From: John Stone (
Date: Mon Jul 30 2007 - 14:32:22 CDT

  If you have overlapping molecular representations, you'll need to
ensure that one is slightly larger, or otherwise "in front" of the other.
OpenGL has a slightly different way of rendering things at identical depth
than Tachyon or other renderers do, so while your overlapping representations
look fine in the VMD window, you'll need to either tweak the atom selections
so there are no longer identical overlapping regions, or you'll need to make
the specially colored regions slightly larger, so they cover up the common
portions of the representation. This is typically done by increasing the
radius or scale of the representations that you're coloring by ColorID,
but you can also just adjust your atom selections so there aren't any
overlaps, and that will also prevent this from occuring. You may wish to
upgrade to VMD 1.8.6 if you're doing a lot of rendering as the quality and
speed achieved by the new versions should greatly exceed that of VMD 1.8.3.

  John Stone

On Mon, Jul 30, 2007 at 10:54:13AM -0700, Henry Yuen wrote:
> I'm using VMD version 1.8.3, and I'm trying to spatially separate a block of
> molecules from another. I used the selections feature in the
> "Representations" box and colored one block of molecules differently (though
> they consist of the same atoms: C and H), using ColorID. However, when I
> render this scene in Tachyon, the resulting image shows that the two blocks
> of molecules are colored according to the default coloring scheme. Any
> ideas?
> Sincerely,
> Henry
> --
> Henry Yuen
> 949-705-9926

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