pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] Anaconda python-bundle package documentation or help

[Tamas H. <bio...@gm...>]

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 
> 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

[PyMOL] Anaconda python-bundle package documentation or help

[Csongor M. <cso...@ub...>]

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/>

Re: [PyMOL] Question Regarding Timeline Python API Availability in Open-Source PyMOL

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

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

Re: [PyMOL] Question Regarding Timeline Python API Availability in Open-Source PyMOL

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

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

Re: [PyMOL] Question Regarding Timeline Python API Availability in Open-Source PyMOL

[Martin U. <mar...@st...>]

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
>
>

[PyMOL] Question Regarding Timeline Python API Availability in Open-Source PyMOL

[Martin U. <mar...@st...>]

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

Re: [PyMOL] [External Email] 2 Molecules superposition

[St j. F. - F. W. <fra...@us...>]

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

You don't often get email from giu...@gm...<mailto:giu...@gm...>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>
[External Email]
If this message comes from an unexpected sender or references a vague/unexpected topic;
Use caution before clicking links or opening attachments.
Please send any concerns or suspicious messages to: Spa...@us...<mailto:Spa...@us...>
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.

Re: [PyMOL] 2 Molecules superposition

[Saurabh G. <sau...@gm...>]

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
>

Re: [PyMOL] Running pymol without launching window in batch

[Saurabh G. <sau...@gm...>]

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

[PyMOL] 2 Molecules superposition

[Giuseppa C. <giu...@gm...>]

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

Re: [PyMOL] Running pymol without launching window in batch

[Gruber, K. (<kar...@un...>]

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

_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pym...@li...
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pym...@li...
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Running pymol without launching window in batch

[Florian N. <mai...@na...>]

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

Re: [PyMOL] Problem launching PyMOL from macOS 13.7.1

[Thomas S. <tho...@sc...>]

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/>

[PyMOL] Problem launching PyMOL from macOS 13.7.1

[Mark S. <sa...@um...>]

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... <mailto:sa...@um...>  |  +972 52 815-0480

[PyMOL] Running pymol without launching window in batch

[Yarrow M. <yar...@gm...>]

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] problem with volumes?

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

anyone else?
Any ideas on how to fix it?

Thanks!

Re: [PyMOL] About license question

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

Hi,

Please reach out to he...@sc... for questions regarding licensing.

Best,
Jarrett J.

On Thu, Dec 5, 2024 at 4:03 AM 左若宇 via PyMOL-users <
pym...@li...> wrote:

> Sorry to bother you, I have registered for EDU-PyMOL for two days, but I
> haven't received the license email yet? Why is this?I sincerely hope to
> receive your reply as soon as possible.
> _______________________________________________
> 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

[PyMOL] About license question

[<192...@qq...>]

Sorry to bother you, I have registered for EDU-PyMOL for two days, but I haven't received the license email yet? Why is this?I sincerely hope to receive your reply as soon as possible.

[PyMOL] PyVOL plugin

[Vitali J. <jir...@gm...>]

Dear PyMol
I am trying to install the PyVol plugin and I have installed the msms on
the computer but still I am not successfully installed the PyVol plugin.
How to set up the MSMS path on windows or on ubuntu?

[image: image.png]
Vol plugin

Re: [PyMOL] CASTp

[Saurabh G. <sau...@gm...>]

Looks like the link has a viewer in the browser itself.
Upon experimenting I found that in the downloaded files, the .mouth and
.poc files are in pdb formats. I simply renamed them and loaded them
alongside the main pdb.
I then showed the other molecule as surface but it looked different than
what I saw on chrome using the url shared earlier.
I later realised the .mouth and .poc have broken fragments that can be open
in the display>sequence menu option in pymol.
I hope you can carry forward from here.
[image: image.png]
Hope it helps.
Regards,
Saurabh Gayali


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

*Saurabh Gayali*
Former Research Scientist [IGIB]
sau...@gm... / +91 8800412916
<http://example.com/>Bangalore, India


On Wed, Nov 20, 2024 at 5:31 PM Vitali James <jir...@gm...> wrote:

> Dear PyMOl users
>
> Can you please help to know how to view the data downloaded from the CASTp
> server.
> I install the plugin but cant view the data obtained from the CASTp
> http://sts.bioe.uic.edu/castp/index.html?3igg
>
> best
> James
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] CASTp

[Vitali J. <jir...@gm...>]

Dear PyMOl users

Can you please help to know how to view the data downloaded from the CASTp
server.
I install the plugin but cant view the data obtained from the CASTp
http://sts.bioe.uic.edu/castp/index.html?3igg

best
James

Re: [PyMOL] Visualisation clashed structures

[Magnus, M. <mm...@fa...>]

Hey,

(I sent the structure in the second e-mail as a zip file, but apparently, the Harvard mail system blocked it)

I also understood what was going on. The structure [2] is a very raw, early stage of our simulation, full of clashes (and the file has no CONECT in it).

When I `set connect_mode, 1` [1] ( = CONECT records), I don’t see any bonds (which makes sense, as there is no CONECT in my PDB file) and PyMOL does not calculate bonds and loads the structure immediately!

Thus, the fix is to `set connect_mode, 1` and use explicit CONECT in my file or load file without CONECT  and use Surface representation to get insights into what’s going on (and calculate RMSD, etc.).

Thanks, the issue is solved.

Magnus

[1] https://pymolwiki.org/index.php/Connect_mode
[2] https://www.dropbox.com/t/kz4LISig75hlwCMj
[sc 2024-10-31 at 12.58.22 2.jpg.jpeg]

Re: [PyMOL] Visualisation clashed structures

[Magnus, M. <mm...@fa...>]

Interestingly,

set auto_show_classified, off

is the best way to solve it (the Line representation works)!

Magnus

[sc 2024-10-31 at 18.56.17.jpeg]

https://pymolwiki.org/index.php/Auto_show_classified

Re: [PyMOL] Visualisation clashed structures

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

Hello,

Hard to say at first glance, but it may be easier to postulate if we have
an example file that hangs.

Best,
Jarrett J

On Wed, Oct 30, 2024 at 7:57 PM Magnus, Marcin <mm...@fa...>
wrote:

> Hey,
>
> I’m working a new method for RNA 3D structure prediction. And yeah, I see
> that the structure is a mess, but I want to be able to load the structure
> into PyMOL. I can do that with Chimera, but PyMOL apparently is trying to
> do something, and this something takes forever to load the model. I love
> PyMOL and have lots of my own plugins to work with RNA 3D structures, I
> would love to be able to use PyMOL for analysis what’s going on in here.
>
> Any ideas, hints, why it takes so long to load it. Is it that PyMOL is
> calculcate bonds between all the atoms and it’s getting overwhelmed but
> this mess?
>
> Any hints are welocome,
>
> Magnus
>
> Elena Rivas lab, MCB, Harvard
> mm...@fa...
> https://mmagnus.github.io/
>
> [image: sc 2024-10-30 at 13.27.07.jpeg.jpeg]
> _______________________________________________
> 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

[PyMOL] Visualisation clashed structures

[Magnus, M. <mm...@fa...>]

Hey,

I’m working a new method for RNA 3D structure prediction. And yeah, I see that the structure is a mess, but I want to be able to load the structure into PyMOL. I can do that with Chimera, but PyMOL apparently is trying to do something, and this something takes forever to load the model. I love PyMOL and have lots of my own plugins to work with RNA 3D structures, I would love to be able to use PyMOL for analysis what’s going on in here.

Any ideas, hints, why it takes so long to load it. Is it that PyMOL is calculcate bonds between all the atoms and it’s getting overwhelmed but this mess?

Any hints are welocome,

Magnus

Elena Rivas lab, MCB, Harvard
mm...@fa...<mailto:mm...@fa...>
https://mmagnus.github.io/

[sc 2024-10-30 at 13.27.07.jpeg.jpeg]