pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] [Job] Staff Associate II (Computational Structural Biology) at Columbia University

[Joel S. <mjs...@al...>]

Hello thank you for your kind update:) attached is my CV/CL feel free to
call me for a virtual interview.

Best,
Joel 🚀

On Tue, Apr 14, 2026 at 3:04 PM Xiang-Jun Lu <3d...@gm...> wrote:

> The *X3DNA-DSSR* resource is at the forefront of structural
> bioinformatics, developing advanced tools for analyzing and modeling
> nucleic acid structures. We are seeking a highly motivated *Staff
> Associate II* to join our team and contribute to our next-generation
> analysis and visualization engine.
>
> To see our resource in action, please visit *wDSSR*, our new web
> interface for dissecting and modeling 3D nucleic acid structures: *https://web.x3dna-dssr.org/
> <https://web.x3dna-dssr.org/>*.
>
> We are looking for a candidate with a strong scientific background in
> structural biology or bioinformatics and a desire to contribute to
> peer-reviewed publications through community-driven data analysis. We value
> individuals who are eager to learn, adapt to new technical challenges, and
> support the global research community.
>
> For the full job description and to submit your application, please visit
> the official Columbia University posting:*https://apply.interfolio.com/183705
> <https://apply.interfolio.com/183705>*
> --
> Xiang-Jun Lu (Ph.D.)
> Email: xia...@x3...
> Web: http://x3dna.org/
> Forum: http://forum.x3dna.org/
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] [Job] Staff Associate II (Computational Structural Biology) at Columbia University

[Xiang-Jun Lu <3d...@gm...>]

The *X3DNA-DSSR* resource is at the forefront of structural bioinformatics,
developing advanced tools for analyzing and modeling nucleic acid
structures. We are seeking a highly motivated *Staff Associate II* to join
our team and contribute to our next-generation analysis and visualization
engine.

To see our resource in action, please visit *wDSSR*, our new web interface
for dissecting and modeling 3D nucleic acid structures:
*https://web.x3dna-dssr.org/
<https://web.x3dna-dssr.org/>*.

We are looking for a candidate with a strong scientific background in
structural biology or bioinformatics and a desire to contribute to
peer-reviewed publications through community-driven data analysis. We value
individuals who are eager to learn, adapt to new technical challenges, and
support the global research community.

For the full job description and to submit your application, please visit
the official Columbia University posting:*https://apply.interfolio.com/183705
<https://apply.interfolio.com/183705>*
--
Xiang-Jun Lu (Ph.D.)
Email: xia...@x3...
Web: http://x3dna.org/
Forum: http://forum.x3dna.org/

Re: [PyMOL] Query for exporting movie

[Jarrett J. <jar...@sc...>]

Hi Tatiana,

We recently released a 3.1 patch that provides two movie export options. If
you're not using PyMOL 3's Timeline to create movies, you would now export
via `File > Export Movie` and then select `Legacy` before exporting.

Best,
Jarrett J.

On Thu, Mar 12, 2026 at 10:40 AM Spatola Rossi, Tatiana via PyMOL-users <
pym...@li...> wrote:

> Hello,
> I have created a movie in pymol which has 240 frames and 1 state. When I
> press play in pymol it shows the movie but when I export it (as mpeg 1) and
> open it with VLC video player it just displays the first frame. Does
> someone know about this?
> Thank you!
> Tatiana
> ------------------------------
>
> Founded in 1821, Heriot-Watt is a leader in ideas and solutions. With
> campuses and students across the entire globe we span the world, delivering
> innovation and educational excellence in business, engineering, design and
> the physical, social and life sciences. This email is generated from the
> Heriot-Watt University Group, which includes:
>
>    1. Heriot-Watt University, a Scottish charity registered under number
>    SC000278
>    2. Heriot- Watt Services Limited (Oriam), Scotland's national
>    performance centre for sport. Heriot-Watt Services Limited is a private
>    limited company registered is Scotland with registered number SC271030 and
>    registered office at Research & Enterprise Services Heriot-Watt University,
>    Riccarton, Edinburgh, EH14 4AS.
>
> The contents (including any attachments) are confidential. If you are not
> the intended recipient of this e-mail, any disclosure, copying,
> distribution or use of its contents is strictly prohibited, and you should
> please notify the sender immediately and then delete it (including any
> attachments) from your system.
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>


-- 

*Jarrett Johnson* | Staff Developer, PyMOL

Re: [PyMOL] Query for exporting movie

[José F. A. <jfr...@gm...>]

En lugar de exportar directamente como MPEG, exporta la película como
una *secuencia
de imágenes (PNG)*.

   1. ​Ve a File > Export Movie > As PNG Images....
   2. ​PyMOL guardará 240 archivos (movie001.png, movie002.png, etc.).
   3. ​Luego, usa un software externo para unirlas. Esto te da la máxima
   calidad y evita errores de compresión.

El flujo de trabajo estándar en bioinformática es:
Renderizar a PNG: Como mencioné arriba, genera la secuencia de imágenes.
Unir con FFmpeg: Es una herramienta gratuita de línea de comandos que crea
vídeos perfectos. El comando sería algo como:
ffmpeg -i movie%03d.png -c:v libx264 -pix_fmt yuv420p mi_pelicula.mp4

Espero sea de ayuda

Saludos

El jue, 12 mar 2026, 15:41, Spatola Rossi, Tatiana via PyMOL-users <
pym...@li...> escribió:

> Hello,
> I have created a movie in pymol which has 240 frames and 1 state. When I
> press play in pymol it shows the movie but when I export it (as mpeg 1) and
> open it with VLC video player it just displays the first frame. Does
> someone know about this?
> Thank you!
> Tatiana
> ------------------------------
>
> Founded in 1821, Heriot-Watt is a leader in ideas and solutions. With
> campuses and students across the entire globe we span the world, delivering
> innovation and educational excellence in business, engineering, design and
> the physical, social and life sciences. This email is generated from the
> Heriot-Watt University Group, which includes:
>
>    1. Heriot-Watt University, a Scottish charity registered under number
>    SC000278
>    2. Heriot- Watt Services Limited (Oriam), Scotland's national
>    performance centre for sport. Heriot-Watt Services Limited is a private
>    limited company registered is Scotland with registered number SC271030 and
>    registered office at Research & Enterprise Services Heriot-Watt University,
>    Riccarton, Edinburgh, EH14 4AS.
>
> The contents (including any attachments) are confidential. If you are not
> the intended recipient of this e-mail, any disclosure, copying,
> distribution or use of its contents is strictly prohibited, and you should
> please notify the sender immediately and then delete it (including any
> attachments) from your system.
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Query for exporting movie

[Spatola R. T. <T.S...@hw...>]

Hello,
I have created a movie in pymol which has 240 frames and 1 state. When I press play in pymol it shows the movie but when I export it (as mpeg 1) and open it with VLC video player it just displays the first frame. Does someone know about this?
Thank you!
Tatiana
________________________________

Founded in 1821, Heriot-Watt is a leader in ideas and solutions. With campuses and students across the entire globe we span the world, delivering innovation and educational excellence in business, engineering, design and the physical, social and life sciences. This email is generated from the Heriot-Watt University Group, which includes:

  1.  Heriot-Watt University, a Scottish charity registered under number SC000278
  2.  Heriot- Watt Services Limited (Oriam), Scotland's national performance centre for sport. Heriot-Watt Services Limited is a private limited company registered is Scotland with registered number SC271030 and registered office at Research & Enterprise Services Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS.

The contents (including any attachments) are confidential. If you are not the intended recipient of this e-mail, any disclosure, copying, distribution or use of its contents is strictly prohibited, and you should please notify the sender immediately and then delete it (including any attachments) from your system.

Re: [PyMOL] Protein structures in 2D?

[Jarrett J. <jar...@sc...>]

As the first command
```
set matrix_mode, 1
fetch 2blx
fetch 2bly
symexp sym2blx, 2blx, (2blx), 4
symexp sym2bly, 2bly, (2bly), 4
align 2bly, 2blx
matrix_copy 2bly, sym2bly*
```

[image: image.png]
Assuming this is what you want.

Best,
Jarrett J.

On Fri, Feb 20, 2026 at 8:34 PM Francisco Murphy Pérez <
fra...@ib...> wrote:

> before matrix_copy...it moves the symmetry mates to other places...(not
> around the original coordinates)
>
> El vie, 20 feb 2026 a la(s) 7:25 p.m., Francisco Murphy Pérez (
> fra...@ib...) escribió:
>
>> before all commands...or just before the matrix_copy command?
>>
>> El vie, 20 feb 2026 a la(s) 4:29 p.m., Jarrett Johnson (
>> jar...@sc...) escribió:
>>
>>> HI Francisco,
>>>
>>> Yes, this is definitely a bug. We'll address this in the next patch. In
>>> the meantime, can you run `set matrix_mode, 1` before doing these commands
>>> and see if that helps?
>>>
>>> Best,
>>> Jarrett J
>>>
>>> On Fri, Feb 20, 2026 at 4:55 PM Francisco Murphy Pérez <
>>> fra...@ib...> wrote:
>>>
>>>> Dear PYMOL users...I found a bug...
>>>> or.. Am I doing something wrong?
>>>>
>>>> got this
>>>> ```
>>>> fetch 2blx
>>>> fetch 2bly
>>>> symexp sym2blx, 2blx, (2blx), 4
>>>> symexp sym2bly, 2bly, (2bly), 4
>>>> align 2bly, 2blx
>>>> matrix_copy 2bly, sym2bly*
>>>> ```
>>>>
>>>> Attached are 2 screenshots, before and after the last command
>>>>
>>>> How do I align symmetry mates?
>>>> Most importantly... is this a feature or a bug?
>>>> (joking...)
>>>>
>>>> Any help is appreciated!
>>>> Thanks
>>>>
>>>> _______________________________________________
>>>> PyMOL-users mailing list
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>> Unsubscribe:
>>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>>
>>>
>>>
>>> --
>>>
>>> *Jarrett Johnson* | Staff Developer, PyMOL
>>>
>>>

-- 

*Jarrett Johnson* | Staff Developer, PyMOL

Re: [PyMOL] Protein structures in 2D?

[Francisco M. P. <fra...@ib...>]

before matrix_copy...it moves the symmetry mates to other places...(not
around the original coordinates)

El vie, 20 feb 2026 a la(s) 7:25 p.m., Francisco Murphy Pérez (
fra...@ib...) escribió:

> before all commands...or just before the matrix_copy command?
>
> El vie, 20 feb 2026 a la(s) 4:29 p.m., Jarrett Johnson (
> jar...@sc...) escribió:
>
>> HI Francisco,
>>
>> Yes, this is definitely a bug. We'll address this in the next patch. In
>> the meantime, can you run `set matrix_mode, 1` before doing these commands
>> and see if that helps?
>>
>> Best,
>> Jarrett J
>>
>> On Fri, Feb 20, 2026 at 4:55 PM Francisco Murphy Pérez <
>> fra...@ib...> wrote:
>>
>>> Dear PYMOL users...I found a bug...
>>> or.. Am I doing something wrong?
>>>
>>> got this
>>> ```
>>> fetch 2blx
>>> fetch 2bly
>>> symexp sym2blx, 2blx, (2blx), 4
>>> symexp sym2bly, 2bly, (2bly), 4
>>> align 2bly, 2blx
>>> matrix_copy 2bly, sym2bly*
>>> ```
>>>
>>> Attached are 2 screenshots, before and after the last command
>>>
>>> How do I align symmetry mates?
>>> Most importantly... is this a feature or a bug?
>>> (joking...)
>>>
>>> Any help is appreciated!
>>> Thanks
>>>
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> Archives: http://www.mail-archive.com/pym...@li...
>>> Unsubscribe:
>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>>
>>
>> --
>>
>> *Jarrett Johnson* | Staff Developer, PyMOL
>>
>>

Re: [PyMOL] Protein structures in 2D?

[Francisco M. P. <fra...@ib...>]

before all commands...or just before the matrix_copy command?

El vie, 20 feb 2026 a la(s) 4:29 p.m., Jarrett Johnson (
jar...@sc...) escribió:

> HI Francisco,
>
> Yes, this is definitely a bug. We'll address this in the next patch. In
> the meantime, can you run `set matrix_mode, 1` before doing these commands
> and see if that helps?
>
> Best,
> Jarrett J
>
> On Fri, Feb 20, 2026 at 4:55 PM Francisco Murphy Pérez <
> fra...@ib...> wrote:
>
>> Dear PYMOL users...I found a bug...
>> or.. Am I doing something wrong?
>>
>> got this
>> ```
>> fetch 2blx
>> fetch 2bly
>> symexp sym2blx, 2blx, (2blx), 4
>> symexp sym2bly, 2bly, (2bly), 4
>> align 2bly, 2blx
>> matrix_copy 2bly, sym2bly*
>> ```
>>
>> Attached are 2 screenshots, before and after the last command
>>
>> How do I align symmetry mates?
>> Most importantly... is this a feature or a bug?
>> (joking...)
>>
>> Any help is appreciated!
>> Thanks
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> --
>
> *Jarrett Johnson* | Staff Developer, PyMOL
>
>

Re: [PyMOL] Protein structures in 2D?

[Jarrett J. <jar...@sc...>]

HI Francisco,

Yes, this is definitely a bug. We'll address this in the next patch. In the
meantime, can you run `set matrix_mode, 1` before doing these commands and
see if that helps?

Best,
Jarrett J

On Fri, Feb 20, 2026 at 4:55 PM Francisco Murphy Pérez <
fra...@ib...> wrote:

> Dear PYMOL users...I found a bug...
> or.. Am I doing something wrong?
>
> got this
> ```
> fetch 2blx
> fetch 2bly
> symexp sym2blx, 2blx, (2blx), 4
> symexp sym2bly, 2bly, (2bly), 4
> align 2bly, 2blx
> matrix_copy 2bly, sym2bly*
> ```
>
> Attached are 2 screenshots, before and after the last command
>
> How do I align symmetry mates?
> Most importantly... is this a feature or a bug?
> (joking...)
>
> Any help is appreciated!
> Thanks
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Staff Developer, PyMOL

[PyMOL] Protein structures in 2D?

[Francisco M. P. <fra...@ib...>]

Dear PYMOL users...I found a bug...
or.. Am I doing something wrong?

got this
```
fetch 2blx
fetch 2bly
symexp sym2blx, 2blx, (2blx), 4
symexp sym2bly, 2bly, (2bly), 4
align 2bly, 2blx
matrix_copy 2bly, sym2bly*
```

Attached are 2 screenshots, before and after the last command

How do I align symmetry mates?
Most importantly... is this a feature or a bug?
(joking...)

Any help is appreciated!
Thanks

Re: [PyMOL] transparency_mode 3 looks ugly

[Francisco M. P. <fra...@ib...>]

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 (kho...@gm...)
escribió:

> Hi
> I see, I'll give it a try.
> Best regards.
> Petro.
>
> On Fri, 6 Feb 2026 at 21:54, Jarrett Johnson <
> jar...@sc...> 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 <kho...@gm...>
>> 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 <
>>> jar...@sc...> 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 <kho...@gm...>
>>>> 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 <
>>>>> jar...@sc...> 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 <
>>>>>> kr...@co...> 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 <kho...@gm...>
>>>>>>> *Sent:* Friday, February 6, 2026 12:42:10 PM
>>>>>>> *To:* pymol-users <pym...@li...>
>>>>>>> *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/pym...@li...
>>>>>>> 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/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] transparency_mode 3 looks ugly

[Khoroshyy P. <kho...@gm...>]

Hi
I see, I'll give it a try.
Best regards.
Petro.

On Fri, 6 Feb 2026 at 21:54, Jarrett Johnson <
jar...@sc...> 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 <kho...@gm...>
> 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 <
>> jar...@sc...> 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 <kho...@gm...>
>>> 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 <
>>>> jar...@sc...> 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 <kr...@co...>
>>>>> 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 <kho...@gm...>
>>>>>> *Sent:* Friday, February 6, 2026 12:42:10 PM
>>>>>> *To:* pymol-users <pym...@li...>
>>>>>> *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/pym...@li...
>>>>>> 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
>
>

Re: [PyMOL] transparency_mode 3 looks ugly

[Jarrett J. <jar...@sc...>]

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 <kho...@gm...> 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 <
> jar...@sc...> 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 <kho...@gm...>
>> 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 <
>>> jar...@sc...> 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 <kr...@co...>
>>>> 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 <kho...@gm...>
>>>>> *Sent:* Friday, February 6, 2026 12:42:10 PM
>>>>> *To:* pymol-users <pym...@li...>
>>>>> *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/pym...@li...
>>>>> 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

Re: [PyMOL] transparency_mode 3 looks ugly

[Khoroshyy P. <kho...@gm...>]

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 <
jar...@sc...> 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 <kho...@gm...>
> 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 <
>> jar...@sc...> 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 <kr...@co...>
>>> 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 <kho...@gm...>
>>>> *Sent:* Friday, February 6, 2026 12:42:10 PM
>>>> *To:* pymol-users <pym...@li...>
>>>> *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/pym...@li...
>>>> Unsubscribe:
>>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>>
>>>
>>>
>>> --
>>>
>>> *Jarrett Johnson* | Staff Developer, PyMOL
>>>
>>>
>
> --
>
> *Jarrett Johnson* | Staff Developer, PyMOL
>
>

Re: [PyMOL] transparency_mode 3 looks ugly

[Jarrett J. <jar...@sc...>]

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 <kho...@gm...> 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 <
> jar...@sc...> 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 <kr...@co...>
>> 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 <kho...@gm...>
>>> *Sent:* Friday, February 6, 2026 12:42:10 PM
>>> *To:* pymol-users <pym...@li...>
>>> *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/pym...@li...
>>> Unsubscribe:
>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>>
>>
>> --
>>
>> *Jarrett Johnson* | Staff Developer, PyMOL
>>
>>

-- 

*Jarrett Johnson* | Staff Developer, PyMOL

Re: [PyMOL] transparency_mode 3 looks ugly

[Khoroshyy P. <kho...@gm...>]

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 <
jar...@sc...> 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 <kr...@co...>
> 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 <kho...@gm...>
>> *Sent:* Friday, February 6, 2026 12:42:10 PM
>> *To:* pymol-users <pym...@li...>
>> *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/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> --
>
> *Jarrett Johnson* | Staff Developer, PyMOL
>
>

Re: [PyMOL] transparency_mode 3 looks ugly

[Jarrett J. <jar...@sc...>]

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 <kr...@co...>
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 <kho...@gm...>
> *Sent:* Friday, February 6, 2026 12:42:10 PM
> *To:* pymol-users <pym...@li...>
> *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/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Staff Developer, PyMOL

Re: [PyMOL] transparency_mode 3 looks ugly

[Roy, K. R. <kr...@Co...>]

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 <kho...@gm...>
Sent: Friday, February 6, 2026 12:42:10 PM
To: pymol-users <pym...@li...>
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] transparency_mode 3 looks ugly

[Khoroshyy P. <kho...@gm...>]

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
Could you provide any guidance on how to resolve this?

Best regards,

Petro Khoroshyy

[PyMOL] 18th Annual CCP4/APS Crystallographic School (2026) in the US

[Xu, Q. <qx...@an...>]

Dear Colleagues,

We are pleased to announce that the 18th annual CCP4/APS Crystallographic School, "From Data Collection to Structure Refinement and Beyond," will be held from July 7th to 14th, 2026, at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. The workshop is co-hosted by CCP4, GMCA and NE-CAT at APS. All details can be found on the school website: http://www.ccp4.ac.uk/schools/APS-2026/index.php.

Dates: July 7th through 14th, 2026 (on-site), June 22nd, 2026 (virtual)
Location: Advanced Photon Source, Argonne National Laboratory, Argonne (near
Chicago), Illinois, USA

The school comprises two parts: a data collection workshop and a crystallographic computing workshop. The data collection workshop includes beamline training, data collection at upgraded GMCA and NE-CAT beamlines, and data processing, using only the participants' crystals. The crystallographic computation workshop will feature many modern crystallographic software packages (including CCP4, PHENIX, XDS, HKL, and DIALS) taught by authors and other experts. This workshop will also introduce elements of CryoEM, such as model building and refinement. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive troubleshooting of the technical difficulties participants face in their projects). An additional virtual day (June 22nd, 2026) will cover sample preparation (cryo-cooling), bioinformatics, and introductory crystallography lectures. We have had considerable success resolving these problems in past years, as attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A draft program can be found on the School website.

Applicants: The workshop strongly encourages students who need expert help with difficulties/challenges in their own projects. Graduate students, postdoctoral researchers, and early-career faculty, along with commercial/industrial researchers, are encouraged to apply. Only about 25 applicants will be selected for participation.

Application: The application deadline is May 15th, 2026, but we strongly encourage interested participants to apply as soon as possible. To apply, visit https://www.ccp4.ac.uk/schools/APS-2026/application.php

Fees: There is a $500 participation fee for selected academic students and $1,500 for industrial researchers. No credit card will be required for registration; students who are selected to participate will be contacted to pay. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals).

We hope to see you at the school.


Charles, Andrey, Graeme and Qingping

[PyMOL] Conference Announcement: 38th Molecular Modelling Workshop in Erlangen, Germany - March 9/10 2026

[Harald L. <har...@fa...>]

<!DOCTYPE html>
<html>
  <head>
    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
  </head>
  <body>
    Dear all, <br>
    <br>
    (apologies for cross posting) <br>
    <br>
    we are delighted to announce here the <br>
    "38th Molecular Modelling Workshop (MMWS)" <br>
    that takes place on Monday 9th and Tuesday 10th March 2026 <br>
    at the Friedrich-Alexander-University in Erlangen, Germany. <br>
    <a class="moz-txt-link-freetext" href="http://mmws2026.mgms-ds.de"
      moz-do-not-send="true">http://mmws2026.mgms-ds.de</a> <br>
    <br>
    The MMWS has a history of giving young scientists (especially 
    graduate students) the opportunity to present their work and dive
    into  discussions with each other, but also the "older experts" of
    the field to gain valuable feedback from academic as well as
    industrial colleagues. Oral and poster contributions are welcome
    from all areas of molecular modelling – from the life sciences,
    computational biology and chemistry, cheminformatics, to materials
    sciences. <br>
    <br>
    The conference is organized by the German Section of the Molecular
    Graphics and Modelling Society (MGMS-DS e.V.). <br>
    <br>
    ####### Plenary Speakers ####### <br>
    We are very happy to announce that three distinguished researchers
    accepted our invitation to present a plenary lecture at the 38th
    MMWS: <br>
    <br>
    Jonathan Essex, Southampton, UK <br>
    Antonella DiPizio, Munich, Germany <br>
    Vlad Cojocaru, Babes Bolyai, Romania <br>
    <br>
    ####### Poster and Lecture Awards ####### <br>
    As in the past years, there will be poster and lecture awards for
    the best student contributions. <br>
    <br>
    ####### Deadlines ####### <br>
    Abstract submission deadline is Februrary 22th, 2026. <br>
    General registration deadline is March 1st, 2026. <br>
    <br>
    The MGMS-DS e.V. offers a limited number of student travel
    bursaries. <br>
    <br>
    We are looking forward to meeting you in Erlangen! <br>
    <br>
    Petra Imhof, President of the MGMS-DS e.V. (<a
      class="moz-txt-link-freetext" href="http://www.mgms-ds.de"
      moz-do-not-send="true">http://www.mgms-ds.de</a>) <br>
    Anselm Horn, Scientific Committee Workshop Organisation 2026 <br>
    <br>
    <a class="moz-txt-link-freetext" href="http://mmws2026.mgms-ds.de"
      moz-do-not-send="true">http://mmws2026.mgms-ds.de</a> <br>
    <pre class="moz-signature" cols="72">-- 
PD Dr. rer. nat. Harald Lanig (Dipl.-Chem.)
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Zentrum für Nationales Hochleistungsrechnen Erlangen (NHR@FAU)
NHR@FAU Geschäftsstelle am Regionalen Rechenzentrum Erlangen (RRZE)
Martensstrasse 1, 91058 Erlangen, Germany
<a class="moz-txt-link-abbreviated moz-txt-link-freetext"
    href="mailto:har...@fa..." moz-do-not-send="true">har...@fa...</a> - hpc.fau.de</pre>
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</html>

Re: [PyMOL] pymol (old version) installation in conda env in ubuntu

[Jarrett J. <jar...@sc...>]

Hi Lei,

Due to recent changes that were made, all PyMOL Incentive versions prior to
2.5.10 were removed from the schrodinger conda channel and our website.

Best,
Jarrett J.

On Tue, Nov 18, 2025 at 11:28 AM Lei Qian <lei...@ou...> wrote:

> Dear users,
>
> I plan to install pymol=2.4.1 and rigimol=1.3 in a conda env (python 3.8)
> in ubuntu.
>
> However, because this 2.4.1 version is very old, it is hard to install
> this pymol version using command: conda install -c schrodinger pymol.
>
> I found the rigimol-1.5-h3fd9d12_2.tar.bz2 for rigimol installation in
> conda, although it still does not match rigimol 1.3. So I would like to
> know if is possible to find the tar.bz2 file of pymol 2.4.1, and where to
> find such tar.bz2 file of pymol 2.4.1
>
> I would appreciate it if you could offer some suggestions.
>
> Thanks!
>
> Lei
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>


-- 

*Jarrett Johnson* | Staff Developer, PyMOL

[PyMOL] pymol (old version) installation in conda env in ubuntu

[Lei Q. <lei...@ou...>]

Dear users,

I plan to install pymol=2.4.1 and rigimol=1.3 in a conda env (python 3.8) in ubuntu.

However, because this 2.4.1 version is very old, it is hard to install this pymol version using command: conda install -c schrodinger pymol.

I found the rigimol-1.5-h3fd9d12_2.tar.bz2 for rigimol installation in conda, although it still does not match rigimol 1.3. So I would like to know if is possible to find the tar.bz2 file of pymol 2.4.1, and where to find such tar.bz2 file of pymol 2.4.1

I would appreciate it if you could offer some suggestions.

Thanks!

Lei

[PyMOL] pymol (old version) installation in conda env in ubuntu

[Lei Q. <lei...@ou...>]

Dear users,

I plan to install pymol=2.4.1 and rigimol=1.3 in a conda env (python 3.8) in ubuntu.

However, because this 2.4.1 version is very old, it is hard to install this pymol version using command: conda install -c schrodinger pymol.

I found the rigimol-1.5-h3fd9d12_2.tar.bz2 for rigimol installation in conda, although it still does not match rigimol 1.3. So I would like to know if is possible to find the tar.bz2 file of pymol 2.4.1, and where to find such tar.bz2 file of pymol 2.4.1

I would appreciate it if you could offer some suggestions.

Thanks!

Lei

[PyMOL] Mutagenesis rotamer states saved as scenes but appearing in movie

[Colin D. <Col...@uw...>]

PyMol 3

Am using the mutagenesis wizard to investigate rotamers for an aa change. I can save each rotamer as a scene in the Scenes sidebar and they appear there as the correct rotamer with clashes, etc as in the main window. I can also add them to the timeline but the movie just shows the original unchanged aa. Is there a way of creating a movie illustrating the various states?