pymol-users Mailing List for PyMOL Molecular Graphics System (Page 2)

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年06月30日
 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

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年12月01日
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)

header intact

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

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

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ドル participation fee for selected academic students and 1,500ドル 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
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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

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

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

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.
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--
Jarrett Johnson | Staff Developer, PyMOL
[https://drive.google.com/uc?id=1zOlB9fluGZyuInRUQgKsdjtjpR5L9z6R&export=download]

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

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.

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ドル participation fee for selected academic students and 1,500ドル 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
________________________________
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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

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
___________________________________________________________________

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

Hello Everyone,
We have just released PyMOL 3.1.4.1 (which is still a digit of pi so the pi
mole remains!) to fix the issues discussed in this thread.
Please give this version a try if you haven't updated recently since many
other small issues have also been fixed in recent patches.
You can download this version from the website (
https://www.pymol.org/#download) and please check back later if 3.1.4.1
isn't showing up for you yet.
Release Notes:
 - Selection names are now properly shown within parentheses again (i.e.
 "(sele)")
 - Fix for selections using the incorrect "Action" menu
 - Wizards that require keyboard input now focus properly
 - Fix for timeline extending off the edge of smaller Mac screens
 - Fix for issues toggling objects after reordering
 - Fix for group members not showing following an empty group
Thank you for your patience and happy PyMOL-ing,
Thomas
Thomas Stewart | Senior Developer I | Product Manager, PyMOL
[image: Schrödinger, Inc.] <https://schrodinger.com/>
On Thu, Mar 20, 2025 at 8:42 PM Engin Özkan <eo...@uc...> wrote:
> Dear Thomas,
>
> Thank you for getting back quickly and on your work on PyMOL. Looking
> forward to testing the patched version.
>
> Best,
>
> Engin
>
>
> On 3/20/25 9:44 AM, Thomas Stewart wrote:
>
> Hello Engin and Vaheh,
>
> Both of these are simply oversights on my part and will be fixed in the
> next patch (3.1.4.1). For this update, I completely rewrote the code for
> the Contents Panel and there appears to be certain ASHLC menus that are not
> pulling the correct set of menu options for their object type.
>
> I will also add the parentheses back to the selections! I'm honestly
> surprised I didn't immediately notice this in my testing but it should be a
> quick fix.
>
> Thank you for reporting these issues and let me know if you find anything
> else.
>
> Thanks again,
> Thomas
>
> Thomas Stewart | Senior Developer I | Product Manager, PyMOL
>
> [image: Schrödinger, Inc.] <https://schrodinger.com/>
>
>
> On Thu, Mar 20, 2025 at 9:08 AM Oganesyan, Vaheh <
> vah...@as...> wrote:
>
>> To add a bit to Engin’s message: under A when selecting "extract" I’m
>> getting "copy" instead. I think it is a bug in 3.1.4.
>>
>>
>>
>> Thank you.
>>
>>
>>
>> Vaheh
>>
>>
>>
>> *From:* Engin Özkan <eo...@uc...>
>> *Sent:* Wednesday, March 19, 2025 8:02 PM
>> *To:* pym...@li...
>> *Subject:* [PyMOL] PyMOL 3.1.4
>>
>>
>>
>> Hi,
>>
>> In the latest version of PyMOL, 3.1.4, I cannot see if an item in the
>> list on the right-hand column is a selection or an object. The
>> parantheses were really useful before. Is this intentional or an
>> oversight?
>>
>> But more urgently, for a selection I made, I no longer see the options
>> under "A" many options I use every session, such as copy to object,
>> extract object, rename selection, align, etc. I am sure I can do these
>> actions via command-line just fine, but not nearly with the same ease of
>> use.
>>
>> Also delete selection has been replaced by delete selections. Why
>> plural? I am scared to click on it, especially now that I don't know
>> which items are selections and which are objects. I'll downgrade for now
>> to be able to use selections effectively in PyMOL; I assume many users
>> also depend on their ability to modify, align and rename selections
>> easily.
>>
>> (And thanks for fixing some of the selection group bugs that popped up
>> with v. 3 early on.)
>>
>> Best,
>>
>> Engin
>>
>> --
>> Engin Özkan, Ph.D.
>> Associate Professor
>> Dept of Biochemistry and Molecular Biology
>> University of Chicago
>>
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>> ------------------------------
>>
>> *Confidentiality Notice: *This message is private and may contain
>> confidential and proprietary information. If you have received this message
>> in error, please notify us and remove it from your system and note that you
>> must not copy, distribute or take any action in reliance on it. Any
>> unauthorized use or disclosure of the contents of this message is not
>> permitted and may be unlawful.
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
> --
> Engin Özkan, Ph.D.
> Associate Professor
> Dept of Biochemistry and Molecular Biology
> University of Chicago
> Phone: (773) 834-5498http://ozkan.uchicago.edu
>
>

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

Hi Thomas, Engin,
Thanks for looking into this. Another thing with Select is that in this Pi
version there is a "delete everything" option, which is very dangerous (it
does delete every single object). It used to be "remove atoms" to remove
only the atoms in the selection.
Best regards,
 Istvan
On Thu, Mar 20, 2025 at 8:59 PM Engin Özkan <eo...@uc...> wrote:
> Dear Thomas,
>
> Thank you for getting back quickly and on your work on PyMOL. Looking
> forward to testing the patched version.
>
> Best,
>
> Engin
>
>
> On 3/20/25 9:44 AM, Thomas Stewart wrote:
>
> Hello Engin and Vaheh,
>
> Both of these are simply oversights on my part and will be fixed in the
> next patch (3.1.4.1). For this update, I completely rewrote the code for
> the Contents Panel and there appears to be certain ASHLC menus that are not
> pulling the correct set of menu options for their object type.
>
> I will also add the parentheses back to the selections! I'm honestly
> surprised I didn't immediately notice this in my testing but it should be a
> quick fix.
>
> Thank you for reporting these issues and let me know if you find anything
> else.
>
> Thanks again,
> Thomas
>
> Thomas Stewart | Senior Developer I | Product Manager, PyMOL
>
> [image: Schrödinger, Inc.] <https://schrodinger.com/>
>
>
> On Thu, Mar 20, 2025 at 9:08 AM Oganesyan, Vaheh <
> vah...@as...> wrote:
>
>> To add a bit to Engin’s message: under A when selecting "extract" I’m
>> getting "copy" instead. I think it is a bug in 3.1.4.
>>
>>
>>
>> Thank you.
>>
>>
>>
>> Vaheh
>>
>>
>>
>> *From:* Engin Özkan <eo...@uc...>
>> *Sent:* Wednesday, March 19, 2025 8:02 PM
>> *To:* pym...@li...
>> *Subject:* [PyMOL] PyMOL 3.1.4
>>
>>
>>
>> Hi,
>>
>> In the latest version of PyMOL, 3.1.4, I cannot see if an item in the
>> list on the right-hand column is a selection or an object. The
>> parantheses were really useful before. Is this intentional or an
>> oversight?
>>
>> But more urgently, for a selection I made, I no longer see the options
>> under "A" many options I use every session, such as copy to object,
>> extract object, rename selection, align, etc. I am sure I can do these
>> actions via command-line just fine, but not nearly with the same ease of
>> use.
>>
>> Also delete selection has been replaced by delete selections. Why
>> plural? I am scared to click on it, especially now that I don't know
>> which items are selections and which are objects. I'll downgrade for now
>> to be able to use selections effectively in PyMOL; I assume many users
>> also depend on their ability to modify, align and rename selections
>> easily.
>>
>> (And thanks for fixing some of the selection group bugs that popped up
>> with v. 3 early on.)
>>
>> Best,
>>
>> Engin
>>
>> --
>> Engin Özkan, Ph.D.
>> Associate Professor
>> Dept of Biochemistry and Molecular Biology
>> University of Chicago
>>
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>> ------------------------------
>>
>> *Confidentiality Notice: *This message is private and may contain
>> confidential and proprietary information. If you have received this message
>> in error, please notify us and remove it from your system and note that you
>> must not copy, distribute or take any action in reliance on it. Any
>> unauthorized use or disclosure of the contents of this message is not
>> permitted and may be unlawful.
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
> --
> Engin Özkan, Ph.D.
> Associate Professor
> Dept of Biochemistry and Molecular Biology
> University of Chicago
> Phone: (773) 834-5498http://ozkan.uchicago.edu
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Dear Thomas,
Thank you for getting back quickly and on your work on PyMOL. Looking 
forward to testing the patched version.
Best,
Engin
On 3/20/25 9:44 AM, Thomas Stewart wrote:
> Hello Engin and Vaheh,
>
> Both of these are simply oversights on my part and will be fixed in 
> the next patch (3.1.4.1). For this update, I completely rewrote the 
> code for the Contents Panel and there appears to be certain ASHLC 
> menus that are not pulling the correct set of menu options for their 
> object type.
>
> I will also add the parentheses back to the selections! I'm honestly 
> surprised I didn't immediately notice this in my testing but it 
> should be a quick fix.
>
> Thank you for reporting these issues and let me know if you find 
> anything else.
>
> Thanks again,
> Thomas
>
> Thomas Stewart | Senior Developer I | Product Manager, PyMOL
>
> Schrödinger, Inc. <https://schrodinger.com/>
>
>
>
> On Thu, Mar 20, 2025 at 9:08 AM Oganesyan, Vaheh 
> <vah...@as...> wrote:
>
> To add a bit to Engin’s message: under A when selecting "extract"
> I’m getting "copy" instead. I think it is a bug in 3.1.4.
>
> Thank you.
>
> Vaheh
>
> *From:*Engin Özkan <eo...@uc...>
> *Sent:* Wednesday, March 19, 2025 8:02 PM
> *To:* pym...@li...
> *Subject:* [PyMOL] PyMOL 3.1.4
>
> Hi,
>
> In the latest version of PyMOL, 3.1.4, I cannot see if an item in the
> list on the right-hand column is a selection or an object. The
> parantheses were really useful before. Is this intentional or an
> oversight?
>
> But more urgently, for a selection I made, I no longer see the
> options
> under "A" many options I use every session, such as copy to object,
> extract object, rename selection, align, etc. I am sure I can do
> these
> actions via command-line just fine, but not nearly with the same
> ease of
> use.
>
> Also delete selection has been replaced by delete selections. Why
> plural? I am scared to click on it, especially now that I don't know
> which items are selections and which are objects. I'll downgrade
> for now
> to be able to use selections effectively in PyMOL; I assume many
> users
> also depend on their ability to modify, align and rename
> selections easily.
>
> (And thanks for fixing some of the selection group bugs that
> popped up
> with v. 3 early on.)
>
> Best,
>
> Engin
>
> -- 
> Engin Özkan, Ph.D.
> Associate Professor
> Dept of Biochemistry and Molecular Biology
> University of Chicago
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives:
> http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
> ------------------------------------------------------------------------
>
> *Confidentiality Notice: *This message is private and may contain
> confidential and proprietary information. If you have received
> this message in error, please notify us and remove it from your
> system and note that you must not copy, distribute or take any
> action in reliance on it. Any unauthorized use or disclosure of
> the contents of this message is not permitted and may be unlawful.
>
> _______________________________________________
> PyMOL-users mailing list
> Archives:
> http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
-- 
Engin Özkan, Ph.D.
Associate Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
Phone: (773) 834-5498
http://ozkan.uchicago.edu

Hello Engin and Vaheh,
Both of these are simply oversights on my part and will be fixed in the
next patch (3.1.4.1). For this update, I completely rewrote the code for
the Contents Panel and there appears to be certain ASHLC menus that are not
pulling the correct set of menu options for their object type.
I will also add the parentheses back to the selections! I'm honestly
surprised I didn't immediately notice this in my testing but it should be a
quick fix.
Thank you for reporting these issues and let me know if you find anything
else.
Thanks again,
Thomas
Thomas Stewart | Senior Developer I | Product Manager, PyMOL
[image: Schrödinger, Inc.] <https://schrodinger.com/>
On Thu, Mar 20, 2025 at 9:08 AM Oganesyan, Vaheh <
vah...@as...> wrote:
> To add a bit to Engin’s message: under A when selecting "extract" I’m
> getting "copy" instead. I think it is a bug in 3.1.4.
>
>
>
> Thank you.
>
>
>
> Vaheh
>
>
>
> *From:* Engin Özkan <eo...@uc...>
> *Sent:* Wednesday, March 19, 2025 8:02 PM
> *To:* pym...@li...
> *Subject:* [PyMOL] PyMOL 3.1.4
>
>
>
> Hi,
>
> In the latest version of PyMOL, 3.1.4, I cannot see if an item in the
> list on the right-hand column is a selection or an object. The
> parantheses were really useful before. Is this intentional or an oversight?
>
> But more urgently, for a selection I made, I no longer see the options
> under "A" many options I use every session, such as copy to object,
> extract object, rename selection, align, etc. I am sure I can do these
> actions via command-line just fine, but not nearly with the same ease of
> use.
>
> Also delete selection has been replaced by delete selections. Why
> plural? I am scared to click on it, especially now that I don't know
> which items are selections and which are objects. I'll downgrade for now
> to be able to use selections effectively in PyMOL; I assume many users
> also depend on their ability to modify, align and rename selections easily.
>
> (And thanks for fixing some of the selection group bugs that popped up
> with v. 3 early on.)
>
> Best,
>
> Engin
>
> --
> Engin Özkan, Ph.D.
> Associate Professor
> Dept of Biochemistry and Molecular Biology
> University of Chicago
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> ------------------------------
>
> *Confidentiality Notice: *This message is private and may contain
> confidential and proprietary information. If you have received this message
> in error, please notify us and remove it from your system and note that you
> must not copy, distribute or take any action in reliance on it. Any
> unauthorized use or disclosure of the contents of this message is not
> permitted and may be unlawful.
>
> _______________________________________________
> PyMOL-users mailing list
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To add a bit to Engin’s message: under A when selecting "extract" I’m getting "copy" instead. I think it is a bug in 3.1.4.
Thank you.
Vaheh
From: Engin Özkan <eo...@uc...>
Sent: Wednesday, March 19, 2025 8:02 PM
To: pym...@li...
Subject: [PyMOL] PyMOL 3.1.4
Hi,
In the latest version of PyMOL, 3.1.4, I cannot see if an item in the
list on the right-hand column is a selection or an object. The
parantheses were really useful before. Is this intentional or an oversight?
But more urgently, for a selection I made, I no longer see the options
under "A" many options I use every session, such as copy to object,
extract object, rename selection, align, etc. I am sure I can do these
actions via command-line just fine, but not nearly with the same ease of
use.
Also delete selection has been replaced by delete selections. Why
plural? I am scared to click on it, especially now that I don't know
which items are selections and which are objects. I'll downgrade for now
to be able to use selections effectively in PyMOL; I assume many users
also depend on their ability to modify, align and rename selections easily.
(And thanks for fixing some of the selection group bugs that popped up
with v. 3 early on.)
Best,
Engin
--
Engin Özkan, Ph.D.
Associate Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
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Hi,
In the latest version of PyMOL, 3.1.4, I cannot see if an item in the 
list on the right-hand column is a selection or an object. The 
parantheses were really useful before. Is this intentional or an oversight?
But more urgently, for a selection I made, I no longer see the options 
under "A" many options I use every session, such as copy to object, 
extract object, rename selection, align, etc. I am sure I can do these 
actions via command-line just fine, but not nearly with the same ease of 
use.
Also delete selection has been replaced by delete selections. Why 
plural? I am scared to click on it, especially now that I don't know 
which items are selections and which are objects. I'll downgrade for now 
to be able to use selections effectively in PyMOL; I assume many users 
also depend on their ability to modify, align and rename selections easily.
(And thanks for fixing some of the selection group bugs that popped up 
with v. 3 early on.)
Best,
Engin
-- 
Engin Özkan, Ph.D.
Associate Professor
Dept of Biochemistry and Molecular Biology
University of Chicago

Hello Istvan,
I actually wasn't even aware of this behavior when I was creating the new
Contents Panel! I couldn't add it in time for this release (3.1.4) but I'll
hopefully have something ready in the near future. There are many small
"features" like this in older versions of PyMOL that are difficult to
discover if you've never seen them used before.
If anyone else has any Contents Panel related features that are now
missing, please feel free to send me an email directly and I will do my
best to restore them in future updates. This PyMOL 3.1.4 update includes a
full reimplementation of the Contents Panel based on a request to improve
performance and stability when a large number of objects are loaded in.
Give this version a try before emailing me with a feature request because
it may already be added!
Thanks,
Thomas
Thomas Stewart | Senior Developer I | Product Manager, PyMOL
[image: Schrödinger, Inc.] <https://schrodinger.com/>
On Sun, Mar 9, 2025 at 6:31 PM Istvan Kolossvary <iko...@gm...>
wrote:
> Hi,
>
> Pymol v2.x has a great feature, which seems not to exist in v3.x any more.
> On Linux, I could hold down the Ctrl key and then hover the cursor
> vertically over the object list to flip through the objects. Moving the
> cursor away from an object turned it off automatically while the next
> object under the cursor was automatically turned on in the display area.
> This feature is extremely useful for example to flip through multiple
> docking poses. (I think it also worked on the Mac using the Cmd key.) Is it
> still available in v3.x, perhaps with other key combinations?
>
> Thanks for any suggestions,
>
> Istvan
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Hi,
Pymol v2.x has a great feature, which seems not to exist in v3.x any more.
On Linux, I could hold down the Ctrl key and then hover the cursor
vertically over the object list to flip through the objects. Moving the
cursor away from an object turned it off automatically while the next
object under the cursor was automatically turned on in the display area.
This feature is extremely useful for example to flip through multiple
docking poses. (I think it also worked on the Mac using the Cmd key.) Is it
still available in v3.x, perhaps with other key combinations?
Thanks for any suggestions,
 Istvan