Hi can you provide a mre? ( https://stackoverflow.com/help/minimal-reproducible-example) and version numbers? you know just to know if it happens the same on this side?
I am not a pymol developer or something like that. Just a mortal guy trying to help. El vie, 6 feb 2026 a la(s) 5:23 p.m., Khoroshyy Petro ([email protected]) escribió: > Hi > I see, I'll give it a try. > Best regards. > Petro. > > On Fri, 6 Feb 2026 at 21:54, Jarrett Johnson < > [email protected]> wrote: > >> Hi, >> >> There is an evaluation period that doesn't require one. Hopefully that >> should be long enough for the fix to migrate to the open-source packages. >> >> Jarrett J >> >> On Fri, Feb 6, 2026 at 3:10 PM Khoroshyy Petro <[email protected]> >> wrote: >> >>> 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 >>>> >>>> >> >> -- >> >> *Jarrett Johnson* | Staff Developer, PyMOL >> >> _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/[email protected] > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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