By LUA script you can set any band longer than actual distance between segments - that way it will push.
Search for "push" scripts to see how it works.

Ah, LUA. The scripting language of the World of Warcraft. Well that's pretty cool, except there's a reason I don't design WoW plugins. :D I'm just saying, since rubber-bands are so easy to make and such a useful tool, it would be great if anti-rubber-bands were easy to make as well. You know, for people who don't know how to use their cookbooks. :P

The only problem I can see is that eventually, a shorter anti-band may be entirely obscured by the protein chain itself. In that event, maybe there should be another scissors-tool for removing anti-bands.

Ugh, this fold isn't working. I needs me some anti-bands! *freezes and pulls by hand* :(

You can always freeze parts, make bands where you want it to go and wiggle to pull (push?) in place.

I know. Sometimes though, you prefer to use a spoon to eat soup instead of a fork or a knife. I figured, since the "rubber banding" tool was already implemented, "negative rubber banding" wouldn't be too difficult. Heck, just expand the attraction limits on the rubberband's slider to include negative values. Wouldn't even need another tool, then. (Though being able to see which bands are negative values would also be helpful, hence why I suggested a new color; that part's not really necessary in the end implementation).

I was about to suggest this on the forums when I saw that there was a feedback section.

Negative band strength could be a possibility.