pymol-users Mailing List for PyMOL Molecular Graphics System (Page 3)

Hi Jarrett,
The issue was I downloaded the "master" zip linked in the instructions subsection of the github page. Using the "pyqt" zip linked from the code button worked.
Cheers,
Irwin
________________________________
From: Jarrett Johnson <jar...@sc...>
Sent: 27 February 2025 11:20:43
To: Irwin Selvam
Cc: pym...@li...
Subject: Re: [PyMOL] Caver3 plugin failure to initialise
Hi Irwin,
I'll ask others to double check on their setups too, but this one should have all imports of tkinter removed. Are you using the specific `pyqt` branch there and not `master`, and is the old one uninstalled first?
Best,
Jarrett J.
On Thu, Feb 27, 2025 at 6:44 PM Irwin Selvam <irw...@db...<mailto:irw...@db...>> wrote:
Hi,
Unfortunately, I'm still getting the same error ("no module named tkinter") and a failure to initialise. Any ideas?
Cheers,
Irwin
________________________________
From: Jarrett Johnson <jar...@sc...<mailto:jar...@sc...>>
Sent: 17 February 2025 00:33:26
To: Irwin Selvam
Cc: pym...@li...<mailto:pym...@li...>
Subject: Re: [PyMOL] Caver3 plugin failure to initialise
Hi Irwin,
A few months ago I worked on converting Caver 3 to use PyQt, I'm unsure if it's in a complete state, but within the next couple of months I'll be sure to finish it up and update the Caver PyMOLWiki page.
https://github.com/JarrettSJohnson/caver-pymol-plugin/tree/pyqt . Should just be able to press the Code button and Download Zip.
Best,
Jarrett J.
On Wed, Feb 12, 2025 at 5:03 AM Irwin Selvam via PyMOL-users <pym...@li...<mailto:pym...@li...>> wrote:
Hi all,
I'm trying to run the Caver3 plugin on PyMOL 2.5.7 on an M2 mac (Sequoia 15.3) but it's failing to initialise due to the "tkinter" module being missing. I've updated python to 3.13.2, which should come with tkinter 8.6. Does anyone have a solution?
Cheers,
Irwin
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--
Jarrett Johnson | Staff Developer, PyMOL
[https://drive.google.com/uc?id=1zOlB9fluGZyuInRUQgKsdjtjpR5L9z6R&export=download]
--
Jarrett Johnson | Staff Developer, PyMOL
[https://drive.google.com/uc?id=1zOlB9fluGZyuInRUQgKsdjtjpR5L9z6R&export=download]

Hi Irwin,
I'll ask others to double check on their setups too, but this one should
have all imports of tkinter removed. Are you using the specific `pyqt`
branch there and not `master`, and is the old one uninstalled first?
Best,
Jarrett J.
On Thu, Feb 27, 2025 at 6:44 PM Irwin Selvam <irw...@db...> wrote:
> Hi,
>
>
> Unfortunately, I'm still getting the same error ("no module named
> tkinter") and a failure to initialise. Any ideas?
>
>
> Cheers,
>
>
> Irwin
> ------------------------------
> *From:* Jarrett Johnson <jar...@sc...>
> *Sent:* 17 February 2025 00:33:26
> *To:* Irwin Selvam
> *Cc:* pym...@li...
> *Subject:* Re: [PyMOL] Caver3 plugin failure to initialise
>
> Hi Irwin,
>
> A few months ago I worked on converting Caver 3 to use PyQt, I'm unsure if
> it's in a complete state, but within the next couple of months I'll be sure
> to finish it up and update the Caver PyMOLWiki page.
>
> https://github.com/JarrettSJohnson/caver-pymol-plugin/tree/pyqt . Should
> just be able to press the Code button and Download Zip.
>
> Best,
> Jarrett J.
>
>
> On Wed, Feb 12, 2025 at 5:03 AM Irwin Selvam via PyMOL-users <
> pym...@li...> wrote:
>
>> Hi all,
>>
>>
>> I'm trying to run the Caver3 plugin on PyMOL 2.5.7 on an M2 mac (Sequoia
>> 15.3) but it's failing to initialise due to the "tkinter" module being
>> missing. I've updated python to 3.13.2, which should come with tkinter 8.6.
>> Does anyone have a solution?
>>
>>
>> Cheers,
>>
>>
>> Irwin
>> _______________________________________________
>> 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

Hi,
Unfortunately, I'm still getting the same error ("no module named tkinter") and a failure to initialise. Any ideas?
Cheers,
Irwin
________________________________
From: Jarrett Johnson <jar...@sc...>
Sent: 17 February 2025 00:33:26
To: Irwin Selvam
Cc: pym...@li...
Subject: Re: [PyMOL] Caver3 plugin failure to initialise
Hi Irwin,
A few months ago I worked on converting Caver 3 to use PyQt, I'm unsure if it's in a complete state, but within the next couple of months I'll be sure to finish it up and update the Caver PyMOLWiki page.
https://github.com/JarrettSJohnson/caver-pymol-plugin/tree/pyqt . Should just be able to press the Code button and Download Zip.
Best,
Jarrett J.
On Wed, Feb 12, 2025 at 5:03 AM Irwin Selvam via PyMOL-users <pym...@li...<mailto:pym...@li...>> wrote:
Hi all,
I'm trying to run the Caver3 plugin on PyMOL 2.5.7 on an M2 mac (Sequoia 15.3) but it's failing to initialise due to the "tkinter" module being missing. I've updated python to 3.13.2, which should come with tkinter 8.6. Does anyone have a solution?
Cheers,
Irwin
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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]

Dear all,
I have just been shocked by our IT department that they will force us into migration to Win11 very soon. I know I am a dinosaur, but I still use and love my old nvidia Quadro/Asus/shutter glasses combi (over 10 years old) for hardware stereo viewing of protein structures under Win10. I am afraid that this will simply not work anymore once I have been upgraded, since nvdia has disabled hardware stereo in its drivers long time ago.
Personally, I cannot understand how modern structural biology can live without it and I would love to still be able view structures in 3D.
I know that the PyMol community is graphics- and tech-savvy, I am therefore asking if you know of any modern day hardware solution for 3D viewing in our favorite programs (PyMol, Coot ...).
Thank you in advance for your advice,
Wulf
Prof. Wulf Blankenfeldt
Struktur und Funktion der Proteine (SFPR)
HZI - Helmholtz-Zentrum f?r Infektionsforschung GmbH
SCIENCE CAMPUS Braunschweig-S?d
Inhoffenstra?e 7, 38124 Braunschweig
Tel. +49 5316181-7000
wul...@he...
www.helmholtz-hzi.de
[cid:Helmholtz_HZI_Logo_RGB_DE_nebeneinander_beschnitt2_1acc279d-0673-4590-b45d-24938b462e30.jpg]
________________________________
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Hi Irwin,
A few months ago I worked on converting Caver 3 to use PyQt, I'm unsure if
it's in a complete state, but within the next couple of months I'll be sure
to finish it up and update the Caver PyMOLWiki page.
https://github.com/JarrettSJohnson/caver-pymol-plugin/tree/pyqt . Should
just be able to press the Code button and Download Zip.
Best,
Jarrett J.
On Wed, Feb 12, 2025 at 5:03 AM Irwin Selvam via PyMOL-users <
pym...@li...> wrote:
> Hi all,
>
>
> I'm trying to run the Caver3 plugin on PyMOL 2.5.7 on an M2 mac (Sequoia
> 15.3) but it's failing to initialise due to the "tkinter" module being
> missing. I've updated python to 3.13.2, which should come with tkinter 8.6.
> Does anyone have a solution?
>
>
> Cheers,
>
>
> Irwin
> _______________________________________________
> 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

Hi all,
I'm trying to run the Caver3 plugin on PyMOL 2.5.7 on an M2 mac (Sequoia 15.3) but it's failing to initialise due to the "tkinter" module being missing. I've updated python to 3.13.2, which should come with tkinter 8.6. Does anyone have a solution?
Cheers,
Irwin

Dear Lei,
the best way to build a new molecule is via the builder in the GUI.
The commands "replace" or "attach" are not well documented. I could 
reproduce your problem and I think PyMOL runs some kind of check routine 
after you issue a replace or attach command and it will reset the atomic 
valence and geometry to sensible values based on the atom environment.
For example, if you construct aniline using the builder the nitrogen has 
geometry=3 and valence=3. If you try to convert it to a sp3-hybridized 
nitrogen via "replace N, 4, 3" it keeps geometry=3 and valence=3. You 
can query the geometry and valence by selecting one or several atoms and 
use the command:
cmd.iterate("sele", "print(name, geom, valence)").
Next you convert the N-conjugated "double bond" of the aromatic system 
to a single bond using the builder. The nitrogen stays planar and the 
geometry ist still 3. Now the command "replace N, 4, 3" works as the 
nitrogen is no longer next to an aromatic system.
Best wishes,
Norbert
Am 06.02.2025 um 17:54 schrieb Lei Qian:
> Dear users,
> Could I ask a question on geometry option in replace command?
> I tried to use Build/Fragment/XXX to replace an atom to a new one, and 
> pymol GUI shows the corresponding replace command.
> However, I found the geometry option always equals to 4.
> For example,
> PyMOL>replace O, 4, 2
> PyMOL>replace N, 4, 3
> PyMOL>replace C, 4, 4
> I tried to replace the atom in different types of bonds: 
> single/double/triple bonds, but the geometry value is always 4.
> Could you please help me figure it out? Thank you very much!
> Best,
> Lei
>
>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives:http://www.mail-archive.com/pym...@li...
> Unsubscribe:https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Dear users,
Could I ask a question on geometry option in replace command?
I tried to use Build/Fragment/XXX to replace an atom to a new one, and pymol GUI shows the corresponding replace command.
However, I found the geometry option always equals to 4.
For example,
PyMOL>replace O, 4, 2
PyMOL>replace N, 4, 3
PyMOL>replace C, 4, 4
I tried to replace the atom in different types of bonds: single/double/triple bonds, but the geometry value is always 4.
Could you please help me figure it out? Thank you very much!
Best,
Lei

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.
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). 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
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

Please, google "pymol iterate objects"
3rd in the hit list: [PyMOL] iterating over list of objects
for i in *cmd.get_object_list()*: cmd.align( i, reference )
On Mon, Jan 27, 2025 at 9:56 AM Csongor MATYAS via PyMOL-users <
pym...@li...> wrote:
> I am trying to iterate over lots of distances that I can generate with
> cmd.distance(name = 'distA_B', selection1 = 'selA', selection2 = 'selB',
> cutoff = 3.6, mode = 2) for example. My only problem is that I don't know
> how to iterate over them. How can one iterate over objects that are not
> selection of atoms?
> (I'm doing this from python using the pymol-bundle, but even in pymol I
> can't find a way to save these into a file or print them or save them in a
> variable somehow)
>
> Kind regards,
> Csongor
>
> DISCLAIMER
>
> Prezentul mesaj și orice documente atașate pot conține informații
> confidențiale sau sensibile care aparțin Universității Babeș-Bolyai din
> Cluj-Napoca. Conținutul mesajului nu poate fi dezvăluit sau utilizat de
> către altcineva decât destinatarul, persoană fizică sau juridică. Dacă ați
> primit acest mesaj dintr-o eroare, vă rugăm să ne anunțati imediat, ca
> răspuns la mesajul de față, și să ștergeți apoi din sistemul dvs. mesajul
> fără a-l copia sau deschide. Prin prezenta vi se notifică faptul că orice
> dezvaluire, copiere, distribuire sau inițierea/omiterea unor acțiuni pe
> baza prezentelor informații sunt strict interzise și atrag răspunderea
> civilă și/sau penală (art. 302 Noul Cod Penal). UBB nu este răspunzătoare
> pentru modificările care pot fi aduse prezentului mesaj și nici pentru
> întârzierile care pot surveni în recepționarea acestuia. De asemenea, nu
> putem garanta integritatea mesajului și nici că acesta este lipsit de
> viruși, interceptări sau interferențe de orice natură. =================
> The contents of this email message and any attachments may contain
> confidential and/or privileged information belonging to Babeș-Bolyai
> University of Cluj-Napoca. This information is intended solely for the
> addressee, natural or legal person, and is legally protected from
> disclosure and may not be used by anyone other than the intended recipient.
> If you are not the intended recipient of this message, or if this message
> has been addressed to you in error, please immediately alert the sender by
> reply email and then delete this message and any attachments. You are
> hereby notified that any use, dissemination, copying, or storage of this
> message or its attachments as well as taking any action in reliance on the
> contents of this information is strictly prohibited and entails civil
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> accepts no liability for any errors or omissions in the contents of this
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> error-free, as information could be intercepted, corrupted, lost,
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>
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> Unsubscribe:
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I am trying to iterate over lots of distances that I can generate with cmd.distance(name = 'distA_B', selection1 = 'selA', selection2 = 'selB', cutoff = 3.6, mode = 2) for example. My only problem is that I don't know how to iterate over them. How can one iterate over objects that are not selection of atoms?
(I'm doing this from python using the pymol-bundle, but even in pymol I can't find a way to save these into a file or print them or save them in a variable somehow)
Kind regards,
Csongor
DISCLAIMER
Prezentul mesaj ?i orice documente ata?ate pot con?ine informa?ii confiden?iale sau sensibile care apar?in Universita?ii Babe?-Bolyai din Cluj-Napoca. Con?inutul mesajului nu poate fi dezvaluit sau utilizat de catre altcineva decât destinatarul, persoana fizica sau juridica. Daca a?i primit acest mesaj dintr-o eroare, va rugam sa ne anun?ati imediat, ca raspuns la mesajul de fa?a, ?i sa ?terge?i apoi din sistemul dvs. mesajul fara a-l copia sau deschide. Prin prezenta vi se notifica faptul ca orice dezvaluire, copiere, distribuire sau ini?ierea/omiterea unor ac?iuni pe baza prezentelor informa?ii sunt strict interzise ?i atrag raspunderea civila ?i/sau penala (art. 302 Noul Cod Penal). UBB nu este raspunzatoare pentru modificarile care pot fi aduse prezentului mesaj ?i nici pentru întârzierile care pot surveni în recep?ionarea acestuia. De asemenea, nu putem garanta integritatea mesajului ?i nici ca acesta este lipsit de viru?i, interceptari sau interferen?e de orice natura. ================= The contents of this email message and any attachments may contain confidential and/or privileged information belonging to Babe?-Bolyai University of Cluj-Napoca. This information is intended solely for the addressee, natural or legal person, and is legally protected from disclosure and may not be used by anyone other than the intended recipient. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply email and then delete this message and any attachments. You are hereby notified that any use, dissemination, copying, or storage of this message or its attachments as well as taking any action in reliance on the contents of this information is strictly prohibited and entails civil and/or criminal liability (under Art. 302 of the New Criminal Code). UBB accepts no liability for any errors or omissions in the contents of this message. Email transmission cannot be guaranteed to be secure or error-free, as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses.
UBBCLUJ <https://www.ubbcluj.ro/ro/politici/>

Dear Csongor,
as far as I know it is not well documented how you can access the python 
objects and its methods or data structures created by the PyMOL API. For 
many tasks one usually finds some information, often PyMOL or python 
scripts. Concerning your example of the hydrogen bonds determined by the 
distance command, the following python script may provide hints:
https://pymolwiki.org/index.php/Get_raw_distances
and: 
https://pymol-users.narkive.com/zHPUseVG/pymol-is-there-a-way-to-count-hydrogen-bond-interactions
When working with the PyMOL distance command to determine hydrogen bonds 
please note that the algorithm is very generous concerning non-linearity 
of the D-H...A angles if you use the default parameters. In addition, it 
will miss some perfect hydrogen bonds.
See
https://research.uni-leipzig.de/straeter/pymol/pymol_hbond.html
and
https://github.com/schrodinger/pymol-open-source/pull/374
Best wishes,
Norbert
Am 22.01.2025 um 15:21 schrieb Csongor MATYAS via PyMOL-users:
> Hey everyone,
>
> I am trying to use pymol from python to have some repetitive tasks 
> done. I've managed to get some basic functions running but I'm running 
> into walls frequently. I couldn't find a tutorial or documentation 
> about this. Am I missing something? I know it's under development but 
> I would assume that some basic instructions would be available 
> somewhere, otherwise the conda package isn't very useful.
>
> I've managed to sort out the cmd.select() function for example but I 
> can't use the data, there is no object or output. All I can do is to 
> cmd.save() selection into a .pdb file. I've managed to select ligand, 
> and then residues around it, I've also been able to use 
> show_contacts() (from link below) between two selections, but I can't 
> access the pairs that suggest hydrogen bonding, it is only a visual 
> thing. Even from pymol, the software, if I do it manually, I don't 
> know how to save those (unless I save it as a pymol session file that 
> is not human readable).
>
> https://wiki.pymol.org/index.php/Show_contacts
>
> Please, if anyone has advice, anything is appreciated 😄
>
> Csongor
>
> DISCLAIMER
>
> Prezentul mesaj și orice documente atașate pot conține informații 
> confidențiale sau sensibile care aparțin Universității Babeș-Bolyai 
> din Cluj-Napoca. Conținutul mesajului nu poate fi dezvăluit sau 
> utilizat de către altcineva decât destinatarul, persoană fizică sau 
> juridică. Dacă ați primit acest mesaj dintr-o eroare, vă rugăm să ne 
> anunțati imediat, ca răspuns la mesajul de față, și să ștergeți apoi 
> din sistemul dvs. mesajul fără a-l copia sau deschide. Prin prezenta 
> vi se notifică faptul că orice dezvaluire, copiere, distribuire sau 
> inițierea/omiterea unor acțiuni pe baza prezentelor informații sunt 
> strict interzise și atrag răspunderea civilă și/sau penală (art. 302 
> Noul Cod Penal). UBB nu este răspunzătoare pentru modificările care 
> pot fi aduse prezentului mesaj și nici pentru întârzierile care pot 
> surveni în recepționarea acestuia. De asemenea, nu putem garanta 
> integritatea mesajului și nici că acesta este lipsit de viruși, 
> interceptări sau interferențe de orice natură. ================= The 
> contents of this email message and any attachments may contain 
> confidential and/or privileged information belonging to Babeș-Bolyai 
> University of Cluj-Napoca. This information is intended solely for the 
> addressee, natural or legal person, and is legally protected from 
> disclosure and may not be used by anyone other than the intended 
> recipient. If you are not the intended recipient of this message, or 
> if this message has been addressed to you in error, please immediately 
> alert the sender by reply email and then delete this message and any 
> attachments. You are hereby notified that any use, dissemination, 
> copying, or storage of this message or its attachments as well as 
> taking any action in reliance on the contents of this information is 
> strictly prohibited and entails civil and/or criminal liability (under 
> Art. 302 of the New Criminal Code). UBB accepts no liability for any 
> errors or omissions in the contents of this message. Email 
> transmission cannot be guaranteed to be secure or error-free, as 
> information could be intercepted, corrupted, lost, destroyed, arrive 
> late or incomplete, or contain viruses.
>
> UBBCLUJ <https://www.ubbcluj.ro/ro/politici/>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives:http://www.mail-archive.com/pym...@li...
> Unsubscribe:https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Dear Csongor,
cmd select creates a named selection. if you do not use a name, the 
default name "sele" will be used. You see this if you use the gui 
version. Plus: https://pymol.org/dokuwiki/doku.php?id=api:cmd:select 
cmd.select("resi 150-160")
cmd.color("red", "sele")
cmd.select("myselection", "resi 150-160")
cmd.color("red", "myselection")
Bests,
Tamas
On 1/22/25 15:21, Csongor MATYAS via PyMOL-users wrote:
> Hey everyone,
>
> I am trying to use pymol from python to have some repetitive tasks 
> done. I've managed to get some basic functions running but I'm running 
> into walls frequently. I couldn't find a tutorial or documentation 
> about this. Am I missing something? I know it's under development but 
> I would assume that some basic instructions would be available 
> somewhere, otherwise the conda package isn't very useful.
>
> I've managed to sort out the cmd.select() function for example but I 
> can't use the data, there is no object or output. All I can do is to 
> cmd.save() selection into a .pdb file. I've managed to select ligand, 
> and then residues around it, I've also been able to use 
> show_contacts() (from link below) between two selections, but I can't 
> access the pairs that suggest hydrogen bonding, it is only a visual 
> thing. Even from pymol, the software, if I do it manually, I don't 
> know how to save those (unless I save it as a pymol session file that 
> is not human readable).
>
> https://wiki.pymol.org/index.php/Show_contacts
>
> Please, if anyone has advice, anything is appreciated 😄
>
> Csongor
>
> DISCLAIMER
>
> Prezentul mesaj și orice documente atașate pot conține informații 
> confidențiale sau sensibile care aparțin Universității Babeș-Bolyai 
> din Cluj-Napoca. Conținutul mesajului nu poate fi dezvăluit sau 
> utilizat de către altcineva decât destinatarul, persoană fizică sau 
> juridică. Dacă ați primit acest mesaj dintr-o eroare, vă rugăm să ne 
> anunțati imediat, ca răspuns la mesajul de față, și să ștergeți apoi 
> din sistemul dvs. mesajul fără a-l copia sau deschide. Prin prezenta 
> vi se notifică faptul că orice dezvaluire, copiere, distribuire sau 
> inițierea/omiterea unor acțiuni pe baza prezentelor informații sunt 
> strict interzise și atrag răspunderea civilă și/sau penală (art. 302 
> Noul Cod Penal). UBB nu este răspunzătoare pentru modificările care 
> pot fi aduse prezentului mesaj și nici pentru întârzierile care pot 
> surveni în recepționarea acestuia. De asemenea, nu putem garanta 
> integritatea mesajului și nici că acesta este lipsit de viruși, 
> interceptări sau interferențe de orice natură. ================= The 
> contents of this email message and any attachments may contain 
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Hey everyone,
I am trying to use pymol from python to have some repetitive tasks done. I've managed to get some basic functions running but I'm running into walls frequently. I couldn't find a tutorial or documentation about this. Am I missing something? I know it's under development but I would assume that some basic instructions would be available somewhere, otherwise the conda package isn't very useful.
I've managed to sort out the cmd.select() function for example but I can't use the data, there is no object or output. All I can do is to cmd.save() selection into a .pdb file. I've managed to select ligand, and then residues around it, I've also been able to use show_contacts() (from link below) between two selections, but I can't access the pairs that suggest hydrogen bonding, it is only a visual thing. Even from pymol, the software, if I do it manually, I don't know how to save those (unless I save it as a pymol session file that is not human readable).
https://wiki.pymol.org/index.php/Show_contacts
Please, if anyone has advice, anything is appreciated 😄
Csongor
DISCLAIMER
Prezentul mesaj și orice documente atașate pot conține informații confidențiale sau sensibile care aparțin Universității Babeș-Bolyai din Cluj-Napoca. Conținutul mesajului nu poate fi dezvăluit sau utilizat de către altcineva decât destinatarul, persoană fizică sau juridică. Dacă ați primit acest mesaj dintr-o eroare, vă rugăm să ne anunțati imediat, ca răspuns la mesajul de față, și să ștergeți apoi din sistemul dvs. mesajul fără a-l copia sau deschide. Prin prezenta vi se notifică faptul că orice dezvaluire, copiere, distribuire sau inițierea/omiterea unor acțiuni pe baza prezentelor informații sunt strict interzise și atrag răspunderea civilă și/sau penală (art. 302 Noul Cod Penal). UBB nu este răspunzătoare pentru modificările care pot fi aduse prezentului mesaj și nici pentru întârzierile care pot surveni în recepționarea acestuia. De asemenea, nu putem garanta integritatea mesajului și nici că acesta este lipsit de viruși, interceptări sau interferențe de orice natură. ================= The contents of this email message and any attachments may contain confidential and/or privileged information belonging to Babeș-Bolyai University of Cluj-Napoca. This information is intended solely for the addressee, natural or legal person, and is legally protected from disclosure and may not be used by anyone other than the intended recipient. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply email and then delete this message and any attachments. You are hereby notified that any use, dissemination, copying, or storage of this message or its attachments as well as taking any action in reliance on the contents of this information is strictly prohibited and entails civil and/or criminal liability (under Art. 302 of the New Criminal Code). UBB accepts no liability for any errors or omissions in the contents of this message. Email transmission cannot be guaranteed to be secure or error-free, as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses.
UBBCLUJ <https://www.ubbcluj.ro/ro/politici/>

Hi Martin,
There are currently no plans to migrate Timeline to open source.
Best,
Jarrett J.
On Mon, Jan 20, 2025 at 1:49 PM Martin Urban <mar...@st...>
wrote:
> Hi Jarrett,
>
> thanks for the quick reply. This is a good thing to know, perhaps it
> should be stated more clearly on the wiki page. Are there any plans for it
> to be open source one day?
>
> Best regards,
> Martin
> On 20.01.2025 19:44, Jarrett Johnson wrote:
>
> Hi Martin,
>
> Timeline and its corresponding Python API is only available for on
> Incentive versions.
>
> Jarrett J.
>
> On Mon, Jan 20, 2025 at 1:42 PM Martin Urban <
> mar...@st...> wrote:
>
>> Dear PyMOL Community,
>>
>> I am exploring the Timeline Python API as described on the PyMOL Wiki (
>> Timeline Python API). However, when I attempt to use
>> timeline_add_composition(), I encounter the following error:
>>
>> *AttributeError: module 'pymol.cmd' has no attribute
>> 'timeline_add_composition'*
>>
>> To investigate further, I tried both the prebuilt wheel file
>> pymol-3.1.0a0-cp311-cp311-win_amd64.whl from the GitHub repository (pymol
>> -open-source-wheels) and a build from source using the commit PYMOL-4365:
>> Filter gizmo and selections from thumbnails and exports. Unfortunately,
>> both approaches resulted in the same error.
>>
>> Could someone clarify whether this API is available in the open-source
>> version of PyMOL or if it is part of the incentive version?
>>
>> Thank you for your time and assistance.
>>
>> Best regards,
>> Martin
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> --
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
>
-- 
*Jarrett Johnson* | Senior Developer, PyMOL

Hi Martin,
Timeline and its corresponding Python API is only available for on
Incentive versions.
Jarrett J.
On Mon, Jan 20, 2025 at 1:42 PM Martin Urban <mar...@st...>
wrote:
> Dear PyMOL Community,
>
> I am exploring the Timeline Python API as described on the PyMOL Wiki (
> Timeline Python API <https://pymolwiki.org/index.php/Timeline_Python_API>).
> However, when I attempt to use timeline_add_composition(), I encounter
> the following error:
>
> *AttributeError: module 'pymol.cmd' has no attribute
> 'timeline_add_composition'*
>
> To investigate further, I tried both the prebuilt wheel file
> pymol-3.1.0a0-cp311-cp311-win_amd64.whl from the GitHub repository (pymol
> -open-source-wheels <https://github.com/cgohlke/pymol-open-source-wheels>)
> and a build from source using the commit PYMOL-4365: Filter gizmo and
> selections from thumbnails and exports. Unfortunately, both approaches
> resulted in the same error.
>
> Could someone clarify whether this API is available in the open-source
> version of PyMOL or if it is part of the incentive version?
>
> Thank you for your time and assistance.
>
> Best regards,
> Martin
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
-- 
*Jarrett Johnson* | Senior Developer, PyMOL

Hi Jarrett,
thanks for the quick reply. This is a good thing to know, perhaps it 
should be stated more clearly on the wiki page. Are there any plans for 
it to be open source one day?
Best regards,
Martin
On 20.01.2025 19:44, Jarrett Johnson wrote:
> Hi Martin,
>
> Timeline and its corresponding Python API is only available for on 
> Incentive versions.
>
> Jarrett J.
>
> On Mon, Jan 20, 2025 at 1:42 PM Martin Urban 
> <mar...@st...> wrote:
>
> Dear PyMOL Community,
>
> I am exploring the Timeline Python API as described on the PyMOL
> Wiki (TimelinePythonAPI
> <https://pymolwiki.org/index.php/Timeline_Python_API>). However,
> when I attempt to use |timeline_add_composition()|, I encounter
> the following error:
>
> /AttributeError: module 'pymol.cmd' has no attribute
> 'timeline_add_composition'/
>
> To investigate further, I tried both the prebuilt wheel file
> |pymol-3.1.0a0-cp311-cp311-win_amd64.whl| from the GitHub
> repository (pymol-open-source-wheels
> <https://github.com/cgohlke/pymol-open-source-wheels>) and a build
> from source using the commit |PYMOL-4365: Filter gizmo and
> selections from thumbnails and exports|. Unfortunately, both
> approaches resulted in the same error.
>
> Could someone clarify whether this API is available in the
> open-source version of PyMOL or if it is part of the incentive
> version?
>
> Thank you for your time and assistance.
>
> Best regards,
> Martin
>
> _______________________________________________
> PyMOL-users mailing list
> Archives:
> http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> -- 
>
> *Jarrett Johnson* | Senior Developer, PyMOL
>
>

Dear PyMOL Community,
I am exploring the Timeline Python API as described on the PyMOL Wiki 
(TimelinePythonAPI 
<https://pymolwiki.org/index.php/Timeline_Python_API>). However, when I 
attempt to use |timeline_add_composition()|, I encounter the following 
error:
/AttributeError: module 'pymol.cmd' has no attribute 
'timeline_add_composition'/
To investigate further, I tried both the prebuilt wheel file 
|pymol-3.1.0a0-cp311-cp311-win_amd64.whl| from the GitHub repository 
(pymol-open-source-wheels 
<https://github.com/cgohlke/pymol-open-source-wheels>) and a build from 
source using the commit |PYMOL-4365: Filter gizmo and selections from 
thumbnails and exports|. Unfortunately, both approaches resulted in the 
same error.
Could someone clarify whether this API is available in the open-source 
version of PyMOL or if it is part of the incentive version?
Thank you for your time and assistance.
Best regards,
Martin

Hello,
Under the plugin menu option there is an included default plugin "alignment" tool which will bring up an alignment GUI.
Best,
Franz
From: Giuseppa Cefalu <giu...@gm...>
Sent: Saturday, January 11, 2025 11:21 PM
To: PyM...@li...
Subject: [External Email][PyMOL] 2 Molecules superposition
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Hello,
I was wondering if there is GUI feature for loading and superimposing 2 proteins. I would like to use pymol for students that do not have any experience using commands.
Thanks,
~Giuseppa
This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

I usually open the second molecule after pymol has loaded first molecule by
just dropping the file on the window.
Afterwards I used align Command: https://pymolwiki.org/index.php/Align
Super command is also useful: https://pymolwiki.org/index.php/Super
Also after loading 2 molecules you can use Align menu under plugin:
[image: image.png]
It has multiple algorithm for alignments.
[image: image.png]
Regards,
Saurabh Gayali
------------------------------
*Saurabh Gayali*
Business Analyst [Excelra], Former Research Scientist [IGIB]
sau...@gm... / +91 8800412916
<http://example.com/>Bangalore, India
On Sun, Jan 12, 2025 at 10:53 AM Giuseppa Cefalu <giu...@gm...>
wrote:
> Hello,
> I was wondering if there is GUI feature for loading and superimposing 2
> proteins. I would like to use pymol for students that do not have any
> experience using commands.
>
> Thanks,
> ~Giuseppa
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

Apart from others' reply, I believe pymol will run .pml files while python
will run .py files.
Regards,
Saurabh Gayali
------------------------------
*Saurabh Gayali*
Business Analyst [Excelra], Former Research Scientist [IGIB]
sau...@gm... / +91 8800412916
<http://example.com/>Bangalore, India
On Tue, Dec 10, 2024 at 3:11 AM Yarrow Madrona <yar...@gm...>
wrote:
> I'm trying to run pymol in batch mode without launching the window. I am
> running PyMOL 3.1.1.
>
> Here is my code for an example script (test.py). I'm trying to run before
> running the real script. In the command line I enter:
> pymol -cq test.py
>
>
> from pymol import cmd
> import time
>
> def main():
> print("Starting PyMOL batch processing...")
> cmd.load("3gbn.pdb")
> do_stuff()
> print("Loaded 3gbn.pdb")
> time.sleep(25) # Ensure commands are processed
> cmd.quit()
>
> if __name__ == "__main_":
> main()
> I don't get any output. If I type:
> pymol -c test.py
> It appears that pymol starts and closes:
>
> [image: image.png]
>
> Any help on how to run a python script with pymol in batch without opening
> the GUI would be appreciated.
> Yarrow
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Hello,
I was wondering if there is GUI feature for loading and superimposing 2 proteins. I would like to use pymol for students that do not have any experience using commands.
Thanks,
~Giuseppa

Dear Yarrow,
The problem in your script is the `if __name__ == "__main__"` clause.
When the script is run using `pymol -cqk test.py`, __name__ refers to the string "pymol".
The following script fetches a structure from the PDB and saves a PNG image. Run it using `pymol -cqk test.py -- <PDB-ID>`. (The flag -k prevents loading pymolrc and plugins.)
```python
from pymol import cmd
def main(pdb_id: str) -> None:
 print(f"Loading PDB-ID {pdb_id.upper()}")
 cmd.fetch(pdb_id)
 png_file_name = f"{pdb_id}.png"
 print(f"Writting image to {png_file_name}")
 cmd.png(png_file_name)
if __name__ == "pymol":
 import sys
 pdb_id = sys.argv[1]
 main(pdb_id)
```
Best regards,
Karl
On 06.01.2025, at 18:04, Florian Nachon <mai...@na...> wrote:
Hello,
It is much easier than that.
Make a pymol script, for example, test.pml:
#
load 3gbn.pdb
select Selection1, resi 80:115
save Selection1.cif, Selection1
quit
#
then run it with the -c option :
pymol test.pml -c
If you want to pass an argument, like the filename of a pdb file to be directly opened, then use the -cp option.
Florian
On 9 Dec 2024, at 22:38, Yarrow Madrona <yar...@gm...> wrote:
I'm trying to run pymol in batch mode without launching the window. I am running PyMOL 3.1.1.
Here is my code for an example script (test.py). I'm trying to run before running the real script. In the command line I enter:
pymol -cq test.py
from pymol import cmd
import time
def main():
print("Starting PyMOL batch processing...")
cmd.load("3gbn.pdb")
do_stuff()
print("Loaded 3gbn.pdb")
time.sleep(25) # Ensure commands are processed
cmd.quit()
if __name__ == "__main_":
main()
I don't get any output. If I type:
pymol -c test.py
It appears that pymol starts and closes:
<image.png>
Any help on how to run a python script with pymol in batch without opening the GUI would be appreciated.
Yarrow
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Archives: http://www.mail-archive.com/pym...@li...
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Hello,
It is much easier than that.
Make a pymol script, for example, test.pml:
#
load 3gbn.pdb
select Selection1, resi 80:115
save Selection1.cif, Selection1
quit
#
then run it with the -c option : 
pymol test.pml -c
If you want to pass an argument, like the filename of a pdb file to be directly opened, then use the -cp option.
Florian
> On 9 Dec 2024, at 22:38, Yarrow Madrona <yar...@gm...> wrote:
> 
> I'm trying to run pymol in batch mode without launching the window. I am running PyMOL 3.1.1.
> 
> Here is my code for an example script (test.py). I'm trying to run before running the real script. In the command line I enter:
> pymol -cq test.py
> 
> 
> from pymol import cmd
> import time
> 
> def main():
> print("Starting PyMOL batch processing...")
> cmd.load("3gbn.pdb")
> do_stuff()
> print("Loaded 3gbn.pdb")
> time.sleep(25) # Ensure commands are processed
> cmd.quit()
> 
> if __name__ == "__main_":
> main()
> I don't get any output. If I type:
> pymol -c test.py
> It appears that pymol starts and closes:
> 
> <image.png>
> 
> Any help on how to run a python script with pymol in batch without opening the GUI would be appreciated.
> Yarrow
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Hello Dr. Saper,
This does appear to be a bug and I was able to reproduce the same behavior
on my Mac. Opening the same pdb repeatedly in the same window should result
in states being added, but there's no reason why PyMOL should be doing this
when double clicking on files. It seems like PyMOL is loading the
structure twice for some reason but this pattern doesn't repeat if you
continue to open the same file.
I will create a ticket to investigate further and hopefully have a fix for
this in the near future. In the meantime, you can delete the second state
using "delete_states {your object name}, 2", though I recognize this is
annoying to type each time and is not a long term solution.
Thanks for reporting this,
Thomas Stewart
On Thu, Dec 12, 2024 at 7:16 AM Mark Saper <sa...@um...> wrote:
> I am running the latest PyMOL 3.1.3 on macOS 13.7,1.
>
> When I double click a .pse or .pdb file, PyMOL opens normally and displays
> the molecule of interest.
> If I think double click on another file, PyMOL opens a new window, the
> molecule displays, but now there is a seoncd state of the moleculeThe GUI
> shows the Global Frames control for switching between scenes. I also get
> this message:
>
> ObjectMolecule: Read crystal symmetry information.
>
> CmdLoad: "" appended into object "231129_EcNfo_WT_P028_9_refine_061", state 2.
>
>
> Is this a bug? Or am I doing something wrong.
>
>
> Mark
> _____________________
> *Mark A. Saper, Ph.D.*
> Visiting Professor
> Dept of Microbiology and Molecular Genetics
> Hebrew University Faculty of Medicine
>
> Associate Professor Emeritus of Biological Chemistry
> University of Michigan Medical School
>
> sa...@um... | +972 52 815-0480
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
-- 
Thomas Stewart | Senior Developer I | Product Manager, PyMOL
[image: Schrödinger, Inc.] <https://schrodinger.com/>