First, we need to ensure that we are making carbon DesignAtom's. Delete everything in the scene, press ".", and have a dialogue like this:
The configuration has these read/write fields: Number Field name Field type Field value 1 Factory for replacement atoms Atom BrennerAtom//C,WireFrame,THERMOSTAT Give the number of a field to edit, or press 0 to exit: 1 This slot implements the protocol Atom. The currently chosen factory is BrennerAtom. Do you want to change the factory and reset to the new factory's default configuration? y The available factories are: Number Name 0 BoringAtom 1 BrennerAtom 2 DesignAtom What is the number of the factory you want? 2 Editing the configuration... The configuration has these read/write fields: Number Field name Field type Field value 1 Atomic Number Positive Integer 6 2 Drawing style Menu Space Fill Give the number of a field to edit, or press 0 to exit: 0 The configuration has these read/write fields: Number Field name Field type Field value 1 Factory for replacement atoms Atom DesignAtom//C,SpaceFill Give the number of a field to edit, or press 0 to exit: 0 Select something first.
Next, ensure that time is started. Press "s", and if the text window says "Stopping time", press "s" again.
Next, start with a pentagon by moving the mouse to the center of the graphics window and pressing "5". The pentagon will appear under the mouse and it will be selected. Then add hexagons around the selected figure by pressing "6":
Next we add pentagons at each of the notches between the hexagons. First, select all five notches:![]()
Then press "5":![]()
The figure's present shape is planar because of the way it has been made. It's natural shape is hemispherical. It hasn't formed itself into a hemisphere because the way it was constructed happens to leave it like like a knife balanced on edge. It's better to control how the knife falls than to let it fall randomly, so select the middle of the figure and push it away from you using shift-right-mouse:![]()
Now add another ring of hexagons by selecting the entire molecule and pressing "6":![]()
The next addition is adding pentagons to notches between hexagons again, but to see the notches we have to turn the figure sideways:![]()
Work around the figure selecting all five notches around the open end, then press "5":![]()
To finish, select the entire figure and fill with hexagons by pressing "6":![]()
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.
Fungimol has more features than it used to have, so building a buckyball is much easier than it used to be. The description above is an easy way to do it. The old version of this page described a more difficult way to do it. The old way used features that still exist and are sometimes useful. Since there is no user documentation for Fungimol other than this tutorial, enthusiastic users of Fungimol will probably want to skim the old version to ensure that they have seen all of the features.