pymol-users — Collaborative support and tips for PyMOL users

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.

[PyMOL] How to drag molecule in the pane with pymol

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

Hello,
I have one molecules and I am importing a second one in the same file. The second molecule comes on top of the first one.
How do I drag the second molecule around so that it does not overlap with the first? If I choose 'drag matrix', I can rotate the second molecule in the z axis. How can I move along the x/y axis?
Thank you

[PyMOL] Get list of bound residues for al poses on PyMol

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

I can find the polar contact between my target and a ligand, but is it possible to get a table with all the bound residues and for all the poses, instead of manually finding the involved residues one by one?
Thank you.

Re: [PyMOL] [EXTERNAL] Question about rotation in latest version of Pymol

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

Hi Katayoun,

You can use the command turn.
Enter 'help turn' at the PyMOL prompt to get the documentation about how to use it.

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: Katayoun Etemadi Some Olyayi <ke...@br...>
Sent: Wednesday, November 15, 2023 10:03 AM
To: pym...@li... <pym...@li...>
Subject: [EXTERNAL] [PyMOL] Question about rotation in latest version of Pymol


Hello,



I’m trying to rotate 2 atoms simultaneously in Pymol, mac version. I am able to do that by using the command: “rotate axis, angle, selection”. But any axis that I use, gives out very long bonds that look definitely wrong. Except for doing it manually, (using command key+ left click) are there any other commands I could use?



Thanks,

Katayoun

[PyMOL] Question about rotation in latest version of Pymol

[Katayoun E. S. O. <ke...@br...>]

Hello,

I’m trying to rotate 2 atoms simultaneously in Pymol, mac version. I am able to do that by using the command: “rotate axis, angle, selection”. But any axis that I use, gives out very long bonds that look definitely wrong. Except for doing it manually, (using command key+ left click) are there any other commands I could use?

Thanks,
Katayoun

Re: [PyMOL] Dss when creating movie from dcd traj

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

Hi Effie,

try to load the trajectory with the option discrete=1:

load trajectory.dcd, discrete=1

Best,

Norbert

Am 09.11.2023 um 19:38 schrieb Effie Artikis:
> Hello,
>
> I’ve uploaded my MD simulation and am trying to create a movie but 
> I’ve noticed that when I play the MD simulation, the secondary 
> structure isn’t updated frame by frame. For example, although it is an 
> unfolding simulation the protein maintains the secondary structure of 
> the initial frame throughout the trajectory. Employing the dss command 
> for any frame applies those secondary structural characteristics to 
> the rest of the frames in the trajectory. Is there a way to update the 
> dss for each frame as the simulation plays?
>
> Thanks!
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Dss when creating movie from dcd traj

[Effie A. <ear...@gm...>]

Hello,

I’ve uploaded my MD simulation and am trying to create a movie but I’ve
noticed that when I play the MD simulation, the secondary structure isn’t
updated frame by frame. For example, although it is an unfolding simulation
the protein maintains the secondary structure of the initial frame
throughout the trajectory. Employing the dss command for any frame applies
those secondary structural characteristics to the rest of the frames in the
trajectory. Is there a way to update the dss for each frame as the
simulation plays?

Thanks!

Re: [PyMOL] How to delete/hide unwanted poses in Pymol?

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

Hi Luigi,

that depends on how the data are read into PyMOL and how the coordinate 
files are structured.

For example, if you read in a pdb file ligand1.pdb, which contains this 
ligand with different poses having different residue numbers and next 
you read in a second pdb file for the second ligand, it may work as follows:

load ligand1.pdb
load ligand2.pdb
# delete the unwanted poses
remove not ((ligand1 and resid 3) or (ligand2 and resid 8))
show sticks

or

load ligand1.pdb
load ligand2.pdb
hide everything
# show only the desired poses
show sticks, (ligand1 and resid 3) or (ligand2 and resid 8)

If you need to do this repeatedly with many poses, a convenient way 
would be to write a script that generates objects for each ligand/pose 
and you can toogle them visible via the menu on the right side of the 
PyMOL interface (commands enable and disable).

If you coordinate files are structured in a different way or if all data 
are in one coordinate file, modifications may be necessary. Perhaps you 
need to distinguish the ligands and poses based on residue names (resn) 
and numbers (resi). Google for "pymol selection algebra" and commands 
show, hide, remove, enable, disable.

With more sophisticated script programming, one may automatically 
generate different objects for each pose read from a pdb file.

Best,

Norbert

Am 09.11.2023 um 11:41 schrieb Luigi Marongiu, PhD via PyMOL-users:
> Hello,
> I have several poses from a docking to a protein and I have different 
> ligands to compare.
> I can load on PyMol the different ligands on a same protein file, and 
> I can look at each pose for the different ligands but only, let's say, 
> in sync: pose 1 of ligand 1 together with pose 1 of ligand 2; pose 2 
> of ligand 1 together with pose 2 of ligand 2; and so forth.
> Let's say that I am interested in comparing pose 3 of ligand 1 and 
> pose 8 of ligand 2.
> How can I hide or delete the unwanted poses?
> Thank you.
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives:http://www.mail-archive.com/pym...@li...
> Unsubscribe:https://sourceforge.net/projects/pymol/lists/pymol-users/unsubsc

[PyMOL] How to delete/hide unwanted poses in Pymol?

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

Hello,
I have several poses from a docking to a protein and I have different ligands to compare.
I can load on PyMol the different ligands on a same protein file, and I can look at each pose for the different ligands but only, let's say, in sync: pose 1 of ligand 1 together with pose 1 of ligand 2; pose 2 of ligand 1 together with pose 2 of ligand 2; and so forth.
Let's say that I am interested in comparing pose 3 of ligand 1 and pose 8 of ligand 2.
How can I hide or delete the unwanted poses?
Thank you.

Re: [PyMOL] help with PyMOL rename command

[<wd...@li...>]

Thank You a lot indeed explanation ways more clear than the wiki one

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


.... I know I should have tried more

 

Again Thanks

Re: [PyMOL] waterbox visulization in pymol

[Matic K. <Mat...@ki...>]

Hi Yeeun,

could it be that you had orthoscopic view (menu Display>Orthoscopic View) enabled in Pymol and not in VMD?

To see the 'grid' I think you usually need Orthoscopic view. I may be wrong. Try the perspective view if that changes things.
So I think this is just a visualisation artefact and does not affect the simulations (if you plan to do that).

Usually all the water molecules are defined in the input file, so I would guess it is not 'several small waterboxes combined into one'.
You can also check by opening the input file in a advanced text editor (Notepad++, Sublime text, ...) and you will be able to count the molecules and see if there is some symmetry defined (probably not).

Best!
Matic


On 22. 10. 23 08:24, 김예은 wrote:
Dear Pymol,
Hello.
I visualized a water box generated by Charmm-gui in pymol.
[image.png]
There is a grid pattern in the waterbox, so I thought several small waterboxes were generated and combined into one.
However, in VMD software, there is no grid pattern in the same waterbox.
[image.png]
Is there any specific visualization method to show the grid pattern in the waterbox in Pymol?
Or, could I think that several small waterboxes were generated and combined into one?

Sincerely,
Yeeun Kim




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[PyMOL] waterbox visulization in pymol

[김예은 <ky...@gm...>]

Dear Pymol,
Hello.
I visualized a water box generated by Charmm-gui in pymol.
[image: image.png]
There is a grid pattern in the waterbox, so I thought several small
waterboxes were generated and combined into one.
However, in VMD software, there is no grid pattern in the same waterbox.
[image: image.png]
Is there any specific visualization method to show the grid pattern in the
waterbox in Pymol?
Or, could I think that several small waterboxes were generated and combined
into one?

Sincerely,
Yeeun Kim

Re: [PyMOL] [EXTERNAL] Student version

[Engin Ö. <eo...@uc...>]

As part of a class, my students had to use this link, 
https://pymol.org/edu/ last week, and we had zero problems.


I think the educational licenses are working just fine. At least most of 
the time.


Engin


On 10/6/23 5:13 AM, Thomas Charles Pochapsky wrote:
>
> Blaine,
>
> Thanks!  I'll try that.
>
> Tom
>
> On 10/6/23 5:58 AM, Mooers, Blaine H.M. (HSC) wrote:
>> Hi Tom,
>>
>> An alternative is to be to show  your students how to install 
>> Anaconda and then install open source PyMOL,
>> which lacks a few minor features of the incentive version but has 
>> more features than the student version.
>> https://anaconda.org/conda-forge/pymol-open-source.
>>
>> It is likely that they will need Anaconda in the future to install 
>> other scientific computing software.
>>
>> 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> 
>>
>> 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>
>> SSRL Users Executive Committee 
>> <https://www-ssrl.slac.stanford.edu/content/about-ssrl/ssrluo-2022-2023-executive-committee-members>
>>
>> Center,
>> ------------------------------------------------------------------------
>> *From:* Thomas Charles Pochapsky <poc...@br...>
>> *Sent:* Friday, October 6, 2023 4:28 AM
>> *To:* pym...@li... 
>> <pym...@li...>
>> *Subject:* [EXTERNAL] [PyMOL] Student version
>> Hi, all.  Did anybody ever reply about the student version of PyMol
>> downloads?  I use it in my class on a regular basis, but I can no longer
>> find the link on the Schrodinger web site.  There is a free download for
>> Maestro, with which I am unfamiliar.   Is this a replacement?
>>
>> Thanks.  Tom
>>
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: 
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>> [mail-archive[.]com]
>> Unsubscribe: 
>> https://urldefense.com/v3/__https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe__;!!GNU8KkXDZlD12Q!6qyXPA9djwzIN-ekBa0_V2y5Q1f2UdHYpkf5NNqCVUc_JacvO8JHPvaC4bKhTKFhhL4H-ldFoxLn3QIHqARfp2zYm2Y$ 
>> [sourceforge[.]net]
>
>
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-- 
Engin Özkan, Ph.D.
Associate Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
Phone: (773) 834-5498
http://ozkan.uchicago.edu