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 > >
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