Building the Projectile (the Hard Way)

Contents

A BuckyBall is symmetric, so first we build one half, then we duplicate the halves and join them together.

Half of the Projectile

In the previous section of the tutorial, we built a ring of six carbons surrounded by six hydrogens. For this section we will not need any hydrogens, and you should start by making a ring of five DesignAtom carbons, each bonded to the next:
Each pentagonal face in the BuckyBall is surrounded by six hexagonal faces. There is a command Shift-E that adds hexagons bordering the selected atoms, so the next step is simply to select all five atoms and type shift-E. If you start time and let things settle, you'll get something like this:
Now we have to add five pentagonal faces, one bordering each adjacent pair of hexagons around the edge. Each pentagonal face will share one atom with one of the hexagons, one atom with the other hexagon, and between them it will share one atom with both of the hexagons. Start by creating another pentagon and place it off to the side. Twist the pentagon so one of its corners points toward the main figure. I've left selected the middle of the three atoms that will be shared. This is the one that is shared by both hexagons and eventually will also be shared by the pentagon:
You might want to save your work now. Generally you'll want to save your work very often, just before you do anything the slightest bit new or unusual. I won't insert any more reminders in the tutorial about saving work.

Stop time, since it's less confusing if the patient isn't wiggling around while you're doing surgery. We will now identify the selected atom with the atom from the pentagon that is nearest to the central figure. Identifying two atoms deletes one of them and gives the other all of the bonds that either of them had originally. To do the identification, select the same atom I did in the picture immediately above, hold the mouse over the leftmost atom of the pentagon, and press ";" (semicolon). This deletes the selected atom while identifying it with the atom under the mouse, and then changes the selection to include the atom under the mouse that now has inherited the links from the recently deleted atom:

Now in several steps we'll identify the other two atoms from the central figure that have to be shared with the corresponding atoms in the pentagon. Select one:
Identify:
Select the other:
Identify:
Repeat four times for each of the other pairs of hexagons bordering the main figure. You can save some work here by making four copies of the existing pentagon instead of making four new ones, distributing the copies around the central figure, and then doing all of the identifications. The identifications eat away all of the atoms bordering the central pentagon, leaving us with this:
Then you can start time and watch everything tighten up:
The connectivity here is fine for half of a buckyball, but it is too flat. Select the central five atoms and push them away from you to give it a more reasonable shape:
You might want to save this as a .pdf file and look at it with Rasmol to verify that the links are the way you expect.

Joining Two Halves

Now we can copy the half-buckyball and join the two copies together. First, make sure time is stopped, select and copy the figure so far, then move one copy around so the two copies are facing each other.
We'll be adding a bunch of hexagonal faces to join the two halves. We won't be adding any more atoms, just links. Each hexagon will consist of four atoms from one figure and two atoms from the other; I selected the atoms for one of the faces in the figure immediately above.

Select an atom for one end of one link:

Then hold the mouse over the other end and press "l":
Repeat nine times, rotating the viewpoint around as required so you can see what you're working on. You don't really have to count the number of times you repeat, since once you create a link that is already there you'll see this message in the text window:
The two objects are already linked
Then you can start time and watch the figure close up:
We could follow the same steps as in the previous section to minimize the energy of this figure, but the fake physics of DesignAtom's works well enough in this case that this does not noticeably change the figure, so there is no need. Save this as buckyball.pdb so we can use it later in the tutorial, then delete all objects in the scene and move on to the next section.
Copyright 2000 Tim Freeman <tim@infoscreen.com>