Unfortunately ChimeraX does not correctly render transparency when there are multiple transparent models, except for the case of multichannel volume data like yours when volumetric style rendering is used. If you want surfaces to see boundaries more clearly you could change the style to mesh. In your case maybe you have just one outermost surface (element Si) that occludes the others and you could change just that one to mesh.

ChimeraX does not correctly render transparency with multiple models because it draws one model at a time and has no way of keeping track of all the different depth layers, only the front-most depth as it does the drawing. Our older Chimera program has the same limitation. In the current ChimeraX graphics when more than one model is transparent, only the frontmost transparent model is shown at each pixel position. You can have opaque models behind transparent ones, but not transparent behind transparent. So another option is to make just the outermost surface transparent, and the inner ones all opaque.

On Jul 24, 2018, at 1:25 PM, Zack Gainsforth <zackg@berkeley.edu> wrote:

Hi,

I’m fairly new to ChimeraX so forgive me if I’m a bit ignorant in this question.

I have volumes acquired by tomographic reconstruction of STEM/EDS data (elemental composition in an electron microscope). I want to visualize several elements together as different colors representing phases. In some cases, the boundary is fairly obvious and can be represented with an isosurface.

When I try to set the transparency of the isosurface so I can see the objects inside it, it simply turns darker color rather than transparent. As an example, here is a silicon isosurface obscuring the other volumes inside it:

<PastedGraphic-17.png>

I’m setting the transparency using the colors dialog box:

<PastedGraphic-19.png>

For comparison, if I make the isosurface invisible to show the objects inside:

<PastedGraphic-18.png>

If instead I use the transparency command:

volume #5 transparency 50

The isosurface turns black:

<PastedGraphic-20.png>

My question is: am I doing this incorrectly?

Thanks,

Zack Gainsforth
Space Sciences Laboratory, UC Berkeley
7 Gauss Way
Berkeley, CA 94720
zackg@ssl.berkeley.edu

_______________________________________________
ChimeraX-users mailing list
ChimeraX-users@cgl.ucsf.edu
Manage subscription:
http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users