I’m sure there are many ways to do this, but this is the way I’ve been doing it most recently:
1) Set up your pymol session. That means importing your structure, turning the background to white, and enabling any other setting to make it the desired quality.
2) I use a custom python script to make a series of commands that make the structure turn slightly, ray-trace the structure (for a high quality image), and export the image to a PNG file. The script that I’ve linked to here makes pymol export 360 images, making the structure spin around completely.
Note: Depending on your settings, this process can take 10 minutes or 3 hours. An easy parameter to change would be the resolution (default setting in the script is 2000). Obviously the settings that are toggled during step 1 can drastically change how long it takes as well.
3) Use ffmpeg (at least, on a mac) to turn the 360 images into a video.
$ ffmpeg -framerate 20 -pattern_type glob -i '*.png' -c:v libx264 -preset slow -profile:v high -level:v 4.0 -pix_fmt yuv420p -vf pad="width=ceil(iw/2)*2:height=ceil(ih/2)*2" -crf 22 -codec:a aac Output.mp4
I used homebrew to install ffmpeg last time I had to do it (brew install ffmpeg). I followed these instructions last time I had to install homebrew.
4) Drag into your powerpoint presentation, and voila!