[Chimera-users] selection line-width

Daniel Gurnon danielgurnon at depauw.edu
Wed Dec 15 10:57:41 PST 2010

The X-ray vision is a good idea, and would be useful in thinking about
interfaces as well as surfaces. But I can imagine some situations where
'x-ray' would be problematic- you would lose some sense of depth if the
green silhouette was always visible as you rotated a model, and multiple
selections would get messy. If transparency is the problem here, would it be
easier to make selections visible through a surface *regardless *of
transparency, but not visible through other objects (i.e., ribbons and bonds
underlying the surface and other models in front of the selection would
conceal the green outline)?

Also, I'm not advocating a permanent increase in the thickness of the
selection outline- I want control over it, so I can thicken it for
presentations to large audiences.


On Wed, Dec 15, 2010 at 1:14 PM, Tom Goddard <goddard at sonic.net> wrote:

>  Hi Daniel,
>   Looking at the code I think it would not  be too hard to thicken the
> green selection outline.  We can test the appearance with a one line
> modification of the C++ code.  I've added this to the feature request list.
>     http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests
> The fact that selected objects don't show a green outline when they are
> under a transparent surface is bug 7777 reported over a year ago.
>     http://plato.cgl.ucsf.edu/trac/chimera/ticket/7777
> The technical problem is that the depth buffer is being written when
> drawing transparent surfaces.  This is needed for one-layer transparent
> surfaces (the default for molecular surfaces) but is not required for
> multi-layer transparent surfaces (the default a few years ago).  Even for
> multi-layer transparent surfaces it is desirable to write the depth buffer
> when multiple transparent models are used to minimize incorrect transparent
> object rendering (depth order wrong).
>   Here's one idea for a solution.  Green selection outlines could be shown
> even for objects hidden behind opaque surfaces and models.  It would be like
> x-ray vision.  I think this may be nice because when selected items are not
> seen because they are covered it is hard to know what is selected.  But it
> may be confusing to see these x-ray silhouettes -- would have to try to
> know.  I think it is easy to try.
>     Tom
> Hi everyone,
> Two requests that would help with interactive demonstrations to large
> audiences:
> In preferences/background, the selection mode can be "fill" or "outline".
> Is it possible to add a line-width option for outline? I want to increase
> the thickness of a selection outline to make it easier for my students to
> see when I'm projecting an image, but I don't want to use the fill option
> and lose residue color information.
> I suspect that's an easy fix, but this one might be more difficult:
> Transparent surfaces are very informative when combined with underlying
> ribbons or stick representations of atoms. But if a residue is visible
> beneath a transparent surface, selecting it (via the command line) does not
> show the selection outline. Is it possible to make that work?
> Thanks,
> Dan
> --
> ____________________________
> Daniel Gurnon, Ph. D.
> Assistant Professor of Chemistry
> DePauw University
> Greencastle, IN 46135
> p: 765-658-6279
> e: danielgurnon at depauw.edu
> _______________________________________________
> Chimera-users mailing listChimera-users at cgl.ucsf.eduhttp://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users


Daniel Gurnon, Ph. D.
Assistant Professor of Chemistry
DePauw University
Greencastle, IN 46135

p: 765-658-6279
e: danielgurnon at depauw.edu
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