recoloring surface does not recolor surface cap

[Elaine Meng]

I added a "front" (rotatable) clip plane but then later decided to change the surface color. The planar cap stayed the old color even if I rotated the whole structure or adjusted the front plane with the mouse. Image attached. It would be nice to allow the cap color to be different from the rest of the surface (e.g. transparent) but in some controllable way.

[Tom Goddard]

I think a nice solution to allow caps to be given their own color and transparency is to give them a model number, a submodel of the clipped surface. Then the color and transparency commands will work on them. Also you can hide and show the cap using Model Panel or command. Also coloring the parent will color the cap. I've made this change. Works nicely.

There are some issues this raises. First we don't have a command specifier to act on the parent and not child models. So if you color the clipped surface #1 with "color #1 blue" it will also color the cap and there is no way to prevent that. Second, some models like Volumes can have multiple surfaces that are not submodels (they have no id number). Clipping those does not make a cap submodel. You only get the cap submodel if the surface you are clipping is a model. I may remedy this by making volume surfaces submodels.

I think the solution of making caps submodels is good enough for now (and better than what Chimera 1 offers).

[Elaine Meng]

Thanks, this solution seems good to me!  I’ve only been working with the molecular surfaces, and this allows separate coloring/transparency as long as you remember to change the main surface first, then the cap.