We have posted an update with several new features today!

Tools: shake will ignore bands that are not on sidechains and should
prevent getting get "stuck". Intermediate results of shake will appear
on the undo graph.

Undo Graph: with the advanced GUI, negative scores will show up in the
undo graph.

Clipboard: copy, cut, and paste have been implemented for OSX.

Scripting: added Lua functions for getting the amino acid type and
hydrophobicity of a segment, also the ability to get the negative score.

GUI fade: the gui will fade out after moving or rotating for several
seconds.

Performance improvements: a number of changes have been made to
improve the performance of the rendering.

Stability: some crashes, such as when zooming out very far, have been
fixed.