Hi Anastasiya, ChimeraX draws only the frontmost transparent layer. You can see opaque objects under transparent surfaces, but not transparent objects under transparent surfaces. This is a limitation of the graphics. To handle multiple layers of transparency requires either ray tracing or slow graphics depth peeling techniques -- we don't have the resources to do this right. Tom

On Jul 13, 2020, at 9:12 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Anastasiya, Unfortunately ChimeraX does not correctly render transparency when there are multiple transparent surfaces, as mentioned in this previous post:

<http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2018-July/000274.html>

The post suggests using mesh instead of transparency.

With large molecular surfaces, the mesh lines may appear too dense, so you may want to recalculate the surfaces with lower gridSpacing (e.g. command "surface grid 1.5" where the default is 0.5); however, that will also make them less smooth in shape. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>

If map surfaces (not molecular surfaces) you can show fewer mesh lines by using a larger step value, e.g. commands:

volume style mesh volume all step 2

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#general>

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Jul 11, 2020, at 8:24 AM, Anastasiya Oguienko <anastdmitr@gmail.com> wrote:

Dear ChimeraX developers,

Hello! Thanks for this amazing tool, I enjoy every second of using it! I have a question about surface imaging: I have several subunits in the protein, and I would like to show surfaces of particular regions of different subunits. However, when one surface is above another, the lower one is not displayed no matter what the transparency value is. Is there a way to display both of the overlapping surfaces?

Thanks in advance!

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