Re: [PyMOL] transparency_mode 3 looks ugly

[Khoroshyy P. <kho...@gm...>]

Hi everyone,

Thank you for the responses.

I am currently using PyMOL version 3.1.0 from conda-forge. I will try the
suggested commands to see if they resolve the issue.

It occurs to me that the problem might be related to the specific colors
used. I haven't tested this in a while, but I don't recall having these
issues with the last version of PyMOL 2. I believe I demonstrated this
during a course about two years ago, though it is possible my memory is
failing me.
Is there a way to print out all settings?
Best.
Petro.

Best regards,

Petro.

On Fri, 6 Feb 2026 at 20:29, Jarrett Johnson <
jar...@sc...> wrote:

> Hi Petro,
>
> I don't think my original reply went through, but can I ask what version
> of PyMOL you're using and what exact commands you're using to create the
> image? On my end at least, with just pulling up an entry, showing surface,
> setting transparency both on cartoon and surface, and setting tmode to 3, I
> don't see what you're observing with the latest PyMOL (3.1.6.1).
>
> Best,
> Jarrett J.
>
> On Fri, Feb 6, 2026 at 2:18 PM Roy, Kushal Raj <kr...@co...>
> wrote:
>
>> 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
>>
>>
>>
>> Get Outlook for iOS <https://aka.ms/o0ukef>
>> ------------------------------
>> *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
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>
>
>
> --
>
> *Jarrett Johnson* | Staff Developer, PyMOL
>
>