Using a Mix Shader with Transparent BSDF gets us the shadows we want, but also affects the object's shading in a way we don't want.
We can fix this using the Light Paths node. The Is Shadow Ray output can be used as the Factor of the Mix Shader.
You can use the color values of the Transparent BSDF to control how much shadow appears.
Areas with many folds ...
The reason is that you have set your Face object to be invisible to all rays except for camera rays. Camera rays are rays that project out from the screen. Once these camera rays hit any rendering object, they cease to be camera rays. For example, once they hit the surface of Helmet, and refract, they turn into transmission rays. For your face to be seen ...
Additionally to Dale Cieslak's answer, you can turn off the Shadow cast for the sphere objects in Cycles.
The objects inside cast a shadow on the insides of the outer objects. And because they are transparent you see these shadows in the image as shown in screenshot 1 of the question and screenshot 1 of Dale's answer (red sphere).
For Cycles, the shadow can ...
I don't know if this is exactly what you are looking for, but I hope it can steer you towards your goal.
The orbitals still appear "transparent" but the colors aren't blending together - you can still see red, yellow, green, and blue clearly:
Basically I added a Layer Weight->Facing connection to each of your shaders, like this:
You can tweak ...
I solved it! It was a very stupid and simple mistake. When I looked closely in the render viewport I could see that the chin was actually transparent. It could be seen more clearly though when moved to another background layer. The problem was I had a transparent BSDF in my shader. After disconnecting it, everything looks fine.
Thanks for you efforts trying ...
I was also seeing black and I redid my nodes but it still didn't work. I finally figured out my issue. I had set max transparency bounces to 0. D'oh. Go to LIGHT PATHS > MAX BOUNCES and ensure you have at least 2 for Transparency.
This is probably a side-note, it may not apply to your case. But in general, if you see shaders with identical settings but different colors being mixed, you should consider mixing the colors before they get to the shader, rather than mixing shaders; it's cheaper.
And, if you don't need Alpha further down your line, you can avoid that, too, by using the ...
If you want to see something on your plane instead of transparency, plug the 2 nodes you use as alpha layers into a Converter > Math > Add, plug this Math into the factor of a Mix Shader, in this Mix Shader plug your current setup plus the background you want to see (here a yellow Diffuse):
I just had the same problem and I check that all the settings were correct (RGBA selected and transparent film also). The problem was happening because I was doing some compositing, which might be your case. In the render tab, top right corner there is a Composite box, change that into View Layer and it should work fine!
Try something like this - it might not be perfect, and may take some tinkering, but you can adjust the clarity/rougness through the Transparency Mix, the Roughness of the Glossy Shader, and the IOR if the Fresnel - between the 3 you should be able to find a mix that comes close. I added a bit of a Noise Texture to some Bump, to give it that "slightly ...
In your case, you have to increase the Max Bounces for Transparency under Render Properties > Light Paths - but increasing the Total bounces is not necessary. The Transparency bounces are independent from the Total bounces. They need to be increased if you're using a Transparent BSDF in your material or for example a Principled Volume in smoke simulations....
You probably need to increase "Max Bounces" values in "Light Paths" in "Render" tab. You need to increase Total and Transparency values.
It is because you have more than default 8 transparent faces along some of light paths in your scene. When the limit is reached, background color is returned, hence you see black spot there.
If you create a material that looks black in EEVEE when you set the Alpha to 0, it is, as moonboots indicated in the comments, because you have the Blend Mode settings for the material set to Opaque as I do in this screenshot:
Now I change only the Blend Mode settings, in this case, to Alpha Hashed, but nothing else changes, and here's a screenshot of the ...
I fixed it by going into the Material Settings menu after selecting the character (Sphere icon with red and black patches). Then, I went to the Settings tab under the Material Menu and unchecked the box that said Show Backface.
I believe this has to do with how AO is generally handled with transparency. It should be fixed based on this very recent commit https://developer.blender.org/rBcccfa597ba6
Try rendering the scene in the latest beta release of Blender 3.0 here https://builder.blender.org/download/daily/
Try using alpha-blend instead of alpha-clip, or try changing the clip threshold (if using alpha clip). Alpha-clip is "all or nothing" when it comes to interpolation, so it can cut things out completely if not set properly.
To see Vertex Alpha in Eevee ...
Switch to Material or Render viewport shading mode
Set under Material Properties > Setting > Blend mode > Alpha Hashed
Viewport shading mode Solid can display only vertex color, not alpha.
Result is quite grainy against smooth 2.79x ... I used Samples set to only 1 to see gradient better.