I had a week-long break in my Blender studies, but now I'm back as enthusiastic as ever! This evening I went through the rest of the 4th chapter - refreshed my memory as well as learned something new - and took another try with that oxygen atom.
I learned a lot of useful things in this 4th chapter of "Essential Blender", although I didn't like it as much as I liked the previous ones. At several points I felt that there were some important points that weren't mentioned. I had to ask my husband several times why this doesn't work like the book lets me understand it works. Most of those problems had to do with what needs to be done in edit mode and what can be done in object mode.
For example, applying the mirror modifier doesn't seem to do anything if I do it in object mode. My husband explained this to me. Mirror modifier mirrors the object around it's center. So if I have a cube that's center is in fact in the middle of that cube (like it is by default), the mirrored object is placed right on top of the original object. If I then move the original cube in object mode, the center of the cube moves with it and mirrored image still stays right on top of the original cube. Instead I need to move the cube in edit mode. In edit mode the center stays put when I move the vertices. This way it's possible to move the cube so that the center is outside the cube's edges. When a mirrored cube is made around this "center", it appears next to the original cube - just on the other side of the center.
Hopefully I explained that right. It took me a while to understand the idea and even longer to try and write it out :) I really think I wouldn't have figured that out for a while if I didn't have someone explaining it. But if we just forget that there's a few unclear points in this chapter, it's quite useful and interesting. With these basic tools that I've learned this far I can imagine to be able to actually do something useful.
I tried to use what I've learned and started to work on the oxygen atom again. First I tried using the array modifier to duplicate an electron. This didn't work - I couldn't get it to move correctly. Finally I ended up using mirror modifier and it worked! :D So now I have the two electrons that belong to the first shell. Unfortunately I don't think the mirror modifier works very well with the second shell where I need to have six electrons. So I need to keep on thinking and trying :) Here's a video of the current oxygen atom, with two electrons in the first shell.