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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