is free to use.

Eventually, Molecule Portrait Maker will become a pay-as-you-go service, with some increased functionality and the ability to create higher resolution images.

How big can my molecule be?

That depends! The first limitation is whether your browser is able to load the molecule in to the JSmol molecule viewer. Very large molecules, such as some viruses, will probably not load.

If you are using a surface representation this can take quite a while for your browser to create, if it is a surface for large numbers of atoms such as large a protein chain. You may have to tell your browser to ‘wait’ a few times if it keeps telling you the page is unresponsive and asking you if you would like to quit. This is perfectly normal.

The second limitation is whether we are able to produce an image of a large model.

Sometimes you will be able to create a model in the molecule viewer, but we will be unable to create the image. The reason for this is that the 3D-model produced by the JSmol molecule viewer is in the form of a 3D-mesh. Unfortunately, this mesh is not fine enough for us to be able to produce nice smooth surfaces, so we have to do some processing of the 3D-model. This processing scales exponentially each time we refine the mesh, and there is a limit to what the servers processing the model can deal with.

The current limitations are approximately:

  • Ball & stick, stick:  1500 atoms & 1500 bonds
  • Spacefill: 3500 atoms
  • Cartoon, trace, surface: 75,000 atoms

You can check how big your model is very easily:

  • Right click anywhere in the molecule viewer and a menu will appear.
  • Hover over the second item in the menu list and you should see a count of the number of atoms and bonds in your model. The name of this item in the menu list should be the same as the file name of the model you uploaded to the viewer.

Can I make images of crystal lattices?

Molecule Portrait Maker is able to load crystal structures, for instance from .cif files, but you might have wondered how to display larger lattices.

At the moment the the Create an Image panel doesn’t have the functionality to display larger lattices, but there is another, very simple, way do this.

  • Right click anywhere in the molecule viewer and a menu will appear.
  • Find ‘Console’ in the menu (usually the 6th item from the bottom) and click on it. This will open a console window where you can enter JSmol scripts in the lower panel. Don’t worry if you are not familiar with JSmol, scripting, or any sort of coding, it’s very straightforward.
  • Paste the following into the lower panel (replace i, j & k with integers, depending on the size of lattice you want):

load “” {i j k};

  • Click the ‘Run’ button in the bottom left of the console window.

Your lattice should now appear, along with the unit cell and the axes (the red, green and blue lines). The axis labels and the unit cell information won’t appear in your final image, but if you want to remove the axes and the unit cell enter the following commands into the lower panel and then click the ‘Run’ button in the bottom left of the console window:

axes off;

set showunitcell off;

If you want to do all of this in one go just paste all three commands into the lower panel like this (replace i, j & k with integers, depending on the size of lattice you want):

load “” {i j k};

axes off;

set showunitcell off;

Then click the ‘Run’ button in the bottom left of the console window.

You should also make sure that your lattice isn’t too large, otherwise we may not be able to create your image. Take a look at the How big can my molecule be? section in the FAQs.

Can I make images from other packages like Pymol or UCSF Chimera?

At the moment Molecule Portrait Maker is limited to making images from the JSmol/Jmol package.

In future releases we hope to be able to add functionality to allow images to be produced from molecular models produced in Pymol and UCSF Chimera.

Lighting - why are some parts of my molecule so dull?

Lights

Molecule Portrait Maker is able to produce photo-realistic images of molecules because it imports a 3D model of your molecule into a 3D scene, complete with camera and lights.

The main light for Molecule Portrait Maker images is to the left (about the 7 o’clock position), above the molecule and behind the camera.

Lighting your molecule

If your image is of the whole molecule then usually lighting isn’t something you need to worry about too much.  Just remember that most of the light is coming from the upper left in the image and so you should orient you model to make sure that the important features in your molecule are able to catch the light coming from the upper left, behind the camera.

Lighting in close ups of large molecules

If your image is a close up view of a large molecule, such as a ligand bound to a protein, then some parts of your molecule might throw shadows over the important parts of your molecule in the image, making it too dull.

You can see in the image on the left that the blue ligand is well lit, but in the image on the right it is dull because of shadows cast on it. These two images are of the same molecule, all that has been changed is the molecule’s orientation.

Lighting1     Lighting2

Remember that the main lighting is coming from the upper left behind the camera. So, if we look at all of the molecule from which the two images above were made we can see that there is nothing between blue ligand and the light coming from the upper left in the first image. However, in the second image part of the green chain is between the blue ligand and the lighting coming from the upper left, behind the camera. These parts of the green chain cast shadows onto the ligand, leaving it dull looking.

Lighting3     Lighting4

So to help light your molecule properly you should:

  • Orient you model to make sure that the important features in your image are able to catch the light coming from the upper left, behind the camera, without being obscured by other parts of the molecule.
  • Don’t forget that in a close up parts of your model that are out of the shot can still cast shadows that appear in your image, just like in real life photography!
  • Remember that you might have to balance a perfect orientation for your molecule with one that properly lights the important features in your image. If only that alpha helix wasn’t there!

Can I use translucent surfaces?

At the moment surfaces are limited to being opaque and a single colour. We are planning to have translucent surfaces and colour mapping to surfaces in a future release.

Can I make higher resolution images?

At the moment Molecule Portrait Maker is limited to making free images that are 600 x 425 pixels.

If you would like a high-resolution version of one of your free images (5000 x 3750 pixels suitable for most publishing uses) we can produce one for you for just £15:

  • Reply to the email containing the download link for your free image, telling us you would like a high-resolution image
  • We will email you an invoice for £15
  • Make payment (credit card, PayPal or bank transfer)
  • We produce your high resolution image and send you an email with a link to download your high-resolution image file

What do I do if I encounter a problem using Molecule Portrait Maker?

If you encounter any problems when using Molecule Portrait Maker do let us know.

Just tell us what the problem is using our contact form.

How do I send feedback?

If you have any comments or feedback on Molecule Portrait Maker we would be delighted to hear from you.

Just contact us using our contact form.

What is Molecule Portrait Maker?

Molecule Portrait Maker lets you create photo-realistic images of molecules in minutes.

Unlike difficult to learn 3D-modelling software and conventional tools for visualizing molecules, Molecule Portrait Maker combines simplicity and speed to turn molecular visualizations into beautiful photo-realistic images.

It is currently FREE to use.

  • Create beautiful visualizations of molecules and then bring them to life as superb photo-realistic images
  • No complex 3D-modelling software to learn
  • Utilizes the widely used JSmol molecule viewer
  • Publication quality images
  • You own the copyright for your images

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