pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Compatibility Issue: Cartoon Representation Disappears After Ray Tracing When Opening Old PSE Files in New PyMOL Versions

[<cz...@fo...>]

Dear PyMOL Community,

I am encountering a version compatibility issue with PyMOL and would appreciate your insights. The problem occurs when opening legacy session files (.pse) created in older PyMOL versions in newer releases (3.1.5.1).

Observed Behavior:


In the original environment (older PyMOL):


Session contains objects with simultaneous cartoon and surface representations



Both have active transparency settings



ray command correctly renders both semi-transparent elements(ray by original version.png)




In newer PyMOL versions (3.1.5.1):



Session loads without errors



ray command execution causes cartoon representation to completely disappear(ray by new version.png)



surface and other representations (e.g., sticks) render normally



Transparency settings appear preserved in GUI but ignored during rendering



The following prompt message appears when loading the PSE file:
PyMOL(TM) 3.1.5.1 - Incentive Product
Copyright (C) Schrodinger, LLC
This Executable Build integrates and extends Open-Source PyMOL.
Detected OpenGL version 2.1. Shaders available.


 Tessellation shaders not available
 Detected GLSL version 1.20.
 OpenGL graphics engine:
  GL_VENDOR:   Apple
  GL_RENDERER: Apple M2
  GL_VERSION:  2.1 Metal - 76.3
 License Expiry date: 2025-12-01 
Appreciate any guidance on resolving this rendering discrepancy while maintaining visualization integrity across versions.

Best regards,
[eva]

[PyMOL] Pymol license not found on cluster

[Nambiar, N. <nna...@vo...>]

Hi,

I'm working on a remote cluster and using pymol without GUI and am
currently getting the license not found error. I installed pymol in a
virtual conda environment. The version of pymol I am running is pymol
3.1.4.1. I downloaded an educational license and renamed it to license.lic
and placed them in 2 folder after finding a similar issue from  earlier on
the board (
https://sourceforge.net/p/pymol/mailman/pymol-users/thread/694...@sc.../
)

/lustre/isaac24/scratch/nnambia1/envs/pymol3env/share/pymol/license.lic
$HOME/.pymol/license.lic

I amstill getting the license not found watermark on my saved images. I
checked the pymol path using the following code too:

import pymol2
p1 = pymol2.PyMOL()
p1.start()
print(os.environ['PYMOL_PATH'])

which printed
out /lustre/isaac24/scratch/nnambia1/envs/pymol3env/share/pymol
For reference I activate the conda env by
conda activate /lustre/isaac24/scratch/nnambia1/envs/pymol3env

Is there a way to direct pymol to the license file and get rid of the
watermark?

Best
Nikhil Nambiar

Re: [PyMOL] Pymol loading pdb files twice

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

Hello,

Sorry, I'm a little late to reply here, but we released 3.1.6.1 early last
week which should hopefully address the issue where files were doubly
loaded.

Jarrett J.

On Thu, May 29, 2025 at 7:45 PM Jarrett Johnson <
jar...@sc...> wrote:

> Hi Kevin,
>
> Looks like we saw this issue as well back in December but seems like it
> slipped through the cracks. We've updated the priority to fix this
> hopefully by the next release. I'll reply here with any future updates.
>
> Best,
> Jarrett J.
>
> On Tue, May 27, 2025 at 1:58 PM Kevin M Jude <kj...@st...> wrote:
>
>> Using Pymol 3.1.3 (for mac from SBgrid) I notice that when I open pymol
>> by double clicking a pdb file in finder or starting up from the command
>> line with a pdb file, it appends a second state:
>>
>>
>>
>> % pymol ~/Downloads/4kc3.pdb
>>
>> PyMOL(TM) 3.1.3 - Incentive Product
>>
>> Copyright (C) Schrodinger, LLC
>>
>>
>>
>> This Executable Build integrates and extends Open-Source PyMOL.
>>
>> License Expiry date: 2025-06-30
>>
>>
>>  Detected OpenGL version 2.1. Shaders available.
>>  Tessellation shaders not available
>>  Detected GLSL version 1.20.
>>  OpenGL graphics engine:
>>   GL_VENDOR:   Apple
>>   GL_RENDERER: Apple M1
>>   GL_VERSION:  2.1 Metal - 88.1
>> HEADER    IMMUNE SYSTEM                           24-APR-13   4KC3
>> TITLE     CYTOKINE/RECEPTOR BINARY COMPLEX
>> COMPND    MOL_ID: 1;
>> COMPND   2 MOLECULE: INTERLEUKIN-33;
>> COMPND   3 CHAIN: A;
>> COMPND   4 FRAGMENT: UNP RESIDUES 112-270;
>>
>> COMPND   5 SYNONYM: IL-33, INTERLEUKIN-1 FAMILY MEMBER 11, IL-1F11, NUCLEAR`
>> COMPND   6 FACTOR FROM HIGH ENDOTHELIAL VENULES, NF-HEV;
>> COMPND   7 ENGINEERED: YES;
>> COMPND   8 MOL_ID: 2;
>> COMPND   9 MOLECULE: INTERLEUKIN-1 RECEPTOR-LIKE 1;
>> COMPND  10 CHAIN: B;
>> COMPND  11 FRAGMENT: UNP RESIDUES 19-321;
>> COMPND  12 SYNONYM: PROTEIN ST2;
>> COMPND  13 ENGINEERED: YES
>>  ObjectMolecule: Read secondary structure assignments.
>>  ObjectMolecule: Read crystal symmetry information.
>>  CmdLoad: "" loaded as "4kc3".
>>
>>  Detected 8 CPU cores.  Enabled multithreaded rendering.
>> HEADER    IMMUNE SYSTEM                           24-APR-13   4KC3
>> TITLE     CYTOKINE/RECEPTOR BINARY COMPLEX
>> COMPND    MOL_ID: 1;
>> COMPND   2 MOLECULE: INTERLEUKIN-33;
>> COMPND   3 CHAIN: A;
>> COMPND   4 FRAGMENT: UNP RESIDUES 112-270;
>>
>> COMPND   5 SYNONYM: IL-33, INTERLEUKIN-1 FAMILY MEMBER 11, IL-1F11, NUCLEAR
>> COMPND   6 FACTOR FROM HIGH ENDOTHELIAL VENULES, NF-HEV;
>> COMPND   7 ENGINEERED: YES;
>> COMPND   8 MOL_ID: 2;
>> COMPND   9 MOLECULE: INTERLEUKIN-1 RECEPTOR-LIKE 1;
>> COMPND  10 CHAIN: B;
>> COMPND  11 FRAGMENT: UNP RESIDUES 19-321;
>> COMPND  12 SYNONYM: PROTEIN ST2;
>> COMPND  13 ENGINEERED: YES
>>  ObjectMolecule: Read secondary structure assignments.
>>  ObjectMolecule: Read crystal symmetry information.
>>  CmdLoad: "" appended into object "4kc3", state 2.
>>
>>
>>
>> While if I load a pdb file into an already running instance of pymol, by
>> drag and drop or File > Open, it behaves as I expect, just loading the file
>> once. I do not see this behavior in version 3.0.0.
>>
>>
>>
>> --
>>
>> Kevin Jude, PhD
>>
>> Structural Biology Research Specialist, Garcia Lab
>>
>> Howard Hughes Medical Institute
>>
>> Stanford University School of Medicine
>>
>> Beckman B177, 279 Campus Drive, Stanford CA 94305
>> _______________________________________________
>> 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] Two issues with the draw command with current pymol version 3.1.5.1

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

Hi Norbert

Sorry, a little late to reply here, but we released 3.1.6.1 early last
week. The second issue where the image is rendered partially from the draw
command should have been addressed.

Unfortunately, the label issue still remains. It seems this has been an
issue In PyMOL for a while. For the draw command by default, PyMOL will
render the image at a higher resolution and scale it back down to remove
jagged edges (Supersampling Antialiasing). However since we draw text at
constant font size regardless of the viewport size, the text shrinks when
we perform the downscaling for the whole image. One way to avoid this is to
set the *antialias *parameter (which is separate from the settings) to zero
(see here <https://pymolwiki.org/index.php/Draw>) which will elide SSAA
pass altogether (you should still be able to use the antialias shader
settings in conjunction with this if you want smoother edges).

Hope that helps,
Jarrett J.

On Thu, May 29, 2025 at 9:00 PM Jarrett Johnson <
jar...@sc...> wrote:

> Hi Norbert,
>
> Thanks very much for the repro steps. I could reproduce this and I believe
> I know where the issue lies (since I caused them 😅). I'll aim to have
> these ironed out by the next patch.
>
> Best,
> Jarrett J
>
> On Fri, May 23, 2025 at 5:38 PM Norbert Straeter <
> st...@bb...> wrote:
>
>> Dear all,
>>
>> I would like to report two issues with the current pymol version
>> 3.1.5.1, which were present as well already in 3.1.4. The two problems
>> were not present in my previous installation of version 3.0.2. The two
>> problems are observed on a windows 11 notebook and on a linux computer.
>> The issues appear with different images, the following is a simple test
>> case:
>>
>> reinitialize
>> viewport 800,600
>> pseudoatom my_atom, pos=[1.0, 2.0, 3.0]
>> show spheres, my_atom
>> set label_position, [0.0, 0.0, 2.0]
>> label my_atom, "my_atom"
>> set label_size, 30
>> set label_color, black
>> zoom my_atom
>>
>> (1) draw command results in smaller label size
>>
>> If you use the draw command after pasting the commands above, the label
>> is plotted much smaller. When using the ray command, the label size is
>> fine. Using pymol 3.0.2 draw and ray commands result in approximately
>> the same label size as in the interactive working window.
>>
>> (2) draw command in conjunction with "set antialias_shader, 2" renders
>> only part of the image
>>
>> If you "set antialias_shader, 2" and use the draw command, only part of
>> the image is rendered. This may seem like a special option, but it is
>> part of the Menu option "Display, Quality, Maximum Quality", which I
>> frequently use. The ray command is not affected. "set antialias_shader,
>> 0" (the default) or "set antialias_shader, 1" cause no problem.
>>
>> Best regards,
>>
>> Norbert
>>
>>
>>
>> _______________________________________________
>> 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] about image generation limitation of the EDU license

[Yonghui Li <fen...@ya...>]

Thanks Jarrett! I've updated it via conda and the water marks are gone.

Thanks for your help!

Best,

Yonghui Li

On 5/30/2025 8:32 AM, Jarrett Johnson wrote:
> Hello,
>
> This issue, I believe, should have already been addressed in our 
> latest patch (3.1.5.1). Can you upgrade and see if you still observe 
> this issue?
>
> Thanks,
> Jarrett J.
>
> On Sat, May 24, 2025 at 8:38 AM Yonghui Li <fen...@ya...> 
> wrote:
>
>     Dear pymol developer and users,
>
>     I recently ran into a problem in generating molecule structures with
>     pymol. Pymol works great in generating about 100k small molecule
>     images.
>     But the problem is the watermark. I've received a EDU license and
>     configured to pymol. But since the 6th image, the watermark begins to
>     show in every image. Is it a limitation of the software or the
>     license?
>     BTW, I am using a server without a GUI, so I did the configuration
>     with
>     CLI. Any suggestions will be appreciated.
>
>     Here is the --diagnostics prints.
>
>       PyMOL(TM) 3.1.3.1 - Incentive Product
>       Copyright (C) Schrodinger, LLC
>
>       This Executable Build integrates and extends Open-Source PyMOL.
>       Detected 12 CPU cores.  Enabled multithreaded rendering.
>     PyMOL>diagnostics
>     PyMOL 3.1.3.1
>     build date: Wed Feb  5 07:42:22 2025 -0800
>     git sha: 698d66e4c6e73b53e79c3954053b380006455f15
>     conda build: py312h2dc6bc7_0
>     https://conda.anaconda.org/schrodinger/linux-64
>
>     License Information:
>       License Expiry date: 2025-12-01
>
>     License Files:
>     /opt/Anaconda3-2024.10-mols/share/pymol/license.lic
>     /opt/schrodinger/licenses/pymol-edu-license.lic
>
>     Operating System:
>     Linux-3.10.0-957.el7.x86_64-x86_64-with-glibc2.17
>     #1 SMP Thu Nov 8 23:39:32 UTC 2018
>
>     OpenGL Driver:
>     (none)
>     (none)
>     (none)
>     PyQt5 5.15.10 (Qt 5.15.2)
>
>     Python:
>     3.12.7 | packaged by conda-forge | (main, Oct  4 2024, 16:05:46) [GCC
>     13.3.0]
>     prefix=/opt/Anaconda3-2024.10-mols
>     executable=/opt/Anaconda3-2024.10-mols/bin/python
>     filesystemencoding=utf-8
>
>     Startup Scripts:
>     (no pymolrc file found)
>
>     Qt, Python and PyMOL Environment Variables:
>     LANG=en_US.UTF-8
>     PYMOL_DATA=/opt/Anaconda3-2024.10-mols/share/pymol/data
>     PYMOL_LICENSE_FILE=/opt/Anaconda3-2024.10-mols/share/pymol/license.lic:/opt/schrodinger/licenses
>     PYMOL_PATH=/opt/Anaconda3-2024.10-mols/share/pymol
>     PYTHONEXECUTABLE=/opt/Anaconda3-2024.10-mols/bin/python
>     PYTHONPATH=/opt/intel2024.0.0/advisor/2024.0/pythonapi
>     QTDIR=/usr/lib64/qt-3.3
>     QTINC=/usr/lib64/qt-3.3/include
>     QTLIB=/usr/lib64/qt-3.3/lib
>     QT_API=pyqt5
>     QT_GRAPHICSSYSTEM_CHECKED=1
>     QT_XKB_CONFIG_ROOT=/opt/Anaconda3-2024.10-mols/lib
>
>     PATH:
>     /opt/Anaconda3-2024.10-
>     mols/bin:/opt/intel2024.0.0/vtune/2024.0/bin64:/opt/intel2024.0.0/mpi/2021.11/
>     opt/mpi/libfabric/bin:/opt/intel2024.0.0/mpi/2021.11/bin:/opt/intel2024.0.0/mk
>     l/2024.0/bin/:/opt/intel2024.0.0/itac/2022.0/bin:/opt/intel2024.0.0/inspector/
>     2024.0/bin64:/opt/intel2024.0.0/dpcpp-ct/2024.0/bin:/opt/intel2024.0.0/dev-uti
>     lities/2024.0/bin:/opt/intel2024.0.0/debugger/2024.0/opt/debugger/bin:/opt/int
>     el2024.0.0/compiler/2024.0/opt/oclfpga/bin:/opt/intel2024.0.0/compiler/2024.0/
>     bin:/opt/intel2024.0.0/advisor/2024.0/bin64:/usr/lib64/qt-
>     3.3/bin:/opt/enviroment-modules.5.0.1/bin:/usr/local/bin:/usr/bin:/usr/local/s
>     bin:/usr/sbin:/opt/ibutils/bin:/public/home/******/.local/bin:/public/home
>     /******//bin
>
>     Diagnostics collected on Sat May 24 19:46:40 2025 -0800
>
>     ---------------------------------------------------------------------------------------------------------------
>
>     The python script is a bit complicate but it basically something like:
>
>     import os
>     #os.environ["PYMOL_LICENSE_FILE"]="/opt/license/pymol-edu-license.lic"
>     import importlib
>     import pymol
>     pymol.pymol_argv = ['pymol', '-qc']
>     from pymol import cmd
>
>     ******#some pre-processing
>
>     pymol.finish_launching()
>
>     os.system("pymol --diagnostics")
>
>     for i in range(len(meta)):
>          print(meta[i]["path"])
>          filename = Path(meta[i]["path"]).stem
>          prefix,p1,p2 = re.findall(r"(.+?)_\w+(\d{3})_\w+(\d{3})",
>     Path(meta[i]["path"]).stem)[0]
>          p1,p2 = int(p1)+1, int(p2)+1
>          xyz_path = basedir / f"{filename}.xyz"
>          get_xyz(meta[i]["path"]).write_file(xyz_path)
>          #cmd.delete('all')
>          cmd.reinitialize()
>          destfile = imgdir / f"{filename}.png"
>          cmd.load(f"{xyz_path}")
>
>          cmd.show('sticks')
>          cmd.show('spheres')
>          cmd.color('gray')
>          cmd.set('stick_radius', 0.15)
>          cmd.set('sphere_scale', 0.3)
>          cmd.color('gray', 'elem C')
>          cmd.color('red', 'elem O')
>          cmd.color('blue', 'elem N')
>          cmd.color('white', 'elem H')
>
>          L, R = f"id {p1}", f"id {p2}"
>          cmd.bond(L, R)
>          cmd.set_bond("stick_color", "orange", L, R)
>          cmd.set_bond("stick_radius", 0.3, L, R)
>          cmd.png(f"{destfile}", ray=1)
>
>
>
>     _______________________________________________
>     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] Two issues with the draw command with current pymol version 3.1.5.1

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

Hi Norbert,

Thanks very much for the repro steps. I could reproduce this and I believe
I know where the issue lies (since I caused them 😅). I'll aim to have
these ironed out by the next patch.

Best,
Jarrett J

On Fri, May 23, 2025 at 5:38 PM Norbert Straeter <st...@bb...>
wrote:

> Dear all,
>
> I would like to report two issues with the current pymol version
> 3.1.5.1, which were present as well already in 3.1.4. The two problems
> were not present in my previous installation of version 3.0.2. The two
> problems are observed on a windows 11 notebook and on a linux computer.
> The issues appear with different images, the following is a simple test
> case:
>
> reinitialize
> viewport 800,600
> pseudoatom my_atom, pos=[1.0, 2.0, 3.0]
> show spheres, my_atom
> set label_position, [0.0, 0.0, 2.0]
> label my_atom, "my_atom"
> set label_size, 30
> set label_color, black
> zoom my_atom
>
> (1) draw command results in smaller label size
>
> If you use the draw command after pasting the commands above, the label
> is plotted much smaller. When using the ray command, the label size is
> fine. Using pymol 3.0.2 draw and ray commands result in approximately
> the same label size as in the interactive working window.
>
> (2) draw command in conjunction with "set antialias_shader, 2" renders
> only part of the image
>
> If you "set antialias_shader, 2" and use the draw command, only part of
> the image is rendered. This may seem like a special option, but it is
> part of the Menu option "Display, Quality, Maximum Quality", which I
> frequently use. The ray command is not affected. "set antialias_shader,
> 0" (the default) or "set antialias_shader, 1" cause no problem.
>
> Best regards,
>
> Norbert
>
>
>
> _______________________________________________
> 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] Pymol loading pdb files twice

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

Hi Kevin,

Looks like we saw this issue as well back in December but seems like it
slipped through the cracks. We've updated the priority to fix this
hopefully by the next release. I'll reply here with any future updates.

Best,
Jarrett J.

On Tue, May 27, 2025 at 1:58 PM Kevin M Jude <kj...@st...> wrote:

> Using Pymol 3.1.3 (for mac from SBgrid) I notice that when I open pymol by
> double clicking a pdb file in finder or starting up from the command line
> with a pdb file, it appends a second state:
>
>
>
> % pymol ~/Downloads/4kc3.pdb
>
> PyMOL(TM) 3.1.3 - Incentive Product
>
> Copyright (C) Schrodinger, LLC
>
>
>
> This Executable Build integrates and extends Open-Source PyMOL.
>
> License Expiry date: 2025-06-30
>
>
>  Detected OpenGL version 2.1. Shaders available.
>  Tessellation shaders not available
>  Detected GLSL version 1.20.
>  OpenGL graphics engine:
>   GL_VENDOR:   Apple
>   GL_RENDERER: Apple M1
>   GL_VERSION:  2.1 Metal - 88.1
> HEADER    IMMUNE SYSTEM                           24-APR-13   4KC3
> TITLE     CYTOKINE/RECEPTOR BINARY COMPLEX
> COMPND    MOL_ID: 1;
> COMPND   2 MOLECULE: INTERLEUKIN-33;
> COMPND   3 CHAIN: A;
> COMPND   4 FRAGMENT: UNP RESIDUES 112-270;
>
> COMPND   5 SYNONYM: IL-33, INTERLEUKIN-1 FAMILY MEMBER 11, IL-1F11, NUCLEAR`
> COMPND   6 FACTOR FROM HIGH ENDOTHELIAL VENULES, NF-HEV;
> COMPND   7 ENGINEERED: YES;
> COMPND   8 MOL_ID: 2;
> COMPND   9 MOLECULE: INTERLEUKIN-1 RECEPTOR-LIKE 1;
> COMPND  10 CHAIN: B;
> COMPND  11 FRAGMENT: UNP RESIDUES 19-321;
> COMPND  12 SYNONYM: PROTEIN ST2;
> COMPND  13 ENGINEERED: YES
>  ObjectMolecule: Read secondary structure assignments.
>  ObjectMolecule: Read crystal symmetry information.
>  CmdLoad: "" loaded as "4kc3".
>
>  Detected 8 CPU cores.  Enabled multithreaded rendering.
> HEADER    IMMUNE SYSTEM                           24-APR-13   4KC3
> TITLE     CYTOKINE/RECEPTOR BINARY COMPLEX
> COMPND    MOL_ID: 1;
> COMPND   2 MOLECULE: INTERLEUKIN-33;
> COMPND   3 CHAIN: A;
> COMPND   4 FRAGMENT: UNP RESIDUES 112-270;
> COMPND   5 SYNONYM: IL-33, INTERLEUKIN-1 FAMILY MEMBER 11, IL-1F11, NUCLEAR
> COMPND   6 FACTOR FROM HIGH ENDOTHELIAL VENULES, NF-HEV;
> COMPND   7 ENGINEERED: YES;
> COMPND   8 MOL_ID: 2;
> COMPND   9 MOLECULE: INTERLEUKIN-1 RECEPTOR-LIKE 1;
> COMPND  10 CHAIN: B;
> COMPND  11 FRAGMENT: UNP RESIDUES 19-321;
> COMPND  12 SYNONYM: PROTEIN ST2;
> COMPND  13 ENGINEERED: YES
>  ObjectMolecule: Read secondary structure assignments.
>  ObjectMolecule: Read crystal symmetry information.
>  CmdLoad: "" appended into object "4kc3", state 2.
>
>
>
> While if I load a pdb file into an already running instance of pymol, by
> drag and drop or File > Open, it behaves as I expect, just loading the file
> once. I do not see this behavior in version 3.0.0.
>
>
>
> --
>
> Kevin Jude, PhD
>
> Structural Biology Research Specialist, Garcia Lab
>
> Howard Hughes Medical Institute
>
> Stanford University School of Medicine
>
> Beckman B177, 279 Campus Drive, Stanford CA 94305
> _______________________________________________
> 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] Plugins with newer PyMOL versions

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

Hi Nikolas,

Welcome to the mailing list! For PyVOL specifically, your best bet might be
to reach out to the authors of the PyVOL plugin via Github issue (seems
like there's been various ones submitted recently)
https://github.com/schlessinger-lab/pyvol . However, it doesn't seem like
it's been updated for quite some time. It may be something we could
possibly consider adopting eventually in the PyMOL Scripts community Github
repo down the road. I'll respond here if we make any progress with that.
For now, I've created
https://github.com/Pymol-Scripts/Pymol-script-repo/issues/160 to track it
and any additions/improvements we can make to it.

Best,
Jarrett J.

On Wed, May 21, 2025 at 4:05 PM Capra, Nikolas via PyMOL-users <
pym...@li...> wrote:

> Hi everyone,
>
> just got here. I’ll break the ice with what may be a bit of a trivial
> question: is anyone experiencing issues with not-so-old plugins and newer
> versions of PyMOL?
>
> My very useful plugins, among which my dearest “PyVOL”, stopped working
> after I have upgraded from PyMOL 2.5.4. I’ve got error messages related to
> the .ini files when trying to run them, so I’m guessing it may have to do
> with the changes in the software’s API (but I’m not sure and neither I’m an
> expert).
>
>
>
> I thank you in advance for your answers and insights.
>
> Cheers,
>
> Nikolas
>
>
>
> ---
>
> Nikolas Capra, PhD
>
> Postdoctoral Research Associate – Single Crystal Diffraction
>
> Neutron Scattering Division
>
> Oak Ridge National Laboratory
>
> Bldg. 8600, K-218-A
>
>
> _______________________________________________
> 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] about image generation limitation of the EDU license

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

Hello,

This issue, I believe, should have already been addressed in our latest
patch (3.1.5.1). Can you upgrade and see if you still observe this issue?

Thanks,
Jarrett J.

On Sat, May 24, 2025 at 8:38 AM Yonghui Li <fen...@ya...> wrote:

> Dear pymol developer and users,
>
> I recently ran into a problem in generating molecule structures with
> pymol. Pymol works great in generating about 100k small molecule images.
> But the problem is the watermark. I've received a EDU license and
> configured to pymol. But since the 6th image, the watermark begins to
> show in every image. Is it a limitation of the software or the license?
> BTW, I am using a server without a GUI, so I did the configuration with
> CLI. Any suggestions will be appreciated.
>
> Here is the --diagnostics prints.
>
>   PyMOL(TM) 3.1.3.1 - Incentive Product
>   Copyright (C) Schrodinger, LLC
>
>   This Executable Build integrates and extends Open-Source PyMOL.
>   Detected 12 CPU cores.  Enabled multithreaded rendering.
> PyMOL>diagnostics
> PyMOL 3.1.3.1
> build date: Wed Feb  5 07:42:22 2025 -0800
> git sha: 698d66e4c6e73b53e79c3954053b380006455f15
> conda build: py312h2dc6bc7_0
> https://conda.anaconda.org/schrodinger/linux-64
>
> License Information:
>   License Expiry date: 2025-12-01
>
> License Files:
> /opt/Anaconda3-2024.10-mols/share/pymol/license.lic
> /opt/schrodinger/licenses/pymol-edu-license.lic
>
> Operating System:
> Linux-3.10.0-957.el7.x86_64-x86_64-with-glibc2.17
> #1 SMP Thu Nov 8 23:39:32 UTC 2018
>
> OpenGL Driver:
> (none)
> (none)
> (none)
> PyQt5 5.15.10 (Qt 5.15.2)
>
> Python:
> 3.12.7 | packaged by conda-forge | (main, Oct  4 2024, 16:05:46) [GCC
> 13.3.0]
> prefix=/opt/Anaconda3-2024.10-mols
> executable=/opt/Anaconda3-2024.10-mols/bin/python
> filesystemencoding=utf-8
>
> Startup Scripts:
> (no pymolrc file found)
>
> Qt, Python and PyMOL Environment Variables:
> LANG=en_US.UTF-8
> PYMOL_DATA=/opt/Anaconda3-2024.10-mols/share/pymol/data
>
> PYMOL_LICENSE_FILE=/opt/Anaconda3-2024.10-mols/share/pymol/license.lic:/opt/schrodinger/licenses
> PYMOL_PATH=/opt/Anaconda3-2024.10-mols/share/pymol
> PYTHONEXECUTABLE=/opt/Anaconda3-2024.10-mols/bin/python
> PYTHONPATH=/opt/intel2024.0.0/advisor/2024.0/pythonapi
> QTDIR=/usr/lib64/qt-3.3
> QTINC=/usr/lib64/qt-3.3/include
> QTLIB=/usr/lib64/qt-3.3/lib
> QT_API=pyqt5
> QT_GRAPHICSSYSTEM_CHECKED=1
> QT_XKB_CONFIG_ROOT=/opt/Anaconda3-2024.10-mols/lib
>
> PATH:
> /opt/Anaconda3-2024.10-
>
> mols/bin:/opt/intel2024.0.0/vtune/2024.0/bin64:/opt/intel2024.0.0/mpi/2021.11/
>
> opt/mpi/libfabric/bin:/opt/intel2024.0.0/mpi/2021.11/bin:/opt/intel2024.0.0/mk
>
> l/2024.0/bin/:/opt/intel2024.0.0/itac/2022.0/bin:/opt/intel2024.0.0/inspector/
>
> 2024.0/bin64:/opt/intel2024.0.0/dpcpp-ct/2024.0/bin:/opt/intel2024.0.0/dev-uti
>
> lities/2024.0/bin:/opt/intel2024.0.0/debugger/2024.0/opt/debugger/bin:/opt/int
>
> el2024.0.0/compiler/2024.0/opt/oclfpga/bin:/opt/intel2024.0.0/compiler/2024.0/
> bin:/opt/intel2024.0.0/advisor/2024.0/bin64:/usr/lib64/qt-
>
> 3.3/bin:/opt/enviroment-modules.5.0.1/bin:/usr/local/bin:/usr/bin:/usr/local/s
> bin:/usr/sbin:/opt/ibutils/bin:/public/home/******/.local/bin:/public/home
> /******//bin
>
> Diagnostics collected on Sat May 24 19:46:40 2025 -0800
>
>
> ---------------------------------------------------------------------------------------------------------------
>
> The python script is a bit complicate but it basically something like:
>
> import os
> #os.environ["PYMOL_LICENSE_FILE"]="/opt/license/pymol-edu-license.lic"
> import importlib
> import pymol
> pymol.pymol_argv = ['pymol', '-qc']
> from pymol import cmd
>
> ******#some pre-processing
>
> pymol.finish_launching()
>
> os.system("pymol --diagnostics")
>
> for i in range(len(meta)):
>      print(meta[i]["path"])
>      filename = Path(meta[i]["path"]).stem
>      prefix,p1,p2 = re.findall(r"(.+?)_\w+(\d{3})_\w+(\d{3})",
> Path(meta[i]["path"]).stem)[0]
>      p1,p2 = int(p1)+1, int(p2)+1
>      xyz_path = basedir / f"{filename}.xyz"
>      get_xyz(meta[i]["path"]).write_file(xyz_path)
>      #cmd.delete('all')
>      cmd.reinitialize()
>      destfile = imgdir / f"{filename}.png"
>      cmd.load(f"{xyz_path}")
>
>      cmd.show('sticks')
>      cmd.show('spheres')
>      cmd.color('gray')
>      cmd.set('stick_radius', 0.15)
>      cmd.set('sphere_scale', 0.3)
>      cmd.color('gray', 'elem C')
>      cmd.color('red', 'elem O')
>      cmd.color('blue', 'elem N')
>      cmd.color('white', 'elem H')
>
>      L, R = f"id {p1}", f"id {p2}"
>      cmd.bond(L, R)
>      cmd.set_bond("stick_color", "orange", L, R)
>      cmd.set_bond("stick_radius", 0.3, L, R)
>      cmd.png(f"{destfile}", ray=1)
>
>
>
> _______________________________________________
> 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 loading pdb files twice

[Kevin M J. <kj...@st...>]

Using Pymol 3.1.3 (for mac from SBgrid) I notice that when I open pymol by double clicking a pdb file in finder or starting up from the command line with a pdb file, it appends a second state:

% pymol ~/Downloads/4kc3.pdb
PyMOL(TM) 3.1.3 - Incentive Product
Copyright (C) Schrodinger, LLC

This Executable Build integrates and extends Open-Source PyMOL.
License Expiry date: 2025-06-30

 Detected OpenGL version 2.1. Shaders available.
 Tessellation shaders not available
 Detected GLSL version 1.20.
 OpenGL graphics engine:
  GL_VENDOR:   Apple
  GL_RENDERER: Apple M1
  GL_VERSION:  2.1 Metal - 88.1
HEADER    IMMUNE SYSTEM                           24-APR-13   4KC3
TITLE     CYTOKINE/RECEPTOR BINARY COMPLEX
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: INTERLEUKIN-33;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: UNP RESIDUES 112-270;
COMPND   5 SYNONYM: IL-33, INTERLEUKIN-1 FAMILY MEMBER 11, IL-1F11, NUCLEAR`
COMPND   6 FACTOR FROM HIGH ENDOTHELIAL VENULES, NF-HEV;
COMPND   7 ENGINEERED: YES;
COMPND   8 MOL_ID: 2;
COMPND   9 MOLECULE: INTERLEUKIN-1 RECEPTOR-LIKE 1;
COMPND  10 CHAIN: B;
COMPND  11 FRAGMENT: UNP RESIDUES 19-321;
COMPND  12 SYNONYM: PROTEIN ST2;
COMPND  13 ENGINEERED: YES
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 CmdLoad: "" loaded as "4kc3".
 Detected 8 CPU cores.  Enabled multithreaded rendering.
HEADER    IMMUNE SYSTEM                           24-APR-13   4KC3
TITLE     CYTOKINE/RECEPTOR BINARY COMPLEX
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: INTERLEUKIN-33;
COMPND   3 CHAIN: A;
COMPND   4 FRAGMENT: UNP RESIDUES 112-270;
COMPND   5 SYNONYM: IL-33, INTERLEUKIN-1 FAMILY MEMBER 11, IL-1F11, NUCLEAR
COMPND   6 FACTOR FROM HIGH ENDOTHELIAL VENULES, NF-HEV;
COMPND   7 ENGINEERED: YES;
COMPND   8 MOL_ID: 2;
COMPND   9 MOLECULE: INTERLEUKIN-1 RECEPTOR-LIKE 1;
COMPND  10 CHAIN: B;
COMPND  11 FRAGMENT: UNP RESIDUES 19-321;
COMPND  12 SYNONYM: PROTEIN ST2;
COMPND  13 ENGINEERED: YES
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 CmdLoad: "" appended into object "4kc3", state 2.

While if I load a pdb file into an already running instance of pymol, by drag and drop or File > Open, it behaves as I expect, just loading the file once. I do not see this behavior in version 3.0.0.

--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305

[PyMOL] about image generation limitation of the EDU license

[Yonghui Li <fen...@ya...>]

Dear pymol developer and users,

I recently ran into a problem in generating molecule structures with 
pymol. Pymol works great in generating about 100k small molecule images. 
But the problem is the watermark. I've received a EDU license and 
configured to pymol. But since the 6th image, the watermark begins to 
show in every image. Is it a limitation of the software or the license? 
BTW, I am using a server without a GUI, so I did the configuration with 
CLI. Any suggestions will be appreciated.

Here is the --diagnostics prints.

  PyMOL(TM) 3.1.3.1 - Incentive Product
  Copyright (C) Schrodinger, LLC

  This Executable Build integrates and extends Open-Source PyMOL.
  Detected 12 CPU cores.  Enabled multithreaded rendering.
PyMOL>diagnostics
PyMOL 3.1.3.1
build date: Wed Feb  5 07:42:22 2025 -0800
git sha: 698d66e4c6e73b53e79c3954053b380006455f15
conda build: py312h2dc6bc7_0 https://conda.anaconda.org/schrodinger/linux-64

License Information:
  License Expiry date: 2025-12-01

License Files:
/opt/Anaconda3-2024.10-mols/share/pymol/license.lic
/opt/schrodinger/licenses/pymol-edu-license.lic

Operating System:
Linux-3.10.0-957.el7.x86_64-x86_64-with-glibc2.17
#1 SMP Thu Nov 8 23:39:32 UTC 2018

OpenGL Driver:
(none)
(none)
(none)
PyQt5 5.15.10 (Qt 5.15.2)

Python:
3.12.7 | packaged by conda-forge | (main, Oct  4 2024, 16:05:46) [GCC 
13.3.0]
prefix=/opt/Anaconda3-2024.10-mols
executable=/opt/Anaconda3-2024.10-mols/bin/python
filesystemencoding=utf-8

Startup Scripts:
(no pymolrc file found)

Qt, Python and PyMOL Environment Variables:
LANG=en_US.UTF-8
PYMOL_DATA=/opt/Anaconda3-2024.10-mols/share/pymol/data
PYMOL_LICENSE_FILE=/opt/Anaconda3-2024.10-mols/share/pymol/license.lic:/opt/schrodinger/licenses
PYMOL_PATH=/opt/Anaconda3-2024.10-mols/share/pymol
PYTHONEXECUTABLE=/opt/Anaconda3-2024.10-mols/bin/python
PYTHONPATH=/opt/intel2024.0.0/advisor/2024.0/pythonapi
QTDIR=/usr/lib64/qt-3.3
QTINC=/usr/lib64/qt-3.3/include
QTLIB=/usr/lib64/qt-3.3/lib
QT_API=pyqt5
QT_GRAPHICSSYSTEM_CHECKED=1
QT_XKB_CONFIG_ROOT=/opt/Anaconda3-2024.10-mols/lib

PATH:
/opt/Anaconda3-2024.10-
mols/bin:/opt/intel2024.0.0/vtune/2024.0/bin64:/opt/intel2024.0.0/mpi/2021.11/
opt/mpi/libfabric/bin:/opt/intel2024.0.0/mpi/2021.11/bin:/opt/intel2024.0.0/mk
l/2024.0/bin/:/opt/intel2024.0.0/itac/2022.0/bin:/opt/intel2024.0.0/inspector/
2024.0/bin64:/opt/intel2024.0.0/dpcpp-ct/2024.0/bin:/opt/intel2024.0.0/dev-uti
lities/2024.0/bin:/opt/intel2024.0.0/debugger/2024.0/opt/debugger/bin:/opt/int
el2024.0.0/compiler/2024.0/opt/oclfpga/bin:/opt/intel2024.0.0/compiler/2024.0/
bin:/opt/intel2024.0.0/advisor/2024.0/bin64:/usr/lib64/qt-
3.3/bin:/opt/enviroment-modules.5.0.1/bin:/usr/local/bin:/usr/bin:/usr/local/s
bin:/usr/sbin:/opt/ibutils/bin:/public/home/******/.local/bin:/public/home
/******//bin

Diagnostics collected on Sat May 24 19:46:40 2025 -0800

---------------------------------------------------------------------------------------------------------------

The python script is a bit complicate but it basically something like:

import os
#os.environ["PYMOL_LICENSE_FILE"]="/opt/license/pymol-edu-license.lic"
import importlib
import pymol
pymol.pymol_argv = ['pymol', '-qc']
from pymol import cmd

******#some pre-processing

pymol.finish_launching()

os.system("pymol --diagnostics")

for i in range(len(meta)):
     print(meta[i]["path"])
     filename = Path(meta[i]["path"]).stem
     prefix,p1,p2 = re.findall(r"(.+?)_\w+(\d{3})_\w+(\d{3})", 
Path(meta[i]["path"]).stem)[0]
     p1,p2 = int(p1)+1, int(p2)+1
     xyz_path = basedir / f"{filename}.xyz"
     get_xyz(meta[i]["path"]).write_file(xyz_path)
     #cmd.delete('all')
     cmd.reinitialize()
     destfile = imgdir / f"{filename}.png"
     cmd.load(f"{xyz_path}")

     cmd.show('sticks')
     cmd.show('spheres')
     cmd.color('gray')
     cmd.set('stick_radius', 0.15)
     cmd.set('sphere_scale', 0.3)
     cmd.color('gray', 'elem C')
     cmd.color('red', 'elem O')
     cmd.color('blue', 'elem N')
     cmd.color('white', 'elem H')

     L, R = f"id {p1}", f"id {p2}"
     cmd.bond(L, R)
     cmd.set_bond("stick_color", "orange", L, R)
     cmd.set_bond("stick_radius", 0.3, L, R)
     cmd.png(f"{destfile}", ray=1)

[PyMOL] header intact

[<487...@qq...>]

header intact

[PyMOL] Two issues with the draw command with current pymol version 3.1.5.1

[Norbert S. <st...@bb...>]

Dear all,

I would like to report two issues with the current pymol version 
3.1.5.1, which were present as well already in 3.1.4. The two problems 
were not present in my previous installation of version 3.0.2. The two 
problems are observed on a windows 11 notebook and on a linux computer. 
The issues appear with different images, the following is a simple test 
case:

reinitialize
viewport 800,600
pseudoatom my_atom, pos=[1.0, 2.0, 3.0]
show spheres, my_atom
set label_position, [0.0, 0.0, 2.0]
label my_atom, "my_atom"
set label_size, 30
set label_color, black
zoom my_atom

(1) draw command results in smaller label size

If you use the draw command after pasting the commands above, the label 
is plotted much smaller. When using the ray command, the label size is 
fine. Using pymol 3.0.2 draw and ray commands result in approximately 
the same label size as in the interactive working window.

(2) draw command in conjunction with "set antialias_shader, 2" renders 
only part of the image

If you "set antialias_shader, 2" and use the draw command, only part of 
the image is rendered. This may seem like a special option, but it is 
part of the Menu option "Display, Quality, Maximum Quality", which I 
frequently use. The ray command is not affected. "set antialias_shader, 
0" (the default) or "set antialias_shader, 1" cause no problem.

Best regards,

Norbert

[PyMOL] Plugins with newer PyMOL versions

[Capra, N. <ca...@or...>]

Hi everyone,

just got here. I’ll break the ice with what may be a bit of a trivial question: is anyone experiencing issues with not-so-old plugins and newer versions of PyMOL?

My very useful plugins, among which my dearest “PyVOL”, stopped working after I have upgraded from PyMOL 2.5.4. I’ve got error messages related to the .ini files when trying to run them, so I’m guessing it may have to do with the changes in the software’s API (but I’m not sure and neither I’m an expert).

I thank you in advance for your answers and insights.

Cheers,
Nikolas

---
Nikolas Capra, PhD
Postdoctoral Research Associate – Single Crystal Diffraction
Neutron Scattering Division
Oak Ridge National Laboratory
Bldg. 8600, K-218-A

Re: [PyMOL] [ccp4bb] Announcement: The 17th CCP4/APS Crystallographic School, June 23rd-30th, 2025, APS

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

Dear Friends,

This is a reminder that we are still accepting application for the upcoming CCP4 crystallography workshop @APS. Thanks.

Qingping

________________________________
From: CCP4 bulletin board <CC...@JI...> on behalf of Xu, Qingping <000...@JI...>
Sent: Monday, January 27, 2025 8:36 AM
To: CC...@JI... <CC...@JI...>
Subject: [ccp4bb] Announcement: The 17th CCP4/APS Crystallographic School, June 23rd-30th, 2025, APS

This Message Is From an External Sender
This message came from outside your organization.

Dear Colleagues,

We are pleased to announce that the 17th annual CCP4/APS Crystallographic School, "From Data Collection to Structure Refinement and Beyond," will be held from June 23rd to 30th, 2025, at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found on the school website: http://www.ccp4.ac.uk/schools/APS-2025/index.php<https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-2025/index.php__;!!G_uCfscf7eWS!efj1mSIiPgk0NgZMHmGe4hJPfYd2OQDHTAN3c3Vrem3MB2NKtbVF54Rrswt012yfTyeTDwQiLmscAeDYLd-jpEoeFbg6-D4$>.

Dates: June 23rd through 30th, 2025 (on-site), June 2nd and 16th (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 GM/CA@APS 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). Two additional virtual days (June 2nd and 16th, 2025) 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<https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-school/publications.php__;!!G_uCfscf7eWS!efj1mSIiPgk0NgZMHmGe4hJPfYd2OQDHTAN3c3Vrem3MB2NKtbVF54Rrswt012yfTyeTDwQiLmscAeDYLd-jpEoeWp70wu8$>). 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 20 applicants will be selected for participation.

Application: The application deadline is May 15th, 2025, we strongly encourage interested participants to apply as soon as possible. To apply, visit https://www.ccp4.ac.uk/schools/APS-2025/application.php<https://urldefense.us/v3/__https://www.ccp4.ac.uk/schools/APS-2025/application.php__;!!G_uCfscf7eWS!efj1mSIiPgk0NgZMHmGe4hJPfYd2OQDHTAN3c3Vrem3MB2NKtbVF54Rrswt012yfTyeTDwQiLmscAeDYLd-jpEoePiMMUbg$>

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, Garib and Qingping


________________________________

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.us/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!G_uCfscf7eWS!efj1mSIiPgk0NgZMHmGe4hJPfYd2OQDHTAN3c3Vrem3MB2NKtbVF54Rrswt012yfTyeTDwQiLmscAeDYLd-jpEoefg6ZIm0$>

Re: [PyMOL] Thermal ellipsoids with principal axes

[Takanori N. <tna...@os...>]

Hi Thomas,

Thank you very much!

 > "ellipsoid_probability" per atom would also be easy, like this:
 >
 > from pymol.editor import iterate_to_list
 > color_indices = iterate_to_list(selection, "color")
 > prob_per_atom = iterate_to_list(selection, "s.ellipsoid_probability")

Apparently this method is a relatively new addition to PyMOL.

For compatibility, I implemented this using `cmd.iterate` with
`s.ellipsoid_probability`. I didn't know I could read per-atom
properties like this.

 > Your scaling factor 32 on "ellipsoid_quality" is a lot higher than
 > PyMOL's native ellipsoids, which use a factor of 12 as far as I can
 > tell.

OK. I kept it as is because 12 looked rather ugly (as mine doesn't use
the sphere impostor shader).

Best regards,

Takanori Nakane

On 5/1/25 16:57, Thomas Holder wrote:
> Hi Takanori,
> 
> This is brilliant. Works like a charm. Thanks a lot for sharing the script.
> 
> Your scaling factor 32 on "ellipsoid_quality" is a lot higher than
> PyMOL's native ellipsoids, which use a factor of 12 as far as I can
> tell.
> 
> "ellipsoid_probability" per atom would also be easy, like this:
> 
> from pymol.editor import iterate_to_list
> color_indices = iterate_to_list(selection, "color")
> prob_per_atom = iterate_to_list(selection, "s.ellipsoid_probability")
> 
> Cheers,
>    Thomas
> 
> On Thu, May 1, 2025 at 8:04 AM Takanori Nakane
> <tna...@os...> wrote:
>>
>> Hi,
>>
>>   > At the moment my code does not support object's TTT matrix
>>   > and per-atom colors. Once I fix these limitations,
>>   > I will put my script to my GitHub or PyMOL wiki.
>>
>> I made my script public at
>> https://gist.github.com/biochem-fan/0a5b690670e90af8946adddc1c40fa6b.
>>
>> Unfortunately I could not find enough time to support the
>> TTT matrix but I hope this is already useful.
>>
>> WARNING: I tried my best to make sure my ellipsoids match
>> PyMOL's native ellipsoids but can never guarantee this is
>> bug free. Please double check before you use my script
>> for serious purposes (e.g. publication).
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>> On 3/28/25 13:11, Takanori Nakane wrote:
>>> Hi,
>>>
>>> I ended up implementing this myself, drawing three ellipses
>>> by CGO over PyMOL's native ellipsoids.
>>> My current style is like the one in
>>> https://www.chem.gla.ac.uk/~louis/software/ortep/index.html.
>>>
>>> At the moment my code does not support object's TTT matrix
>>> and per-atom colors. Once I fix these limitations,
>>> I will put my script to my GitHub or PyMOL wiki.
>>>
>>> I also want to implement the "cutting out one octant" feature
>>> like ORTEP but that would require completely hiding
>>> PyMOL's native ellipsoids and drawing everything from scratch.
>>>
>>> Best regards,
>>>
>>> Takanori Nakane
>>>
>>> On 3/25/25 22:30, Takanori Nakane wrote:
>>>> Dear PyMOL users,
>>>>
>>>> I am preparing figures for small molecular crystallography.
>>>> I know I can plot thermal ellipsoids in PyMOL but can I add
>>>> principal axes on the surface (or cut out one octant)?
>>>>
>>>> I would like to draw something like ORTEP:
>>>> https://www.chem.gla.ac.uk/~louis/software/ortep/fig2.gif.
>>>>
>>>> Do I have to code CGO objects?
>>>>
>>>> Best regards,
>>>>
>>>> Takanori Nakane
>>>>
>>>>
>>>> _______________________________________________
>>>> PyMOL-users mailing list
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>> Unsubscribe:
>>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Thermal ellipsoids with principal axes

[Thomas H. <th...@th...>]

Hi Takanori,

This is brilliant. Works like a charm. Thanks a lot for sharing the script.

Your scaling factor 32 on "ellipsoid_quality" is a lot higher than
PyMOL's native ellipsoids, which use a factor of 12 as far as I can
tell.

"ellipsoid_probability" per atom would also be easy, like this:

from pymol.editor import iterate_to_list
color_indices = iterate_to_list(selection, "color")
prob_per_atom = iterate_to_list(selection, "s.ellipsoid_probability")

Cheers,
  Thomas

On Thu, May 1, 2025 at 8:04 AM Takanori Nakane
<tna...@os...> wrote:
>
> Hi,
>
>  > At the moment my code does not support object's TTT matrix
>  > and per-atom colors. Once I fix these limitations,
>  > I will put my script to my GitHub or PyMOL wiki.
>
> I made my script public at
> https://gist.github.com/biochem-fan/0a5b690670e90af8946adddc1c40fa6b.
>
> Unfortunately I could not find enough time to support the
> TTT matrix but I hope this is already useful.
>
> WARNING: I tried my best to make sure my ellipsoids match
> PyMOL's native ellipsoids but can never guarantee this is
> bug free. Please double check before you use my script
> for serious purposes (e.g. publication).
>
> Best regards,
>
> Takanori Nakane
>
> On 3/28/25 13:11, Takanori Nakane wrote:
> > Hi,
> >
> > I ended up implementing this myself, drawing three ellipses
> > by CGO over PyMOL's native ellipsoids.
> > My current style is like the one in
> > https://www.chem.gla.ac.uk/~louis/software/ortep/index.html.
> >
> > At the moment my code does not support object's TTT matrix
> > and per-atom colors. Once I fix these limitations,
> > I will put my script to my GitHub or PyMOL wiki.
> >
> > I also want to implement the "cutting out one octant" feature
> > like ORTEP but that would require completely hiding
> > PyMOL's native ellipsoids and drawing everything from scratch.
> >
> > Best regards,
> >
> > Takanori Nakane
> >
> > On 3/25/25 22:30, Takanori Nakane wrote:
> >> Dear PyMOL users,
> >>
> >> I am preparing figures for small molecular crystallography.
> >> I know I can plot thermal ellipsoids in PyMOL but can I add
> >> principal axes on the surface (or cut out one octant)?
> >>
> >> I would like to draw something like ORTEP:
> >> https://www.chem.gla.ac.uk/~louis/software/ortep/fig2.gif.
> >>
> >> Do I have to code CGO objects?
> >>
> >> Best regards,
> >>
> >> Takanori Nakane
> >>
> >>
> >> _______________________________________________
> >> PyMOL-users mailing list
> >> Archives: http://www.mail-archive.com/pym...@li...
> >> Unsubscribe:
> >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Thermal ellipsoids with principal axes

[Takanori N. <tna...@os...>]

Hi,

 > At the moment my code does not support object's TTT matrix
 > and per-atom colors. Once I fix these limitations,
 > I will put my script to my GitHub or PyMOL wiki.

I made my script public at 
https://gist.github.com/biochem-fan/0a5b690670e90af8946adddc1c40fa6b.

Unfortunately I could not find enough time to support the
TTT matrix but I hope this is already useful.

WARNING: I tried my best to make sure my ellipsoids match
PyMOL's native ellipsoids but can never guarantee this is
bug free. Please double check before you use my script
for serious purposes (e.g. publication).

Best regards,

Takanori Nakane

On 3/28/25 13:11, Takanori Nakane wrote:
> Hi,
> 
> I ended up implementing this myself, drawing three ellipses
> by CGO over PyMOL's native ellipsoids.
> My current style is like the one in
> https://www.chem.gla.ac.uk/~louis/software/ortep/index.html.
> 
> At the moment my code does not support object's TTT matrix
> and per-atom colors. Once I fix these limitations,
> I will put my script to my GitHub or PyMOL wiki.
> 
> I also want to implement the "cutting out one octant" feature
> like ORTEP but that would require completely hiding
> PyMOL's native ellipsoids and drawing everything from scratch.
> 
> Best regards,
> 
> Takanori Nakane
> 
> On 3/25/25 22:30, Takanori Nakane wrote:
>> Dear PyMOL users,
>>
>> I am preparing figures for small molecular crystallography.
>> I know I can plot thermal ellipsoids in PyMOL but can I add
>> principal axes on the surface (or cut out one octant)?
>>
>> I would like to draw something like ORTEP:
>> https://www.chem.gla.ac.uk/~louis/software/ortep/fig2.gif.
>>
>> Do I have to code CGO objects?
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe: 
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] 'Extent' representation in PyMOL

[Daniel M. <mar...@ho...>]

Hi Jarrett,
I see now. Thanks a lot for taking the time to answer!

Best,
D.
________________________________
De: Jarrett Johnson <jar...@sc...>
Enviado: sábado, 12 de abril de 2025 16:56
Para: Daniel Martinez <mar...@ho...>
Cc: pym...@li... <pym...@li...>
Asunto: Re: [PyMOL] 'Extent' representation in PyMOL

Hi Dani,

The extent should simply be the bounding box that contains all of the map density data in cartesian space.

Best,
Jarrett J

On Sat, Apr 12, 2025 at 7:27 AM Daniel Martinez <mar...@ho...<mailto:mar...@ho...>> wrote:
Dear PyMOL user community,
I’ve been trying to understand exactly what the 'extent' representation refers to in PyMOL.
It’s listed as a type of Map representation in the following reference:
https://pymol.org/dokuwiki/doku.php?id=representation
However, I haven’t been able to find any further documentation or explanation about it.
Could anyone provide some insight or point me to where it might be described?
Thank you in advance!
Best regards,
Dani.
_______________________________________________
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

[https://drive.google.com/uc?id=1zOlB9fluGZyuInRUQgKsdjtjpR5L9z6R&export=download]

Re: [PyMOL] 'Extent' representation in PyMOL

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

Hi Dani,

The extent should simply be the bounding box that contains all of the map
density data in cartesian space.

Best,
Jarrett J

On Sat, Apr 12, 2025 at 7:27 AM Daniel Martinez <mar...@ho...>
wrote:

> Dear PyMOL user community,
> I’ve been trying to understand exactly what the *'extent'* representation
> refers to in PyMOL.
> It’s listed as a type of *Map representation* in the following reference:
> https://pymol.org/dokuwiki/doku.php?id=representation
> However, I haven’t been able to find any further documentation or
> explanation about it.
> Could anyone provide some insight or point me to where it might be
> described?
> Thank you in advance!
> Best regards,
> Dani.
> _______________________________________________
> 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] 'Extent' representation in PyMOL

[Daniel M. <mar...@ho...>]

Dear PyMOL user community,
I’ve been trying to understand exactly what the 'extent' representation refers to in PyMOL.
It’s listed as a type of Map representation in the following reference:
https://pymol.org/dokuwiki/doku.php?id=representation
However, I haven’t been able to find any further documentation or explanation about it.
Could anyone provide some insight or point me to where it might be described?
Thank you in advance!
Best regards,
Dani.

Re: [PyMOL] [ccp4bb] Announcement: The 17th CCP4/APS Crystallographic School, June 23rd-30th, 2025, APS

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

Dear friends,

This is a reminder of that registration is still open for the upcoming 2025 CCP4/APS workshop. If you have any questions, please let us know.

Charles, Andrey, Garib and Qingping

________________________________
From: CCP4 bulletin board <CC...@JI...> on behalf of Xu, Qingping <000...@JI...>
Sent: Monday, January 27, 2025 8:36 AM
To: CC...@JI... <CC...@JI...>
Subject: [ccp4bb] Announcement: The 17th CCP4/APS Crystallographic School, June 23rd-30th, 2025, APS

This Message Is From an External Sender
This message came from outside your organization.

Dear Colleagues,

We are pleased to announce that the 17th annual CCP4/APS Crystallographic School, "From Data Collection to Structure Refinement and Beyond," will be held from June 23rd to 30th, 2025, at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found on the school website: http://www.ccp4.ac.uk/schools/APS-2025/index.php<https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-2025/index.php__;!!G_uCfscf7eWS!efj1mSIiPgk0NgZMHmGe4hJPfYd2OQDHTAN3c3Vrem3MB2NKtbVF54Rrswt012yfTyeTDwQiLmscAeDYLd-jpEoeFbg6-D4$>.

Dates: June 23rd through 30th, 2025 (on-site), June 2nd and 16th (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 GM/CA@APS 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). Two additional virtual days (June 2nd and 16th, 2025) 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<https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-school/publications.php__;!!G_uCfscf7eWS!efj1mSIiPgk0NgZMHmGe4hJPfYd2OQDHTAN3c3Vrem3MB2NKtbVF54Rrswt012yfTyeTDwQiLmscAeDYLd-jpEoeWp70wu8$>). 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 20 applicants will be selected for participation.

Application: The application deadline is May 15th, 2025, we strongly encourage interested participants to apply as soon as possible. To apply, visit https://www.ccp4.ac.uk/schools/APS-2025/application.php<https://urldefense.us/v3/__https://www.ccp4.ac.uk/schools/APS-2025/application.php__;!!G_uCfscf7eWS!efj1mSIiPgk0NgZMHmGe4hJPfYd2OQDHTAN3c3Vrem3MB2NKtbVF54Rrswt012yfTyeTDwQiLmscAeDYLd-jpEoePiMMUbg$>

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, Garib and Qingping


________________________________

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.us/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!G_uCfscf7eWS!efj1mSIiPgk0NgZMHmGe4hJPfYd2OQDHTAN3c3Vrem3MB2NKtbVF54Rrswt012yfTyeTDwQiLmscAeDYLd-jpEoefg6ZIm0$>

Re: [PyMOL] 3.1.3.1 no viewport sizing with the movie timeline panel toggled on?

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

Hi Rachelle,

This is a known issue and something we plan to address hopefully in the
near future!

Jarrett J.

On Wed, Apr 2, 2025 at 2:55 PM Gaudet, Rachelle <ga...@mc...>
wrote:

> Hello,
>
>
>
> I’m getting a weird behavior with PyMOL 3.1.3.1: When I toggle on the
> movie timeline panel (clicking on the camera icon), the PyMOL window
> changes, such that the aspect ratio of the display window is now very wide
> and not what I’d like it to be. I also cannot decrease the PyMOL window
> width with the timeline on. It seems to be locked at a minimal width,
> perhaps to fit all the buttons at the bottom of the movie timeline panel?
>
>
>
> The one “fix” I’ve found is to change the width of the Contents Panel
> (increasing it to decrease the width of the display window). But I do this
> manually, so I don’t really have precision like I did in PyMOL 2 with the
> “viewport” command. (The “viewport” command still works with the movie
> panel toggled off, but doesn’t work properly with the movie panel toggled
> on.)
>
>
>
> I realize I can change the aspect ratio of the movie when I’m saving it.
> But it is useful to plan and build the movie with the intended aspect ratio
> in view.
>
>
>
> Any tips?
>
>
>
> Best,
>
> Rachelle
>
>
>
> ___________________________________________________________________
>
>  Rachelle Gaudet, Ph.D.
>
>  Professor and Chair
>
>  Department of Molecular and Cellular Biology
> <https://www.mcb.harvard.edu/>
>
>  Co-Director of Graduate Studies, Biophysics
> <https://biophysics.fas.harvard.edu/>
>  Harvard University
>  52 Oxford Street, Northwest Labs room 311.13
>
>  Cambridge, MA 02138
>  Voice: (617) 495-5616    e-mail: ga...@mc...
>
>  https://projects.iq.harvard.edu/gaudetlab/home
>
> ___________________________________________________________________
>
>
> _______________________________________________
> 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] 3.1.3.1 no viewport sizing with the movie timeline panel toggled on?

[Gaudet, R. <ga...@mc...>]

Hello,

I'm getting a weird behavior with PyMOL 3.1.3.1: When I toggle on the movie timeline panel (clicking on the camera icon), the PyMOL window changes, such that the aspect ratio of the display window is now very wide and not what I'd like it to be. I also cannot decrease the PyMOL window width with the timeline on. It seems to be locked at a minimal width, perhaps to fit all the buttons at the bottom of the movie timeline panel?

The one "fix" I've found is to change the width of the Contents Panel (increasing it to decrease the width of the display window). But I do this manually, so I don't really have precision like I did in PyMOL 2 with the "viewport" command. (The "viewport" command still works with the movie panel toggled off, but doesn't work properly with the movie panel toggled on.)

I realize I can change the aspect ratio of the movie when I'm saving it. But it is useful to plan and build the movie with the intended aspect ratio in view.

Any tips?

Best,
Rachelle

___________________________________________________________________
 Rachelle Gaudet, Ph.D.
 Professor and Chair
 Department of Molecular and Cellular Biology<https://www.mcb.harvard.edu/>
 Co-Director of Graduate Studies, Biophysics<https://biophysics.fas.harvard.edu/>
 Harvard University
 52 Oxford Street, Northwest Labs room 311.13
 Cambridge, MA 02138
 Voice: (617) 495-5616    e-mail: ga...@mc...<mailto:ga...@mc...>
 https://projects.iq.harvard.edu/gaudetlab/home
___________________________________________________________________

Re: [PyMOL] Thermal ellipsoids with principal axes

[Takanori N. <tna...@os...>]

Hi,

I ended up implementing this myself, drawing three ellipses
by CGO over PyMOL's native ellipsoids.
My current style is like the one in
https://www.chem.gla.ac.uk/~louis/software/ortep/index.html.

At the moment my code does not support object's TTT matrix
and per-atom colors. Once I fix these limitations,
I will put my script to my GitHub or PyMOL wiki.

I also want to implement the "cutting out one octant" feature
like ORTEP but that would require completely hiding
PyMOL's native ellipsoids and drawing everything from scratch.

Best regards,

Takanori Nakane

On 3/25/25 22:30, Takanori Nakane wrote:
> Dear PyMOL users,
> 
> I am preparing figures for small molecular crystallography.
> I know I can plot thermal ellipsoids in PyMOL but can I add
> principal axes on the surface (or cut out one octant)?
> 
> I would like to draw something like ORTEP:
> https://www.chem.gla.ac.uk/~louis/software/ortep/fig2.gif.
> 
> Do I have to code CGO objects?
> 
> Best regards,
> 
> Takanori Nakane
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: 
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe