Hi Jarrett, I will try that, but don't I need a license for it?
Best, Petro On Fri, 6 Feb 2026 at 21:00, Jarrett Johnson < [email protected]> wrote: > 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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