Hi, I think there's actually a bug still present in the open-source version (which is what conda-forge is based off of)! I see exactly what you're observing, and I will file an issue on the Github repository later today. If you pull PyMOL from the `schrodinger` conda channel or use the latest version from pymol.org, transparency mode 3 should work fine.
Best, Jarrett J. On Fri, Feb 6, 2026 at 2:50 PM Khoroshyy Petro <[email protected]> wrote: > 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 < > [email protected]> 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 <[email protected]> >> 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 <[email protected]> >>> *Sent:* Friday, February 6, 2026 12:42:10 PM >>> *To:* pymol-users <[email protected]> >>> *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 >>> _______________________________________________ >>> PyMOL-users mailing list >>> Archives: http://www.mail-archive.com/[email protected] >>> Unsubscribe: >>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe >> >> >> >> -- >> >> *Jarrett Johnson* | Staff Developer, PyMOL >> >> -- *Jarrett Johnson* | Staff Developer, PyMOL
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