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.
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.
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!