pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] [Help]About using PyMOL for Master's thesis

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

Hello Haruki,

My name is Thomas Stewart and I'm one of the PyMOL developers at
Schrodinger. You can use an educational license to fulfill course or
program requirements such as a Master's thesis or dissertation. We hope to
reword the website in the near future to make it more clear when
educational and academic licenses should each be used.

Thanks,
Thomas Stewart

On Thu, Feb 15, 2024 at 4:08 AM MF SOEJIMA Haruki <
soe...@st...> wrote:

> To whom it may concern,
>
> My name is Haruki Soejima and I am studying at the Graduate School of
> Marine Biosciences, Kitasato University, Japan.
> The purpose of this e-mail is to ask you a question about the license of
> PyMOL.
>
> I used the “Educational-Use-Only PyMOL” in my study for my Master's
> thesis. However, I have just discovered that I must purchase a license for
> “PyMOL” for academic purposes.
> Is my Master's thesis educational or academic?
> I will pay the cost as soon as possible if it is academic.
>
> Please don't hesitate to contact us with any further queries.
> I look forward to hearing from you.
>
> Best regards,
> Haruki Soejima
>
> ーーーーーーーーーーーーーーーーー
> 北里大学 大学院
> 海洋生命科学研究科
> 水族病理学研究室
> MF22013
> 副島 晴希（ソエジマ ハルキ）
> 電話：080‐5698‐3992
> メール：soe...@st...
> ーーーーーーーーーーーーーーーーー
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] [Help]About using PyMOL for Master's thesis

[MF S. H. <soe...@st...>]

To whom it may concern,

My name is Haruki Soejima and I am studying at the Graduate School of
Marine Biosciences, Kitasato University, Japan.
The purpose of this e-mail is to ask you a question about the license of
PyMOL.

I used the “Educational-Use-Only PyMOL” in my study for my Master's thesis.
However, I have just discovered that I must purchase a license for “PyMOL”
for academic purposes.
Is my Master's thesis educational or academic?
I will pay the cost as soon as possible if it is academic.

Please don't hesitate to contact us with any further queries.
I look forward to hearing from you.

Best regards,
Haruki Soejima

ーーーーーーーーーーーーーーーーー
北里大学 大学院
海洋生命科学研究科
水族病理学研究室
MF22013
副島 晴希（ソエジマ ハルキ）
電話：080‐5698‐3992
メール：soe...@st...
ーーーーーーーーーーーーーーーーー

Re: [PyMOL] draw sticks between given coordinates

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

Hi,

Probably you need to explicitly define bonds.

Relevant pages are:

https://pymolwiki.org/index.php/Bond
https://pymolwiki.org/index.php/Unbond
https://pymolwiki.org/index.php/Sticks

If these points are not atoms, you can use CGOs instead:
https://pymolwiki.org/index.php/CGO_Shapes

Best regards,

Takanori Nakane

On 2/7/24 19:25, Daniele Notarmuzi wrote:
> Hello!
> 
> I am trying to draw sticks given a set of coordinates and sometimes I 
> succeed, sometimes I do not. In my silly mind, what I would like to do 
> is to give two set of 3D coordinates and have a stick drawn between 
> them. For example, given the set of coordinates
> 
> 0.0 0.0 0.0            # coord 1 start
> 1.0 0.0 0.0            # coord 1 end
> 0.0 0.0 0.0            # coord 2 start
> 0.0 1.0 0.0            # coord 2 end
> 1.0 0.0 0.0            # coord 3 start
> 0.0 1.0 0.0            # coord 3 end
> 
> I would like to obtain a triangle. This actually happens. However, if I 
> replace all the 1.0 with 2.0, I only get the two short sides of the 
> triangle and if I replace the 1.0 with 3.0 I get nothing.
> 
> I deduce that there is a certain distance below which a stick is drawn 
> (?). I do not see how to make this criterion work for my problem, given 
> that there could be coordinates that are very close but do not need to 
> be connected and coordinates that are very far and that do need to be 
> connected.
> 
> So my question is: how to draw sticks between points, given the "head" 
> and the "tail" coordinates of each stick I want to draw?
> 
> Thank you in advance.
> 
> PS: sorry if the question is silly, I have looked around and found 
> nothing...
> 
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] draw sticks between given coordinates

[Daniele N. <dan...@gm...>]

Hello!

I am trying to draw sticks given a set of coordinates and sometimes I
succeed, sometimes I do not. In my silly mind, what I would like to do is
to give two set of 3D coordinates and have a stick drawn between them. For
example, given the set of coordinates

0.0 0.0 0.0            # coord 1 start
1.0 0.0 0.0            # coord 1 end
0.0 0.0 0.0            # coord 2 start
0.0 1.0 0.0            # coord 2 end
1.0 0.0 0.0            # coord 3 start
0.0 1.0 0.0            # coord 3 end

I would like to obtain a triangle. This actually happens. However, if I
replace all the 1.0 with 2.0, I only get the two short sides of the
triangle and if I replace the 1.0 with 3.0 I get nothing.

I deduce that there is a certain distance below which a stick is drawn (?).
I do not see how to make this criterion work for my problem, given that
there could be coordinates that are very close but do not need to be
connected and coordinates that are very far and that do need to be
connected.

So my question is: how to draw sticks between points, given the "head" and
the "tail" coordinates of each stick I want to draw?

Thank you in advance.

PS: sorry if the question is silly, I have looked around and found
nothing...

Re: [PyMOL] Questions about licenses

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

I would suggest you to use the PyMol open Source version for Research
Publications.
https://github.com/schrodinger/pymol-open-source

Regards,
Saurabh Gayali

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

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

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On Sun, Jan 14, 2024 at 12:56 AM ALEX ZATUCHNEY via PyMOL-users <
pym...@li...> wrote:

> Hello, all.
> My name is Alex Zatuchney, and I am a full-time high school student that
> is looking to use PyMOL to generate renders for both self-study and a
> possible research paper for the AP Research program. At some point, I would
> like to publish this research. Since I am a full-time student, would I be
> able to include PyMOL renders in a hypothetical research paper with the
> free, educational-use license?
>
> Thank you so much in advance,
> Alex
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Questions about licenses

[ALEX Z. <aza...@hc...>]

Hello, all.
My name is Alex Zatuchney, and I am a full-time high school student that is
looking to use PyMOL to generate renders for both self-study and a possible
research paper for the AP Research program. At some point, I would like to
publish this research. Since I am a full-time student, would I be able to
include PyMOL renders in a hypothetical research paper with the free,
educational-use license?

Thank you so much in advance,
Alex

[PyMOL] Error when opening PyMOL installed through Anaconda

[Naveen R. <nav...@gm...>]

Hello all,

I recently brought a new laptop (Windows 11) and had installed Anaconda along with their python interpreter. When it came time to install PyMOL, I saw on the website that it was possible to install PyMOL through Anaconda.

This was very convenient for me, as with my previous laptop (Windows 10), I ran into issues having two python installs on the same device. Installing PyMOL through Anaconda in the base (root) environment would save me from a potential hassle.

I ran the command on the PyMOL website (conda install -c conda-forge -c schrodinger pymol-bundle) in the Anaconda prompt, installing PyMOL in the default environment. When I tried to open PyMOL through the desktop, nothing happens.

However, when I try to open PyMOL through the Anaconda Navigator, I get the following error message:
Traceback (most recent call last):
File "C:\ProgramData\anaconda3\Scripts\pymol-script.py", line 6, in from pymol import launch
File "C:\ProgramData\anaconda3\Lib\site-packages\pymol\__init__.py", line 620, in import pymol._cmd
ImportError: DLL load failed while importing _cmd: The specified module could not be found.

After this error, I installed PyMOL through the installer (to check if it was an issue with the PyMOL version) and it worked. With this in mind I carried out the following troubleshooting steps:

  *   Install PyMOL through Anaconda (with the command from the website) on another PC that has not PyMOL installed before.
  *   Compare the installed packages in the install from Anaconda and from the installer. Resolve the differences in the Anaconda install.
  *   Install PyMOL through Anaconda using other commands I found on the internet, including the one used to install a previous versions of PyMOL.

All of the afformentioned steps were unsucessful in getting the Anaconda install to open.

I have also compared the "__init__.py" from the Anaconda and installer installs and they are the same. I have also attempted to find the "__cmd" file in the installer install but was unsucessful. I am at a loss as to what is causing the installer install to go through but the Anaconda install to fail.

I was hoping if others have a fix for this so that the Anaconda installation opens as I have tried looking for a solution online but failed to find anything useful.

Hope you have a nice day.

Best Wishes,
Naveen Ravichandran

[PyMOL] RMSD per residue graph for multiple aligned PDB files

[Tomas M. <tom...@gm...>]

Dear All,

I have multiple aligned PDB files loaded in PyMOL, each representing
different conformations of the same protein. I'm interested in
creating a graph displaying RMSD per residue, similar to those shown
at https://www.ks.uiuc.edu/Training/Tutorials/science/aars/aars_html.bak/node22.html
or https://www.compchems.com/how-to-compute-the-rmsf-using-gromacs/#the-gmx-rmsf-command.

I'm wondering if anyone has a script available that can calculate RMSD
per residue and write the data to a text file for graph generation. If
so, would they be able to share it with everyone?

Thank you for your help.

Best wishes,
Tomas

[PyMOL] Measuring angle between two RNA helices in pymol

[Shekhar J. <she...@st...>]

Dear All,

I want to measure the angle between two RNA helices. I tried using script
"angle_between_helices.py" but it does not work for RNA structure.

Does anybody in the community have an idea or know a method to calculate
angle between two helices in pymol, please?

Regards,
Shekhar

[PyMOL] Cartoon Representation of Non-standard nucleic acid in PyMol

[Priyasha M. <maj...@gm...>]

Dear All,

I am working with a genomic sequence. There is a modification in one of the
nucleic acid of this DNA sequence. When I am viewing this in pymol, I can
see it in sticks and it looks disconnected from the rest of DNA backbone. I
am not able to see it in cartoon format. Can someone tell me how to show
this Non-Standard nucleic acid in cartoon representation connected to the
backbone,as it is a part of it?
Thank you

Regards,
Priyasha Majee

Re: [PyMOL] Writing a trajectory file

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

Hi Istvan,

The psico extension provides a "save_traj" command.

https://pymolwiki.org/index.php/save_traj
https://pymolwiki.org/index.php/psico

Cheers,
  Thomas

On Mon, Dec 4, 2023 at 5:11 PM Istvan Kolossvary <iko...@gm...> wrote:
>
> Hi, I was wondering, does Pymol have a way to save a trajectory directly in .dcd, .xtc, .gro, or some other popular file format?
>
> Thanks for any suggestions,
>
>    Istvan
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Writing a trajectory file

[Istvan K. <iko...@gm...>]

Thank you, Thomas! I was so hoping something like that exists. :) It is
about saving a movie and the associated coordinates with it for further
analysis.

Thanks again. Best,

   Istvan


On Mon, Dec 4, 2023 at 2:28 PM Thomas Holder <th...@th...>
wrote:

> Hi Istvan,
>
> The psico extension provides a "save_traj" command.
>
> https://pymolwiki.org/index.php/save_traj
> https://pymolwiki.org/index.php/psico
>
> Cheers,
>   Thomas
>
> On Mon, Dec 4, 2023 at 5:11 PM Istvan Kolossvary <iko...@gm...>
> wrote:
> >
> > Hi, I was wondering, does Pymol have a way to save a trajectory directly
> in .dcd, .xtc, .gro, or some other popular file format?
> >
> > Thanks for any suggestions,
> >
> >    Istvan
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pym...@li...
> > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>

Re: [PyMOL] Writing a trajectory file

[Petro <sub...@kh...>]

Hi.
I doubt it.
I also would say that mdanalysys or pytraj will be better for big
trajectories.
If trajectory is big, Pymol will struggle.
Petro.

On Mon, 4 Dec 2023, 17:06 Istvan Kolossvary, <iko...@gm...> wrote:

> Hi, I was wondering, does Pymol have a way to save a trajectory directly
> in .dcd, .xtc, .gro, or some other popular file format?
>
> Thanks for any suggestions,
>
>    Istvan
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Writing a trajectory file

[Istvan K. <iko...@gm...>]

Hi, I was wondering, does Pymol have a way to save a trajectory directly in
.dcd, .xtc, .gro, or some other popular file format?

Thanks for any suggestions,

   Istvan

Re: [PyMOL] Pymol Getting rid of the Colorbar

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

No worries. Glad it worked.

Jarrett J.

On Wed, Nov 29, 2023 at 12:09 AM Anna Elmanova <ann...@un...>
wrote:

> Dear Jarrett,
>
> Thanks a lot, that is exactly what I was looking for.
>
> I thought I used the option, but probably have used something else
> instead. I tried it on my commands and it worked. Many thanks!
> Best regards,
>
> Anna
> On 29.11.2023 04:47, Jarrett Johnson wrote:
>
> Hi Anna,
>
> Toggling an object's activity by clicking on the GUI uses the underlying *disable
> *command. If you already know the name of the color ramp, you can simply
> type
>
> *disable my_ramp*
>
> otherwise, if you want to hide any and all color ramps, you can use an
> API-only command (which is also submittable via PyMOL's command-line):
>
> *for ramp in cmd.get_names_of_type("object:ramp"): cmd.disable(ramp)*
>
> Hope this helps,
> Jarrett J.
>
> On Tue, Nov 28, 2023 at 10:39 AM Anna Elmanova <ann...@un...>
> wrote:
>
>> Dear colleagues,
>>
>> I am using Pymol electrostatic potential to surface mapping quite often.
>> But I have the issue that if I use command line mode, I always get the
>> colorbar. I would prefer to use custom colorbar, which I can make e.g.
>> in photoshop, but to hide the colorbar by default. Whenever I try to do
>> so, I lose the potentials on the surface also. Can this be resolved? I
>> would be grateful for help. In the GUI I can just turn off the bar, but
>> there is no log message for the command. I need to hide it from the
>> command line, therefore I am asking..
>>
>> Thank you for suggestions.
>>
>> --
>> Best regards,
>> Anna Elmanova
>>
>>
>> PhD student at Leibniz-Institut für Photonische Technologien e.V.
>> (Leibniz-IPHT) and Friedrich Schiller Universität Jena
>>
>>
>> +49 3641 948359
>> Technische Optik Gebäude (Lessingstraße 8)
>> Raum 229
>>
>>
>>
>> _______________________________________________
>> 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
>
> --
> Best regards,
> Anna Elmanova
>
>
> PhD student at Leibniz-Institut für Photonische Technologien e.V. (Leibniz-IPHT) and Friedrich Schiller Universität Jena
>
>
> +49 3641 948359
> Technische Optik Gebäude (Lessingstraße 8)
> Raum 229
>
>

-- 

*Jarrett Johnson* | Senior Developer, PyMOL

Re: [PyMOL] Pymol Getting rid of the Colorbar

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

Hi Anna,

Toggling an object's activity by clicking on the GUI uses the
underlying *disable
*command. If you already know the name of the color ramp, you can simply
type

*disable my_ramp*

otherwise, if you want to hide any and all color ramps, you can use an
API-only command (which is also submittable via PyMOL's command-line):

*for ramp in cmd.get_names_of_type("object:ramp"): cmd.disable(ramp)*

Hope this helps,
Jarrett J.

On Tue, Nov 28, 2023 at 10:39 AM Anna Elmanova <ann...@un...>
wrote:

> Dear colleagues,
>
> I am using Pymol electrostatic potential to surface mapping quite often.
> But I have the issue that if I use command line mode, I always get the
> colorbar. I would prefer to use custom colorbar, which I can make e.g.
> in photoshop, but to hide the colorbar by default. Whenever I try to do
> so, I lose the potentials on the surface also. Can this be resolved? I
> would be grateful for help. In the GUI I can just turn off the bar, but
> there is no log message for the command. I need to hide it from the
> command line, therefore I am asking..
>
> Thank you for suggestions.
>
> --
> Best regards,
> Anna Elmanova
>
>
> PhD student at Leibniz-Institut für Photonische Technologien e.V.
> (Leibniz-IPHT) and Friedrich Schiller Universität Jena
>
>
> +49 3641 948359
> Technische Optik Gebäude (Lessingstraße 8)
> Raum 229
>
>
>
> _______________________________________________
> 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] Vacuum Electrostatics error

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

Hi Joel,

This is unfortunately an oversight on my part. This fix unfortunately never
made its way to a patched version. I will make sure it does for the next
patch. In the meantime, if you ever do come across this issue, the
workaround is to disable undo from the Edit menu.

Best,
Jarrett J

On Tue, Nov 28, 2023 at 3:50 PM Joel Tyndall <joe...@ot...>
wrote:

> Hi all,
>
>
>
> I tried to help Anna with her issue around the colour bar  (which seemed
> unusual) only to find that I cannot generate the electrostatic maps at all
> on 2 different PCs running windows (10 I believe).
>
>
>
> The error is Pop-error: invalid source selection name ‘assign_tmp1’
>
>
>
> Running 2.5.1
>
>
>
> Joel
>
>
>
>
>
> Joel Tyndall | BSc(Hons) PhD
>
> Professor in Medicinal Chemistry
> School of Pharmacy | He Rau Kawakawa
> University of Otago | Te Whare Wānanga o Otāgo
>
> PO Box 56 9054
>
> Dunedin | Ōtepoti
>
> New Zealand | Aotearoa
>
> Website | pharmacy.otago.ac.nz
>
>
>
>
> _______________________________________________
> 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] Vacuum Electrostatics error

[Joel T. <joe...@ot...>]

Hi all,

I tried to help Anna with her issue around the colour bar  (which seemed unusual) only to find that I cannot generate the electrostatic maps at all on 2 different PCs running windows (10 I believe).

The error is Pop-error: invalid source selection name ‘assign_tmp1’

Running 2.5.1

Joel


Joel Tyndall | BSc(Hons) PhD

Professor in Medicinal Chemistry
School of Pharmacy | He Rau Kawakawa
University of Otago | Te Whare Wānanga o Otāgo
PO Box 56 9054
Dunedin | Ōtepoti
New Zealand | Aotearoa
Website | pharmacy.otago.ac.nz

[PyMOL] Pymol Getting rid of the Colorbar

[Anna E. <ann...@un...>]

Dear colleagues,

I am using Pymol electrostatic potential to surface mapping quite often. 
But I have the issue that if I use command line mode, I always get the 
colorbar. I would prefer to use custom colorbar, which I can make e.g. 
in photoshop, but to hide the colorbar by default. Whenever I try to do 
so, I lose the potentials on the surface also. Can this be resolved? I 
would be grateful for help. In the GUI I can just turn off the bar, but 
there is no log message for the command. I need to hide it from the 
command line, therefore I am asking..

Thank you for suggestions.

-- 
Best regards,
Anna Elmanova


PhD student at Leibniz-Institut für Photonische Technologien e.V. (Leibniz-IPHT) and Friedrich Schiller Universität Jena


+49 3641 948359
Technische Optik Gebäude (Lessingstraße 8)
Raum 229

Re: [PyMOL] [EXTERNAL] How to install APBS on PyMol

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

If you have not already done so, you might try looking here: https://pdb2pqr.readthedocs.io/en/latest/using/examples.html#parameterizing-ligands-with-the-pdb2pqr-web-server.
You need to apply the right partial charges to your small molecule with PSB2PQR to be able to apply APBS to it.

The version of PyMOL that you installed with apt-get is probably the open source version.
Next time, please include your operating system.

Best regards,

Blaine


Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Physiology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center, Rm. 466
975 NE 10th Street<https://maps.google.com/?q=975+NE+10th+Street&entry=gmail&source=g>, BRC 466
Oklahoma City, OK 73104-5419

Central Time Zone (follows Daylight Savings Time)

office: (405) 271-8300   lab: (405) 271-8313

Faculty webpage<https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd-1> <https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd-1>
Director: Laboratory of Biomolecular Structure and Function (X-ray crystallography lab)<https://research.ouhsc.edu/research-support/core-laboratory-services/laboratory-of-biomolecular-structure-and-function>
Ex-chair: SSRL Users Executive Committee<https://www-ssrl.slac.stanford.edu/content/about-ssrl/ssrluo-2022-2023-executive-committee-members>
Charter member: NIH Maximizing Investigators’ Research Award B (MRAB) Study section<https://public.csr.nih.gov/StudySections/DBIB/MBBC/MRAB>
Guest-editor: Special Issue "Nucleic Acid Crystallography Volume II"<https://www.mdpi.com/journal/crystals/special_issues/Nucleic_Acid_Crystallography> submission deadline June 25, 2024
Co-Chair: Oklahoma Data Science Workshop<https://mediasite.ouhsc.edu/Mediasite/Channel/python>
________________________________
From: Luigi Marongiu, PhD <mar...@pr...>
Sent: Sunday, November 26, 2023 8:17 AM
To: Luigi Marongiu, PhD <mar...@pr...>
Cc: Mooers, Blaine H.M. (HSC) <Bla...@ou...>; pym...@li... <pym...@li...>
Subject: Re: [PyMOL] [EXTERNAL] How to install APBS on PyMol

Hello,
I installed PyMol 2.5.7 and ran APBS electrostatic. However, I got the error:

Error encountered: No heavy atoms found. You may also see this message if PDB2PQR does not have parameters for any residue in your protein.

The point is: I am evaluating molecules (acesulfame potassium, in this case) and not whole proteins. If the APBS has worked but could not compute, then I the answer is asnwered.
Thank you.


Sent with Proton Mail<https://urldefense.com/v3/__https://proton.me/__;!!GNU8KkXDZlD12Q!91FP9SLBNsqS8eThZ_0UNDUVLqeM5sdLcs0RhpVWuFCYTgv9UkS6FbV83OX2HQXD-I2v7ruXzzTA7TXsjauNBxLT5p2XpyGj$> secure email.

On Sunday, November 26th, 2023 at 1:13 PM, Luigi Marongiu, PhD via PyMOL-users <pym...@li...> wrote:

Hello,
I am using Version 2.5.0, if I not mistaken, I installed it via apt-get:

sudo apt-get -y install pymol

In the legacy tab, there is nothing...
Thank you

On Saturday, November 25th, 2023 at 6:38 PM, Mooers, Blaine H.M. (HSC) <Bla...@ou...> wrote:

Hi Luigi ,

Please include the version of PyMOL that you are using.
The APBS Tools are under the "legacy plugins" in the incentive version (2.5.7).
These are absent in the open source PyMOL (2.5.0).

There was a relatively recent change in the Python libraries used to generate
the widgets in PyMOL. You may have gotten an error about a missing Pnw module
when trying to load the plugin with a recent version of the open source PyMOL.
To use the plugin on the Wiki, you try an older version of PyMOL.
Hopefully, someone who is more knowledgeable about plugins will provide a better answer.

Best regards,

Blaine


________________________________
From: Luigi Marongiu, PhD via PyMOL-users <pym...@li...>
Sent: Saturday, November 25, 2023 2:02 AM
To: pym...@li... <pym...@li...>
Subject: [EXTERNAL] [PyMOL] How to install APBS on PyMol

Hello,
I tried to install APBS by launching Plugin manager and giving the URL of the app:

http://www.pymolwiki.org/index.php/apbsplugin<https://urldefense.com/v3/__http://www.pymolwiki.org/index.php/apbsplugin__;!!GNU8KkXDZlD12Q!5OL49CYDTO_Y03Eujw_t8KCDxMhOCpyG5rcuA3v1BiSdj2qbkMPr4ANlxDKnjXAhAEivMy4Avk2qqgNNSdDfhzZCogbMEtzeGog$>

The file has been written in ~/.pymol/startup but I got the error:

Plugin "apbsplugin" has been installed but initialization failed.

How do I properly launch this app? Please note I relaunched PyMol several times.
Thank you.

Sent with Proton Mail<https://urldefense.com/v3/__https://proton.me/__;!!GNU8KkXDZlD12Q!5OL49CYDTO_Y03Eujw_t8KCDxMhOCpyG5rcuA3v1BiSdj2qbkMPr4ANlxDKnjXAhAEivMy4Avk2qqgNNSdDfhzZCogbMu60SyAw$> secure email.

Re: [PyMOL] [EXTERNAL] How to install APBS on PyMol

[Luigi M. P. <mar...@pr...>]

Hello,
I installed PyMol 2.5.7 and ran APBS electrostatic. However, I got the error:

Error encountered: No heavy atoms found. You may also see this message if PDB2PQR does not have parameters for any residue in your protein.

The point is: I am evaluating molecules (acesulfame potassium, in this case) and not whole proteins. If the APBS has worked but could not compute, then I the answer is asnwered.
Thank you.

Sent with [Proton Mail](https://proton.me/) secure email.

On Sunday, November 26th, 2023 at 1:13 PM, Luigi Marongiu, PhD via PyMOL-users <pym...@li...> wrote:

> Hello,
> I am using Version 2.5.0, if I not mistaken, I installed it via apt-get:
>
> sudo
>
> apt-get
>
> -y
>
> install
>
> pymol
>
> In the legacy tab, there is nothing...
> Thank you
>
> On Saturday, November 25th, 2023 at 6:38 PM, Mooers, Blaine H.M. (HSC) <Bla...@ou...> wrote:
>
>> Hi Luigi ,
>>
>> Please include the version of PyMOL that you are using.
>> The APBS Tools are under the "legacy plugins" in the incentive version (2.5.7).
>> These are absent in the open source PyMOL (2.5.0).
>>
>> There was a relatively recent change in the Python libraries used to generate
>> the widgets in PyMOL. You may have gotten an error about a missing Pnw module
>> when trying to load the plugin with a recent version of the open source PyMOL.
>> To use the plugin on the Wiki, you try an older version of PyMOL.
>> Hopefully, someone who is more knowledgeable about plugins will provide a better answer.
>>
>> Best regards,
>>
>> Blaine
>>
>> ---------------------------------------------------------------
>>
>> From: Luigi Marongiu, PhD via PyMOL-users <pym...@li...>
>> Sent: Saturday, November 25, 2023 2:02 AM
>> To: pym...@li... <pym...@li...>
>> Subject: [EXTERNAL] [PyMOL] How to install APBS on PyMol
>>
>> Hello,
>> I tried to install APBS by launching Plugin manager and giving the URL of the app:
>>
>> [http://www.pymolwiki.org/index.php/apbsplugin](https://urldefense.com/v3/__http://www.pymolwiki.org/index.php/apbsplugin__;!!GNU8KkXDZlD12Q!5OL49CYDTO_Y03Eujw_t8KCDxMhOCpyG5rcuA3v1BiSdj2qbkMPr4ANlxDKnjXAhAEivMy4Avk2qqgNNSdDfhzZCogbMEtzeGog$)
>>
>> The file has been written in ~/.pymol/startup but I got the error:
>>
>> Plugin "apbsplugin" has been installed but initialization failed.
>>
>> How do I properly launch this app? Please note I relaunched PyMol several times.
>> Thank you.
>>
>> Sent with [Proton Mail](https://urldefense.com/v3/__https://proton.me/__;!!GNU8KkXDZlD12Q!5OL49CYDTO_Y03Eujw_t8KCDxMhOCpyG5rcuA3v1BiSdj2qbkMPr4ANlxDKnjXAhAEivMy4Avk2qqgNNSdDfhzZCogbMu60SyAw$) secure email.

Re: [PyMOL] [EXTERNAL] How to install APBS on PyMol

[Luigi M. P. <mar...@pr...>]

Hello,
I am using Version 2.5.0, if I not mistaken, I installed it via apt-get:

sudo

apt-get

-y

install

pymol

In the legacy tab, there is nothing...
Thank you

On Saturday, November 25th, 2023 at 6:38 PM, Mooers, Blaine H.M. (HSC) <Bla...@ou...> wrote:

> Hi Luigi ,
>
> Please include the version of PyMOL that you are using.
> The APBS Tools are under the "legacy plugins" in the incentive version (2.5.7).
> These are absent in the open source PyMOL (2.5.0).
>
> There was a relatively recent change in the Python libraries used to generate
> the widgets in PyMOL. You may have gotten an error about a missing Pnw module
> when trying to load the plugin with a recent version of the open source PyMOL.
> To use the plugin on the Wiki, you try an older version of PyMOL.
> Hopefully, someone who is more knowledgeable about plugins will provide a better answer.
>
> Best regards,
>
> Blaine
>
> ---------------------------------------------------------------
>
> From: Luigi Marongiu, PhD via PyMOL-users <pym...@li...>
> Sent: Saturday, November 25, 2023 2:02 AM
> To: pym...@li... <pym...@li...>
> Subject: [EXTERNAL] [PyMOL] How to install APBS on PyMol
>
> Hello,
> I tried to install APBS by launching Plugin manager and giving the URL of the app:
>
> [http://www.pymolwiki.org/index.php/apbsplugin](https://urldefense.com/v3/__http://www.pymolwiki.org/index.php/apbsplugin__;!!GNU8KkXDZlD12Q!5OL49CYDTO_Y03Eujw_t8KCDxMhOCpyG5rcuA3v1BiSdj2qbkMPr4ANlxDKnjXAhAEivMy4Avk2qqgNNSdDfhzZCogbMEtzeGog$)
>
> The file has been written in ~/.pymol/startup but I got the error:
>
> Plugin "apbsplugin" has been installed but initialization failed.
>
> How do I properly launch this app? Please note I relaunched PyMol several times.
> Thank you.
>
> Sent with [Proton Mail](https://urldefense.com/v3/__https://proton.me/__;!!GNU8KkXDZlD12Q!5OL49CYDTO_Y03Eujw_t8KCDxMhOCpyG5rcuA3v1BiSdj2qbkMPr4ANlxDKnjXAhAEivMy4Avk2qqgNNSdDfhzZCogbMu60SyAw$) secure email.

Re: [PyMOL] How to install APBS on PyMol

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

Hi Luigi,

I assume you are running Open source PyMOL 2.X and tried to install the 
apbsplugin.py file via the Plugin manager. I just tried this and got the 
same error from the Plugin manager. I am no expert here, but I assume 
this is related to the fact that this plugin uses the Tkinter GUI and 
python2. This will not work with PyMOL 2.X, which is based on Qt5 and 
python3. One possibility is to try to install an older PyMOL version 
1.X. Very likely the heavily used apbs plugin will work. Alternatively, 
use the Schrödinger PyMOL version. Even after the license has expired, 
many options will still work, probably also the APBS plugin.

I do not know if anybody works on adapting important plugins such as 
abps to open source PyMOL 2.X. Without such tools open source PyMOL is 
limited and many users might switch to ChimeraX which has developed a lot.

Best,

Norbert

Am 25.11.2023 um 09:02 schrieb Luigi Marongiu, PhD via PyMOL-users:
> Hello,
> I tried to install APBS by launching Plugin manager and giving the URL 
> of the app:
> http://www.pymolwiki.org/index.php/apbsplugin
> The file has been written in ~/.pymol/startup but I got the error:
>
> Plugin "apbsplugin" has been installed but initialization failed.
>
> How do I properly launch this app? Please note I relaunched PyMol 
> several times.
> Thank you.
>
> Sent with Proton Mail <https://proton.me/> secure email.
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives:http://www.mail-archive.com/pym...@li...
> Unsubscribe:https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] [EXTERNAL] How to install APBS on PyMol

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

Hi Luigi ,

Please include the version of PyMOL that you are using.
The APBS Tools are under the "legacy plugins" in the incentive version (2.5.7).
These are absent in the open source PyMOL (2.5.0).

There was a relatively recent change in the Python libraries used to generate
the widgets in PyMOL. You may have gotten an error about a missing Pnw module
when trying to load the plugin with a recent version of the open source PyMOL.
To use the plugin on the Wiki, you try an older version of PyMOL.
Hopefully, someone who is more knowledgeable about plugins will provide a better answer.

Best regards,

Blaine


________________________________
From: Luigi Marongiu, PhD via PyMOL-users <pym...@li...>
Sent: Saturday, November 25, 2023 2:02 AM
To: pym...@li... <pym...@li...>
Subject: [EXTERNAL] [PyMOL] How to install APBS on PyMol

Hello,
I tried to install APBS by launching Plugin manager and giving the URL of the app:

http://www.pymolwiki.org/index.php/apbsplugin<https://urldefense.com/v3/__http://www.pymolwiki.org/index.php/apbsplugin__;!!GNU8KkXDZlD12Q!5OL49CYDTO_Y03Eujw_t8KCDxMhOCpyG5rcuA3v1BiSdj2qbkMPr4ANlxDKnjXAhAEivMy4Avk2qqgNNSdDfhzZCogbMEtzeGog$>

The file has been written in ~/.pymol/startup but I got the error:

Plugin "apbsplugin" has been installed but initialization failed.

How do I properly launch this app? Please note I relaunched PyMol several times.
Thank you.

Sent with Proton Mail<https://urldefense.com/v3/__https://proton.me/__;!!GNU8KkXDZlD12Q!5OL49CYDTO_Y03Eujw_t8KCDxMhOCpyG5rcuA3v1BiSdj2qbkMPr4ANlxDKnjXAhAEivMy4Avk2qqgNNSdDfhzZCogbMu60SyAw$> secure email.

[PyMOL] How to install APBS on PyMol

[Luigi M. P. <mar...@pr...>]

Hello,
I tried to install APBS by launching Plugin manager and giving the URL of the app:

http://www.pymolwiki.org/index.php/apbsplugin

The file has been written in ~/.pymol/startup but I got the error:

Plugin "apbsplugin" has been installed but initialization failed.

How do I properly launch this app? Please note I relaunched PyMol several times.
Thank you.

Sent with [Proton Mail](https://proton.me/) secure email.