This was done entirely with Powerpoint; though I generated the molecular models in CN3D, the labels, the emphasis masking, everything else was Powerpoint-only (no Photoshop required!). It took me quite a while to put this slide together, but it can be done very rapidly once you know the process.
First, I pasted the molecular model image, then cropped and resized to cover the entire image. Next, I de-emphasized the area around the focus points of my image by creating a large grey oval, making it mostly transparent, and applying an edge-softening effect to the shape. The hard part was creating the focus points: Powerpoint does not have a function that allows you to 'cut holes' in shapes that you've made, so I had to devise a workaround to get the enzyme cofactors of interest to shine through the de-emphasis mask:
- Create the 'emphasis ovals' by selecting a dashed, red outline and no fill
- Copy the entire background molecular model image
- Crop the background image to the area of interest, so it has exactly the same height and width as the emphasis oval
- Select the cropped image and 'save as picture' to an easily-accessible directory
- Repeat (2) and (3) for each emphasis oval
- For each emphasis oval, switch the fill to 'picture', selecting the pictures you just cropped and saved
When you've inserted an image as a 'fill' on a shape, you can apply sorts of effects to the shape, change it to freeform, edit the defining points, and get some really neat results: link
Powerpoint is an often-abused artform... I saw some pretty horrific things on an industry internship a few years ago. It's a visual aid, so keep the text to the minimum! If your Powerpoint doesn't look like anyone else's, you're probably on the right track.