Hi Francois,

As Elaine said multi-layer transparency is not supported in ChimeraX (or Chimera).  The reason is that the graphics code to handle it efficiently without slowing down rendering for the 99.9% of the time when users don't need it is too complex for our limited funding and few programmers to handle.  Sorry about that.  Here is the bug report Elaine made

https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7488

and an earlier one from a few years ago discussing the same issue

https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/3838

  Tom


On Aug 22, 2022, at 9:19 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Francois,
You can open that same bild file in ChimeraX to see for yourself -- unfortunately, however, the problem with transparency is the same.
<https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html>

ChimeraX also has the same problems with multiple transparent models as Chimera, see:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html#transparency-limitations>
<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2018-July/000274.html>

This BILD problem is additional, however, as the spheres are all in the same model (not multiple models) if you open them from a single file. I'll make a ChimeraX ticket for the problem with your name as reporter, so that you would receive notifications if anything happens.

To see the problem with multiple models, you can create the spheres with the "shape" command -- the transparency may work in certain places but not in others, which is the gist of the problem.  Some of the spheres will not look transparent at all, but might look transparent if you open some other structure and put it behind them.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html>

Here are the shape commands to make the same spheres as in your BILD file (also attached as shape.cxc):

color name tgreen 0,100,0,75
color name torange 100,65,0,75
color name tgrey 50,50,50,75
shape sphere radius 1.5 center -0.542700,0.122500,-0.047867 color tgreen
shape sphere radius 1.5 center 1.060560,-1.270600,-0.236620 color tgreen
shape sphere radius 1.25 center 0.611100,-2.324200,-0.346200 color torange
shape sphere radius 1.25 center 1.108100,2.092000,0.140700 color torange
shape sphere radius 1.25 center -3.097400,0.651000,0.062700 color torange
shape sphere radius 1.5 center -0.542700,0.122500,-0.047867 color tgrey
shape sphere radius 1.5 center 1.060560,-1.270600,-0.236620 color tgrey
shape sphere radius 1.5 center -1.453700,2.784800,0.269900 color tgrey
shape sphere radius 1.5 center 3.272900,0.026100,-0.134900 color tgrey
shape sphere radius 1.5 center -2.354000,-1.959600,-0.245900 color tgrey

Sorry about the limitations,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
<shape.cxc>
On Aug 21, 2022, at 11:48 PM, Francois Berenger via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear chimera hackers,

In the old Chimera (not X), if I put two transparent spheres in a .bild file:
one sphere can completely hide the other (e.g. a small one inside of a bigger one).

While, if there was true transparency, no sphere should completely hide another.

Is this better handled in ChimeraX?

I _love_ .bild files, because it is so easy to generate them in order to annotate
a 3D molecular system then view all of it (molecules + annotations) in Chimera.
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html

Thanks a lot,
F.

PS: here is an example problematic .bild file for the old chimera
---
.color green
.transparency 0.750000
.sphere -0.542700 0.122500 -0.047867 1.500000
.sphere 1.060560 -1.270600 -0.236620 1.500000
.color orange
.transparency 0.750000
.sphere 0.611100 -2.324200 -0.346200 1.250000
.sphere 1.108100 2.092000 0.140700 1.250000
.sphere -3.097400 0.651000 0.062700 1.250000
.color grey
.transparency 0.750000
.sphere -0.542700 0.122500 -0.047867 1.500000
.sphere 1.060560 -1.270600 -0.236620 1.500000
.sphere -1.453700 2.784800 0.269900 1.500000
.sphere 3.272900 0.026100 -0.134900 1.500000
.sphere -2.354000 -1.959600 -0.245900 1.500000
---
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