Re: [ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2

2023-02-06 Thread Julia Griese
Oh, I hadn’t thought of trying that, that works!

Obviously it would still be great if this issue was fixed (I guess it’s MacOS 
rather than PyMOL that’s to blame here), but this is a decent workaround.

Thanks!

/Julia

--
Dr. Julia Griese
Assistant Professor/Docent
Department of Cell and Molecular Biology
Uppsala University
BMC, Box 596
SE-75124 Uppsala
Sweden

email: julia.gri...@icm.uu.se
phone: +46-(0)18-471 4982
http://www.icm.uu.se/structural-biology/griese-lab/

From: CCP4 bulletin board  on behalf of Nicholas Clark 

Reply-To: Nicholas Clark 
Date: Monday, February 6, 2023 at 12:46
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: [ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2



-- Forwarded message -
From: Nicholas Clark mailto:ndcla...@buffalo.edu>>
Date: Mon, Feb 6, 2023 at 6:44 AM
Subject: Re: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2
To: Julia Griese mailto:julia.gri...@icm.uu.se>>

Julia,

I have the same issue with PyMOL. After it opens the blank session, if you 
return to the file explorer and try to reopen the file it will open the session 
correctly. Seems what you’re trying to open gets “lost” while loading PyMOL.

Best,

Nick Clark

On Mon, Feb 6, 2023 at 5:38 AM Julia Griese 
mailto:julia.gri...@icm.uu.se>> wrote:
Hi all,

I’ve recently upgraded to MacOS Ventura (yes, I regret giving in to my 
computer’s nagging) and am now encountering some issues with Coot and PyMOL. 
The issues persist after updating to version 13.2.

Regarding Coot version 0.9.8.7: The rotate/translate zone 
function does not work properly. Everything works when using the slider bars in 
the dialog, and translating with the mouse works, but rotating with the mouse 
does not work. The region to be rotated disappears from view. I can make do 
with the slider bars, but feel that I have much better fine control and it’s 
much faster when using the mouse to rotate. Has anyone else encountered this 
problem and knows of a workaround?
(I’m aware of the workaround for the main window disappearing when you delete 
items.)

Regarding PyMOL version 2.5.4 (had the same issue with 2.4.1): When I try to 
open any kind of file that is set to open in PyMOL by default (pdb or cif 
coordinates, pse), PyMOL opens, but to an empty session. I can only open PyMOL 
files through the File Open dialog, having to navigate through the entire 
folder structure first, which obviously takes much longer. Has anyone else 
encountered this issue and knows how to fix it?


Best,

Julia

--
Dr. Julia Griese
Assistant Professor/Docent
Department of Cell and Molecular Biology
Uppsala University
BMC, Box 596
SE-75124 Uppsala
Sweden

email: julia.gri...@icm.uu.se
phone: +46-(0)18-471 4982
http://www.icm.uu.se/structural-biology/griese-lab/








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--
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908
--
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908



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[ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2

2023-02-06 Thread Nicholas Clark
-- Forwarded message -
From: Nicholas Clark 
Date: Mon, Feb 6, 2023 at 6:44 AM
Subject: Re: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2
To: Julia Griese 


Julia,

I have the same issue with PyMOL. After it opens the blank session, if you
return to the file explorer and try to reopen the file it will open the
session correctly. Seems what you’re trying to open gets “lost” while
loading PyMOL.

Best,

Nick Clark

On Mon, Feb 6, 2023 at 5:38 AM Julia Griese  wrote:

> Hi all,
>
>
>
> I’ve recently upgraded to MacOS Ventura (yes, I regret giving in to my
> computer’s nagging) and am now encountering some issues with Coot and
> PyMOL. The issues persist after updating to version 13.2.
>
>
>
> *Regarding Coot version 0.9.8.7 :* The rotate/translate
> zone function does not work properly. Everything works when using the
> slider bars in the dialog, and translating with the mouse works, but
> rotating with the mouse does not work. The region to be rotated disappears
> from view. I can make do with the slider bars, but feel that I have much
> better fine control and it’s much faster when using the mouse to rotate.
> Has anyone else encountered this problem and knows of a workaround?
>
> (I’m aware of the workaround for the main window disappearing when you
> delete items.)
>
>
>
> *Regarding PyMOL version 2.5.4 *(had the same issue with 2.4.1): When I
> try to open any kind of file that is set to open in PyMOL by default (pdb
> or cif coordinates, pse), PyMOL opens, but to an empty session. I can only
> open PyMOL files through the File Open dialog, having to navigate through
> the entire folder structure first, which obviously takes much longer. Has
> anyone else encountered this issue and knows how to fix it?
>
>
>
>
>
> Best,
>
>
>
> Julia
>
>
>
> --
>
> Dr. Julia Griese
>
> Assistant Professor/Docent
>
> Department of Cell and Molecular Biology
>
> Uppsala University
>
> BMC, Box 596
>
> SE-75124 Uppsala
>
> Sweden
>
>
>
> email: julia.gri...@icm.uu.se
>
> phone: +46-(0)18-471 4982
>
> http://www.icm.uu.se/structural-biology/griese-lab/
> 
>
>
>
>
>
>
>
>
> När du har kontakt med oss på Uppsala universitet med e-post så innebär
> det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör
> det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
>
> E-mailing Uppsala University means that we will process your personal
> data. For more information on how this is performed, please read here:
> http://www.uu.se/en/about-uu/data-protection-policy
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
>
-- 
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908
-- 
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908



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[ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2

2023-02-06 Thread Julia Griese
Hi all,

I’ve recently upgraded to MacOS Ventura (yes, I regret giving in to my 
computer’s nagging) and am now encountering some issues with Coot and PyMOL. 
The issues persist after updating to version 13.2.

Regarding Coot version 0.9.8.7: The rotate/translate zone function does not 
work properly. Everything works when using the slider bars in the dialog, and 
translating with the mouse works, but rotating with the mouse does not work. 
The region to be rotated disappears from view. I can make do with the slider 
bars, but feel that I have much better fine control and it’s much faster when 
using the mouse to rotate. Has anyone else encountered this problem and knows 
of a workaround?
(I’m aware of the workaround for the main window disappearing when you delete 
items.)

Regarding PyMOL version 2.5.4 (had the same issue with 2.4.1): When I try to 
open any kind of file that is set to open in PyMOL by default (pdb or cif 
coordinates, pse), PyMOL opens, but to an empty session. I can only open PyMOL 
files through the File Open dialog, having to navigate through the entire 
folder structure first, which obviously takes much longer. Has anyone else 
encountered this issue and knows how to fix it?


Best,

Julia

--
Dr. Julia Griese
Assistant Professor/Docent
Department of Cell and Molecular Biology
Uppsala University
BMC, Box 596
SE-75124 Uppsala
Sweden

email: julia.gri...@icm.uu.se
phone: +46-(0)18-471 4982
http://www.icm.uu.se/structural-biology/griese-lab/








När du har kontakt med oss på Uppsala universitet med e-post så innebär det att 
vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du 
läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/

E-mailing Uppsala University means that we will process your personal data. For 
more information on how this is performed, please read here: 
http://www.uu.se/en/about-uu/data-protection-policy



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