Problems with changing opacity by atom

[stared]

I wrote:

function highlightFrom(start) {
    return new pv.color.ColorOp(function(atom, out, index) {
      if (atom.index() > start) {
        out[index+0] = 1.0; // R
        out[index+1] = 0.0; // G
        out[index+2] = 0.0; // B
        out[index+3] = 1.0; // A
      } else {
        out[index+0] = 0.0;
        out[index+1] = 1.0;
        out[index+2] = 0.0;
        out[index+3] = 0.5;
      }
    });
  }

  viewer.forEach(function(go) {
    go.colorBy(highlightFrom(50));
  });

(As a side note, convention out[index+1] is begging for some description in docs; it wasn't intuitive for me and it took me some time guessing; at least comments (this // R // G // B // A) would be really nice.)

However, opacity does not work as intended: (i.e. it rather mixes with white than makes thing semi-transparent):

Is there way to make parts of a structure transparent or semi-transparent (either with colorBy or something like setOpacity)? (Setting opacity would be even nicer, as I don't intend to change a color.)

[biasmv]

Hi,

I believe you are experiencing the problems outlined here: #55. The part of the geometry you are highlighting (N-term) is always rendered before the rest of the protein. It would work correctly for the C-term.

I've started implementing a special highlighting pass in a local branch a while ago (see screenshot) It essentially abuses the alpha color channel for implementing a glow around the selected part. If there is interest, I can spend some time to get it ready for prime-time.

I agree, the docs are not very clear on what the indices mean. I'll update them to make it clearer.

[biasmv]

@stared: here are the updated docs: http://pv.readthedocs.org/en/latest/coloring.html#adding-a-new-color-operation