Why make molecular models in Google Sketchup? Because it’s free, simple to use, and gives nice results that can customized as desired. All it takes is a basic knowledge of how to navigate, copy, move, and make groups and components in Sketchup.
(If you don’t yet know how to do those things, you might check out the video training tutorials at the official Google Sketchup site. And of course that’s also a good place to find Sketchup if you don’t have it installed on your computer already!)
To begin making simple molecular models in Sketchup, first start up the Sketchup application on your computer and go to the Google Sketchup 3D Warehouse. You can do that within Sketchup, without having to use an external web browser. Simply go to the Sketchup menu bar and select File>3D Warehouse>Get Models.
A window will open up on top of the Sketchup application. In the search box, enter: Modeling Molecules Basic Tool Kit.
You’ll see something like this:
You’ll want to click on the button that says ‘Download Model.’
Now you’ve got four differently-colored atoms and single and double bonds in your Sketchup application, looking like so:
And you’re probably wondering, “Is that all?” Well, I said it was simple!
But as we go along, we’ll add more atomic balls, more bonds, and sample molecules, all of which will be available for free in the Google Sketchup 3D Warehouse. For now, let’s start with the basics and make a simple molecule.
The first thing you’ll have to do, of course, is ‘explode’ the tool kit component. If you don’t know how to do this or anything else with components and/or groups, I strongly recommend that you view the tutorials at the Google Sketchup web site mentioned previously. Exploding components is very simple and despite the terminology, also very safe.
Okay, in this first blog entry, we’re going to make the simplest molecule of all, a hydrogen molecule. For this you’ll need two hydrogen atoms and a bond. We’ll discuss element-colors in another blog entry, but for now all you need to know is that hydrogen is represented by the white ball.
So you should copy, move, and paste until you’ve got something that looks like this:
(BTW, you’ll notice I changed the background to a pale bluish-greenish. I did this so that the white of the hydrogen would stand out more. The color choice is suggestive of an aqueous solution, but of course you can make your background any color you like.)
Now of course, we could just move the atoms and bonds together by eye, but that might be time-consuming and sloppy. Fortunately, there’s a simple trick that makes precisely-connecting the atoms and bonds much easier.
The trick is to go to the menu and select View>Face Style>X-Ray. And now you’ve got:
You’ll notice that each of the atoms has in its center a coordinate axis with three intersecting planes. The ends of the bonds also have this same do-hickey, which from here on out we’ll refer to as a ‘tri-plane.’ The intersection point of the three planes in the tri-plane, let’s call the ‘center-point.’
And since a picture sometimes explains better than words:
Your job, should you decide to accept it, is to match the atom tri-plane center-point with the bond tri-plane center-point. This is very easy to do because fortunately Sketchup has been designed to figure out what you want to do and ‘snap’ things together.
So let’s connect an atom with a bond.
1. Click on an atom and a blue box will appear around it (which you already knew).
2. Zoom in on the center-point of the ‘tri-plane.’
3. Click on the ‘move’ icon on the tool bar (or select ‘move’ from the tools menu). Your mouse cursor should change from an arrow to a cross of four arrows.
4. Hover (don’t click yet) the mouse cursor over the center-point of the tri-plane. You should see a little violet dot appear like so:
(And yes, you should also see the words ‘Endpoint in Group’ in a little white box as shown.)
5. Click your mouse to ‘snag’ the atom, then (very important) release the mouse button. Using your Sketchup zoom, pan, and moving skills, move the atom so that its centerpoint hovers over the center-point of one of the bond tri-planes, like so:
6. Google Sketchup should have ‘intuitively’ figured out that you wanted to superimpose the tri-plane center-points and therefore matched their positions exactly. All you have to do now is once again click.
7. Now do the same for the other atom and the other end of the bond.
8. To return to normal view, click View>Face Styles>X-Ray again and the view will ‘de-x-ray’ like so:
(The dotted line in the background is the vertical coordinate axis for the Sketchup file drawing space.)
9. You now have a hydrogen molecule. Now select all three components — the two atoms and the bond — and make a group/component. Then you can move and copy as much as you like.
10. You can also export pictures using File>Export>2D Graphic. That’s how I ended up with this:
(I guess they’re flying in formation or something.)
Well, that’s your first molecular model. Tomorrow, let’s make a model of a slightly more complex molecule — otherwise known as water.