Finish: Add 3D arrow depth effect using Paint Shop Pro
Admittedly, I am probably the last one left who still uses Paint Shop Pro 8.0 (it's from 2003!). But it's easy and fast at what I want it to do: Cut and paste parts from large images. You are free to use Photo Shop, Paint, or another software that does the same for your. The point is the same.
If there was a molecular visualization program that could add colorful 3D arrows into the molecule structure file, this step would be unnecessary.
1. In the Illustrator session go to File -> Export.
2. Export the figure to a png file with a resolution of at least 300 ppi.
3. Now go back to the illustrator session and hide all the Waves layers and the FRET layer.
4. Export the figure once more using the exact same settings, but with a new filename.
5. Open both exported figures in Paint Shop Pro, or similar software.
6. The purpose now, is to manually cut all parts of the molecule that are hidden behind an arrow but should instead be located in the foreground in front of the arrow. This procedure is exemplified by the large 3D energy transfer arrow in the front.
7. In Paint Shop Pro I use the 'Freehand Selection Tool' the manually copy parts from the right image to the left image.
8. This procedure is done for all parts of the molecule that should be located in front of the 3D arrows.
The finished figure: