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 > >
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