Re: [PyMOL] transparency_mode 3 looks ugly

[Roy, K. R. <kr...@Co...>]

Hello,


I guess the problem occurs when you make both cartoon + surface transparent in real-time with transparency_mode=3, the OpenGL renderer in PyMOL simply sucks at compositing multiple transparent objects.


try this:


set transparency_mode, 1

set backface_cull, 0

set two_sided_lighting, 1
unset ray_shadows

then render with

ray

I hope it helps.


Cheers!

Kushal Raj Roy



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________________________________
From: Khoroshyy Petro <kho...@gm...>
Sent: Friday, February 6, 2026 12:42:10 PM
To: pymol-users <pym...@li...>
Subject: [PyMOL] transparency_mode 3 looks ugly

Hi pymollers,

I hope this mailing list is still active. I have noticed a decrease in traffic since AI release, but I hope there are still knowledgeable people.

I am having trouble with transparency rendering when setting both cartoon and surface to transparent with transparency_mode set to 3. While both surfaces are visible, the resulting image quality is poor. Please see link to the picture for reference.
https://photos.app.goo.gl/corhXXpVmdsytmxg6<https://urldefense.com/v3/__https://photos.app.goo.gl/corhXXpVmdsytmxg6__;!!LkSTlj0I!CTMrAviBOj_OX3hjz4gyCljs15ODYJbA8cY62GpxnhBZrHuef3-Z-GYeVvUj-1G6OOWetEFaKSLXxRHxHGiOteg$>
Could you provide any guidance on how to resolve this?

Best regards,

Petro Khoroshyy