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
