Building the Barrel

Contents

It is rumored that a 10,10 buckytube will provide a snug fit around a buckyball. We clearly don't have a snug fit in our buckygun, but nevertheless for this tutorial we'll use a 10,10 buckytube as the barrel. To make the barrel, first we must count our hexagons, then fill in the figure to make a cylinder, then put a cap on the end.

Strings of Hexagons

To make a 10,10 buckytube, we first need to count 10 hexagons twice. Make a hexagon out of DesignAtom's, and orient it so that two edges are vertical, stop time, make a copy of it, and leave the copy selected:
Now move the right hexagon so its left two atoms coincide with the right two atoms of the left hexagon. One sensitive way to tell if they are in the same place is to adjust the depth of the right hexagon and watch the atoms that are supposed to coincide. If there is no sudden change in shading as the front atom changes, then they are in the right place.
Now press ":", which is shift-semicolon. This searches the scene for atoms that are in the same place as each other, and identifies them. If anything is selected, the search only includes atoms where at least one atom of the pair is selected. If you put the atoms close enough, you ought to get this message in the text window:
Did 2 identifications
Repeat this to make a chain of four.
Repeat again to get 8, and again to get 16. We need to count to 10 starting from 0, so trim the chain of 16 hexagons down to 11, numbered 0 through 10. Copy the 10 hexagons, twist the copy so it points up and to the right 60 degress, and then translate it so that the hex at the left end of the copy is next to the hex at the right end of the original:
Ideally we'd like to identify the leftmost hex of the copy with the rightmost hex of the original, but I can't ever get them to be close enough to each other for shift-semicolon to identify all six. So instead, just trim off the rightmost four atoms of the original, and bring the corresponding two atoms of the copy to coincide with the right two remaining atoms of the original, deselect all, and press shift-semicolon again:
As a check, start time and stop time again. If you've done this right up to this point, there shouldn't be much rearrangement when the physics is turned on. If some of your identify's missed, then the atoms that nearly coincide will abruptly move so they no longer coincide, and you know that you need to explicitly identify those two atoms.

Now we need to arrange this figure so it goes around a tube, and identify the leftmost hexagon with the rightmost hexagon. To do this, twist the viewpoint around until the leftmost and rightmost hexagons are the same height on the screen:

and then rotate the point of view so it is edge-on without changing the depth of either end:
Now, if we can fold it up so the right end of this line coincides with the left end of this line, and we avoid changing the depth of anything, everything will be properly oriented. Grab the right third of the line and translate and twist it to fold it upward:
And then fold half of that over again:
Repeat similar actions with the left half, but don't let the hexagons at the end coincide yet:
Now rotate the point of view so that you can look down on the figure from above. You'll probably see some depth dislocations that weren't visible before, but don't worry about that:
Move the two ends so they are close to each other, and at about the same 120 degree angle that we had when we made the join earlier. I've selected the four atoms that I'll be removing in the next step:
Now, as we did before, trim off four atoms from one of the ends and identify the two atoms remaining of that hex with two atoms of the hex on the other end. In this case it's likely to be difficult to get the atoms to coincide, so just use semicolon to identify the two pairs of atoms. Then start time and watch everything pull together:
Now we've defined the part of our tube that determines the shape, so all that remains to do with the tube is to fill in the rest with graphite.

Filling in the Tube

Our tube needs more length, and eventually we will have to square off the ends.

Giving it more length is easy. Just select the entire figure and press "6" to add hexagons along the edge. This will leave the new edge selected, so it is useful to press "6" repeatedly. Be sure to give the DesignAtom's a few seconds to relax between repetitions, so the figure retains a reasonable shape as it grows. Pressing "6" three times gives this somewhat wrinkled tube:

A good way to eliminate the wrinkles is to rotate the figure so you are looking down the tube:
and then select the top half of the figure and move it upward and let it pull back together. Then select the right half of the figure and move it to the right and let it pull back together. The figure will become more round:
We will call this process "blocking" after the procedure that is done to knitted sweaters when they are wrinkled because they have just been made.

Now we can square off the ends. Turn the tube so its length is horizontal and you are looking at its side:

Select the diagonally cut ends and try to cleanly remove them:
Look at the tube and trim off any spare atoms individually until it looks like this at each end:
Now that the ends are square, if we make it longer it will stay square. Repeatedly press "6" until the figure has 500 atoms, blocking it whenever it starts to look ugly. To count the atoms, select the entire molecule, position the cursor over the background, press "/", and look at the text window. When you're done you'll have something like this:

Capping the Tube

The end of the tube has 10 pairs of atoms protruding, so we need a cap with fivefold symmetry. Let's start with a pentagon, and surround it with hexagons like we did at the beginning of making the projectile:
We don't have enough atoms on the perimeter of our cap yet to match them up with the atoms on the end of the tube. If we add more hexes to the edge of the cap, it won't increase the number of atoms on the perimeter; we need to add five septagons. Here I've arranged them around the cap and selected the atoms we will be identifying next:
Identify each of the three selected atoms on the center of the cap with the corresponding selected atom on the septagon, and proceed similarly around the cap. Once again I've selected the atoms we'll be using for the next step:
Hexagons between the septagons gives us the desired perimeter, and about the right size, so just select the atoms indicated above and press "6":
Now identify each of the 20 atoms around the perimeter of the cap with the corresponding atom at the end of the tube, and start time:
Although it makes no difference in simulations, the barrel is more chemically plausible if we add hydrogen termination to the other end of the barrel. Use shift-comma to start generating hydrogens, and link each one to the corresponding atom at the end of the barrel:
Save this as barrel.pdb. Minimizing this system does not appreciably change it, so we can skip the minimization step and move directly to Loading the Gun
Copyright 2000 Tim Freeman <tim@infoscreen.com>