On Feb 21, 2012, at 11:25 AM, Elaine Meng wrote:

setattr p color 1,0,0,.5
setattr p display 0

... where you could put the atomspec of the two endpoint atoms at the end of each command to control only that pseudobond, instead of all pseudobonds.

If you don't like the way the change in transparency looks, another alternative is to have the breaking bond become gradually thinner (attribute "radius") while the forming bond becomes thicker.

It's just as awkward to script because you would need a setattr command each frame the motion is happening (luckily it's easy to have motions go on as other commands are executed, just don't use a "wait" command after the motion command).

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu