add ribbon "surface" capping

[Greg Couch]

After adding the clip_cap attribute to ribbons (two separate "= new_drawing(.*ribbon" lines in atomic/structure.py, the caps don't work as well as one would like. There are separate ribbon drawing per-chain.

1) After "open 3fx2; clip", the tubes are clipped, but not the strands
2) Then "rainbow" causes the caps to disappear
3) Then "clip front -.1" causes the original caps to appear, but would like the coloring to match (perhaps this should be a separate request)

So adding ribbon caps has been left out for now.

[Greg Couch]

Talking with TomG, the strands are not clipped because of the redundant vertices for the rectangular cross sections. And the caps disappearing is a bug that might be due to the ribbons being regenerated after the caps.

[Tom Goddard]

While caps on cut ribbons look a bit nicer, it may not be worth the slower clip motion required to computed those caps. This is is even more serious with atoms and bonds which also are not capped when clipped. For the cap color, a clip cap can cross multiple residues with different colors so matching the color is only easy if the ribbon has a single color. I believe the ribbon always has vertex colors (even when it is a single color) so it is not easy to tell it is a single color.