[PyMOL] where can I ask questions? Is there any forum?

[Elizabeth Tsakelidou]

Hey

I would like to know what is the best way to install and work protein-ligand 
docking.
I have Windows 11 and I tried Anaconda PyMOL but I think this way
you cannot have all plugins available.
So, what if I tried ubuntu with all is available on GitHub?
Can I do this?
The query arises because it is said that if you want to install linux in windows
you better use cygwin.
What do you think?
Thanks

Elizabeth

Sent from Outlook
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Re: [PyMOL] where can I ask questions? Is there any forum?

[Tamas Hegedus]

Hi,

I think that you have two issues:

#1 pymol autodock/vina plugin; it should work on windows, since it is written 
in python. The issue u might encounter: it may have written in an older python 
version than the pymol install

#2 you have to perform the docking with autodock or autodock vina. I think that 
these will not run on win.
You also have to prepare the prot and small molecule w autodocktools. Some gui 
apps might have preparation wizard.

Bests



⁣Az Android BlueMail letöltése ​

2024. ápr. 1. 17:23-n, 17:23-kor, Elizabeth Tsakelidou  
ezt írta:
>
>Hey
>
>I would like to know what is the best way to install and work
>protein-ligand docking.
>I have Windows 11 and I tried Anaconda PyMOL but I think this way
>you cannot have all plugins available.
>So, what if I tried ubuntu with all is available on GitHub?
>Can I do this?
>The query arises because it is said that if you want to install linux
>in windows
>you better use cygwin.
>What do you think?
>Thanks
>
>Elizabeth
>
>Sent from Outlook
>
>
>
>
>
>
>
>
>___
>PyMOL-users mailing list
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Re: [PyMOL] where can I ask questions? Is there any forum?

[Dr. Vijay Masand]

Dear Elizabeth
A simple solution is to use DockingApp in Windows. Downliad it from
following site:
http://www.computationalbiology.it/software.html
It is very easy to use it. Contact if you need any help.
From
Dr. Vijay H. Masand


On Mon, 1 Apr, 2024, 8:55 pm Elizabeth Tsakelidou, 
wrote:

>
> Hey
>
> I would like to know what is the best way to install and work
> protein-ligand docking.
> I have Windows 11 and I tried Anaconda PyMOL but I think this way
> you cannot have all plugins available.
> So, what if I tried ubuntu with all is available on GitHub?
> Can I do this?
> The query arises because it is said that if you want to install linux in
> windows
> you better use cygwin.
> What do you think?
> Thanks
>
> Elizabeth
>
> Sent from Outlook 
> ___
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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Re: [PyMOL] where can I ask questions? Is there any forum?

[Elizabeth Tsakelidou]

Thank you very much for your reply.
I will work some things that are seemingly working
for the moment
and if I see this does not lead anywhere, I ll come back to you.

Greetings,
Elizabeth

Sent from Outlook


From: Dr. Vijay Masand 
Sent: Monday, April 1, 2024 5:02 PM
To: Elizabeth Tsakelidou 
Cc: pymol-users 
Subject: Re: [PyMOL] where can I ask questions? Is there any forum?

Dear Elizabeth
A simple solution is to use DockingApp in Windows. Downliad it from following 
site:
http://www.computationalbiology.it/software.html
It is very easy to use it. Contact if you need any help.
From
Dr. Vijay H. Masand


On Mon, 1 Apr, 2024, 8:55 pm Elizabeth Tsakelidou, 
mailto:tsake...@hotmail.com>> wrote:

Hey

I would like to know what is the best way to install and work protein-ligand 
docking.
I have Windows 11 and I tried Anaconda PyMOL but I think this way
you cannot have all plugins available.
So, what if I tried ubuntu with all is available on GitHub?
Can I do this?
The query arises because it is said that if you want to install linux in windows
you better use cygwin.
What do you think?
Thanks

Elizabeth

Sent from Outlook

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[PyMOL] create new object from selection - version 3.0

[Joel Mackay via PyMOL-users]

Hi
I've always found the command allowing you to create a 'cloned' object from a 
selection to be extremely useful. That is, select a chain (for example) and 
then use:

Action > copy to object > new

This seems to be disabled in version 3. You can extract a chain that you've 
selected, but not make a fresh copy. Am I just missing something?

[It also seems a bit strange that submenus now don't disappear as you scroll 
down the list of possible actions, until you reach the next command that has a 
submenu - it's a bit disconcerting]

Thanks
Joel


[cid:image001.png@01DA84FA.CEE5D470]
-
Professor Joel Mackay
School of Life and Environmental Sciences
THE UNIVERSITY OF SYDNEY

A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave
The University of Sydney | NSW | 2006 | Australia
T: +61 2 9351 3906
E: joel.mac...@sydney.edu.au  | W: 
www.mackaymatthewslab.org

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Re: [PyMOL] create new object from selection - version 3.0

[Jarrett Johnson]

Hi Joel,

Thanks for your feedback. You're correct in both assessments. I can
reproduce the first issue (the `copy to object` menu should produce a
submenu), and should be able to get a fix for that very soon. There are
some submenu quirks that are still being ironed out; some of which, at
least for linux, are also being addressed this week--but all still ongoing.

Best,
Jarrett J.

On Mon, Apr 1, 2024 at 10:16 PM Joel Mackay via PyMOL-users <
pymol-users@lists.sourceforge.net> wrote:

> Hi
>
> I’ve always found the command allowing you to create a ‘cloned’ object
> from a selection to be extremely useful. That is, select a chain (for
> example) and then use:
>
>
>
> Action > copy to object > new
>
>
>
> This seems to be disabled in version 3. You can extract a chain that
> you’ve selected, but not make a fresh copy. Am I just missing something?
>
>
>
> [It also seems a bit strange that submenus now don’t disappear as you
> scroll down the list of possible actions, until you reach the next command
> that has a submenu – it’s a bit disconcerting]
>
>
>
> Thanks
> Joel
>
>
>
>
>
>
> -
>
> *Professor Joel Mackay*
>
> School of Life and Environmental Sciences
>
> THE UNIVERSITY OF SYDNEY
>
>
>
> A: School of Life and Environmental Sciences | Rm 674, Building G08 |
> Butlin Ave
>
> The University of Sydney | NSW | 2006 | Australia
>
> T: +61 2 9351 3906
>
> E: joel.mac...@sydney.edu.au  | W: www.mackaymatthewslab.org
> 
>
>
> ___
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>


-- 

*Jarrett Johnson* | Senior Developer, PyMOL
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Re: [PyMOL] create new object from selection - version 3.0

[Joel Mackay via PyMOL-users]

Thanks very much for the response Jarrett – great to know it’s been ID-ed and 
is in the process of being mended.
J


-
Professor Joel Mackay
School of Life and Environmental Sciences
THE UNIVERSITY OF SYDNEY

A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave
The University of Sydney | NSW | 2006 | Australia
T: +61 2 9351 3906
E: joel.mac...@sydney.edu.au  | W: 
www.mackaymatthewslab.org

From: Jarrett Johnson 
Sent: Tuesday, April 2, 2024 2:57 PM
To: Joel Mackay 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] create new object from selection - version 3.0

Hi Joel,

Thanks for your feedback. You're correct in both assessments. I can reproduce 
the first issue (the `copy to object` menu should produce a submenu), and 
should be able to get a fix for that very soon. There are some submenu quirks 
that are still being ironed out; some of which, at least for linux, are also 
being addressed this week--but all still ongoing.

Best,
Jarrett J.

On Mon, Apr 1, 2024 at 10:16 PM Joel Mackay via PyMOL-users 
mailto:pymol-users@lists.sourceforge.net>> 
wrote:
Hi
I’ve always found the command allowing you to create a ‘cloned’ object from a 
selection to be extremely useful. That is, select a chain (for example) and 
then use:

Action > copy to object > new

This seems to be disabled in version 3. You can extract a chain that you’ve 
selected, but not make a fresh copy. Am I just missing something?

[It also seems a bit strange that submenus now don’t disappear as you scroll 
down the list of possible actions, until you reach the next command that has a 
submenu – it’s a bit disconcerting]

Thanks
Joel


[cid:image001.png@01DA8513.C8E14410]
-
Professor Joel Mackay
School of Life and Environmental Sciences
THE UNIVERSITY OF SYDNEY

A: School of Life and Environmental Sciences | Rm 674, Building G08 | Butlin Ave
The University of Sydney | NSW | 2006 | Australia
T: +61 2 9351 3906
E: joel.mac...@sydney.edu.au  | W: 
www.mackaymatthewslab.org

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--

Jarrett Johnson | Senior Developer, PyMOL
[Image removed by sender.]

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