There are 4 messages totaling 3805 lines in this issue.
Topics of the day:
1. Quartz/Coot 0.9.8.96 (4)
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Date: Sun, 23 Aug 2026 09:07:49 +0200
From: Oliver H. Weiergräber
<[email protected]>
Subject: Re: Quartz/Coot 0.9.8.96
Hello Engin and Matthew,
Using Coot 0.9.8.96 (ccp4) on a Macbook Air M2 (running latest OS and
XQuartz, as mentioned above), this is what I am getting (see attached
screenshot).
As you can see, the bottom row (for display of status information) is
mostly drawn black, and there is an additional horizontal area on top
which should not be there. Btw, the icons displayed there are actually
copies of the main toolbar on the right, and their number may change
when resizing the window. Clearly a case of graphics corruption.
Of course I tried deleting the .coot-preferences directory as well as
local state files, without effect.
Best,
Oliver
On 22.08.26 21:12, Engin Özkan wrote:
For extra data on this, everything I could test was fine with an M1
MacBook Pro and Xquartz 2.8.6 (stable) on Tahoe 26.6.2. All pop-up
windows I tried worked as intended. This is with 0.9.8.96 (installed via
ccp4, version 9.0.017).
The only issue I have is a thin row of corrupted space (same thickness
as the menu bar) under the menu bar, or sequence viewer when turned on,
but it does not affect usability much. An upgrade to 2.8.7beta3 does not
fix this issue, so I would not suggest it yet.
Engin
On 8/22/26 12:41 PM, Matthew Snee wrote:
Hi Oliver
I have tested two macs now using xquartz 2.8.6 and coot 0.9.8.93 EL
and both an M4 MAX studio and an M2 MacBook Air with the latest Tahoe.
I tested looking at maps and some refinement features etc.. Obviously
I cant test everything but dialogue boxes and stuff are all working
fine for me.
I'm not recommending anyone assumes it will work with their hardware,
but I thought everyone was in the same boat as me where it wouldn't
even launch?
Best wishes
Matthew.
Sent from Outlook for iOS<https://aka.ms/o0ukef>
------------------------------------------------------------------------
*From:* Oliver H. Weiergräber<[email protected]>
*Sent:* Saturday, August 22, 2026 6:12 pm
*To:* Matthew Snee<[email protected]>;
[email protected] <[email protected]>
*Subject:* Re: [ccp4bb] Quartz/Coot 0.9.8.96
Dear Matthew,
For me, using Tahoe 26.6.2 and XQuartz 2.8.6, Coot 0.9 starts up with a
partly corrupted workspace.
Are you maybe referring to XQuartz 2.8.7beta?
Best,
Oliver
On 21.08.26 18:27, Matthew Snee wrote:
Hi All
Just to let everyone know, but the latest Xquartz or Tahoe update
appears to have fixed the (OpenGL) issue in Xquartz that broke Coot 0.9
versions for mac.
*Matthew Snee, PhD*
Post-doctoral Research Associate
The Baldock Lab | Michael Smith Building C3.214 | Wellcome Trust Centre
for Cell-Matrix Research |Division of Cell Matrix Biology & Regenerative
Medicine| School of Biological Sciences| Faculty of Biology, Medicine
and Health, University of Manchester, Oxford Road, Manchester M13 9PT
Lab Tel: +44 (0)161 306 2869
cell-matrix-research
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------------------------------
Date: Sun, 23 Aug 2026 00:22:03 -0700
From: Kedar Sharma<[email protected]>
Subject: Re: Quartz/Coot 0.9.8.96
Hi all,
I have updated to xquartz 2.8.7 beta 3 and coot 0.9.8.96 working fine. I
am using Mac Tahoe 26.6.2.
Best
Kedar
On Sun, Aug 23, 2026 at 12:08 AM Oliver H. Weiergräber<
[email protected]> wrote:
Hello Engin and Matthew,
Using Coot 0.9.8.96 (ccp4) on a Macbook Air M2 (running latest OS and
XQuartz, as mentioned above), this is what I am getting (see attached
screenshot).
As you can see, the bottom row (for display of status information) is
mostly drawn black, and there is an additional horizontal area on top
which should not be there. Btw, the icons displayed there are actually
copies of the main toolbar on the right, and their number may change
when resizing the window. Clearly a case of graphics corruption.
Of course I tried deleting the .coot-preferences directory as well as
local state files, without effect.
Best,
Oliver
On 22.08.26 21:12, Engin Özkan wrote:
For extra data on this, everything I could test was fine with an M1
MacBook Pro and Xquartz 2.8.6 (stable) on Tahoe 26.6.2. All pop-up
windows I tried worked as intended. This is with 0.9.8.96 (installed via
ccp4, version 9.0.017).
The only issue I have is a thin row of corrupted space (same thickness
as the menu bar) under the menu bar, or sequence viewer when turned on,
but it does not affect usability much. An upgrade to 2.8.7beta3 does not
fix this issue, so I would not suggest it yet.
Engin
On 8/22/26 12:41 PM, Matthew Snee wrote:
Hi Oliver
I have tested two macs now using xquartz 2.8.6 and coot 0.9.8.93 EL
and both an M4 MAX studio and an M2 MacBook Air with the latest Tahoe.
I tested looking at maps and some refinement features etc.. Obviously
I cant test everything but dialogue boxes and stuff are all working
fine for me.
I'm not recommending anyone assumes it will work with their hardware,
but I thought everyone was in the same boat as me where it wouldn't
even launch?
Best wishes
Matthew.
Sent from Outlook for iOS<https://aka.ms/o0ukef>
------------------------------------------------------------------------
*From:* Oliver H. Weiergräber<[email protected]>
*Sent:* Saturday, August 22, 2026 6:12 pm
*To:* Matthew Snee<[email protected]>;
[email protected] <[email protected]>
*Subject:* Re: [ccp4bb] Quartz/Coot 0.9.8.96
Dear Matthew,
For me, using Tahoe 26.6.2 and XQuartz 2.8.6, Coot 0.9 starts up with a
partly corrupted workspace.
Are you maybe referring to XQuartz 2.8.7beta?
Best,
Oliver
On 21.08.26 18:27, Matthew Snee wrote:
Hi All
Just to let everyone know, but the latest Xquartz or Tahoe update
appears to have fixed the (OpenGL) issue in Xquartz that broke Coot
0.9
versions for mac.
*Matthew Snee, PhD*
Post-doctoral Research Associate
The Baldock Lab | Michael Smith Building C3.214 | Wellcome Trust
Centre
for Cell-Matrix Research |Division of Cell Matrix Biology &
Regenerative
Medicine| School of Biological Sciences| Faculty of Biology, Medicine
and Health, University of Manchester, Oxford Road, Manchester M13 9PT
Lab Tel: +44 (0)161 306 2869
cell-matrix-research
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------------------------------
Date: Sun, 23 Aug 2026 02:49:41 -0500
From: Engin Özkan<[email protected]>
Subject: Re: Quartz/Coot 0.9.8.96
Hi Oliver,
Yes, that's the thin row of corrupted space at the top, similar to the
picture Matthew had attached. But you can load maps and coordinates, and
everything works in my hands.
The loss of the bottom row is the only lost functionality I can see (I
had missed it). That is significant, indeed. Though you can make up for
that by running coot from a terminal and looking at the output there, I
believe. It beats immediate crashing, as has been the case lately.
Coot 0.9 will not likely see any updates, so this is a temporary
solution until we all manage to move to Coot 1.
Engin
On 8/23/26 2:07 AM, Oliver H. Weiergräber wrote:
Hello Engin and Matthew,
Using Coot 0.9.8.96 (ccp4) on a Macbook Air M2 (running latest OS and
XQuartz, as mentioned above), this is what I am getting (see attached
screenshot).
As you can see, the bottom row (for display of status information) is
mostly drawn black, and there is an additional horizontal area on top
which should not be there. Btw, the icons displayed there are actually
copies of the main toolbar on the right, and their number may change
when resizing the window. Clearly a case of graphics corruption.
Of course I tried deleting the .coot-preferences directory as well as
local state files, without effect.
Best,
Oliver
On 22.08.26 21:12, Engin Özkan wrote:
For extra data on this, everything I could test was fine with an M1
MacBook Pro and Xquartz 2.8.6 (stable) on Tahoe 26.6.2. All pop-up
windows I tried worked as intended. This is with 0.9.8.96 (installed
via ccp4, version 9.0.017).
The only issue I have is a thin row of corrupted space (same
thickness as the menu bar) under the menu bar, or sequence viewer
when turned on, but it does not affect usability much. An upgrade to
2.8.7beta3 does not fix this issue, so I would not suggest it yet.
Engin
On 8/22/26 12:41 PM, Matthew Snee wrote:
Hi Oliver
I have tested two macs now using xquartz 2.8.6 and coot 0.9.8.93 EL
and both an M4 MAX studio and an M2 MacBook Air with the latest Tahoe.
I tested looking at maps and some refinement features etc..
Obviously I cant test everything but dialogue boxes and stuff are
all working fine for me.
I'm not recommending anyone assumes it will work with their
hardware, but I thought everyone was in the same boat as me where
it wouldn't even launch?
Best wishes
Matthew.
Sent from Outlook for iOS<https://aka.ms/o0ukef>
------------------------------------------------------------------------
*From:* Oliver H. Weiergräber<[email protected]>
*Sent:* Saturday, August 22, 2026 6:12 pm
*To:* Matthew Snee<[email protected]>;
[email protected] <[email protected]>
*Subject:* Re: [ccp4bb] Quartz/Coot 0.9.8.96
Dear Matthew,
For me, using Tahoe 26.6.2 and XQuartz 2.8.6, Coot 0.9 starts up with a
partly corrupted workspace.
Are you maybe referring to XQuartz 2.8.7beta?
Best,
Oliver
On 21.08.26 18:27, Matthew Snee wrote:
Hi All
Just to let everyone know, but the latest Xquartz or Tahoe update
appears to have fixed the (OpenGL) issue in Xquartz that broke
Coot 0.9
versions for mac.
*Matthew Snee, PhD*
Post-doctoral Research Associate
The Baldock Lab | Michael Smith Building C3.214 | Wellcome Trust
Centre
for Cell-Matrix Research |Division of Cell Matrix Biology &
Regenerative
Medicine| School of Biological Sciences| Faculty of Biology, Medicine
and Health, University of Manchester, Oxford Road, Manchester M13 9PT
Lab Tel: +44 (0)161 306 2869
cell-matrix-research
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------------------------------
Date: Sun, 23 Aug 2026 10:12:25 +0200
From: Oliver H. Weiergräber
<[email protected]>
Subject: Re: Quartz/Coot 0.9.8.96
Hi Engin,
Sorry, I had missed Matthew's attachment -- so we are all seeing the
same things.
For those still relying on Coot 0.9, the Bandicoot project may be the
way to go:https://github.com/fraser-lab/bandicoot
Best,
Oliver
On 23.08.26 09:49, Engin Özkan wrote:
Hi Oliver,
Yes, that's the thin row of corrupted space at the top, similar to the
picture Matthew had attached. But you can load maps and coordinates, and
everything works in my hands.
The loss of the bottom row is the only lost functionality I can see (I
had missed it). That is significant, indeed. Though you can make up for
that by running coot from a terminal and looking at the output there, I
believe. It beats immediate crashing, as has been the case lately.
Coot 0.9 will not likely see any updates, so this is a temporary
solution until we all manage to move to Coot 1.
Engin
On 8/23/26 2:07 AM, Oliver H. Weiergräber wrote:
Hello Engin and Matthew,
Using Coot 0.9.8.96 (ccp4) on a Macbook Air M2 (running latest OS and
XQuartz, as mentioned above), this is what I am getting (see attached
screenshot).
As you can see, the bottom row (for display of status information) is
mostly drawn black, and there is an additional horizontal area on top
which should not be there. Btw, the icons displayed there are actually
copies of the main toolbar on the right, and their number may change
when resizing the window. Clearly a case of graphics corruption.
Of course I tried deleting the .coot-preferences directory as well as
local state files, without effect.
Best,
Oliver
On 22.08.26 21:12, Engin Özkan wrote:
For extra data on this, everything I could test was fine with an M1
MacBook Pro and Xquartz 2.8.6 (stable) on Tahoe 26.6.2. All pop-up
windows I tried worked as intended. This is with 0.9.8.96 (installed
via ccp4, version 9.0.017).
The only issue I have is a thin row of corrupted space (same
thickness as the menu bar) under the menu bar, or sequence viewer
when turned on, but it does not affect usability much. An upgrade to
2.8.7beta3 does not fix this issue, so I would not suggest it yet.
Engin
On 8/22/26 12:41 PM, Matthew Snee wrote:
Hi Oliver
I have tested two macs now using xquartz 2.8.6 and coot 0.9.8.93 EL
and both an M4 MAX studio and an M2 MacBook Air with the latest Tahoe.
I tested looking at maps and some refinement features etc..
Obviously I cant test everything but dialogue boxes and stuff are
all working fine for me.
I'm not recommending anyone assumes it will work with their
hardware, but I thought everyone was in the same boat as me where
it wouldn't even launch?
Best wishes
Matthew.
Sent from Outlook for iOS<https://aka.ms/o0ukef>
------------------------------------------------------------------------
*From:* Oliver H. Weiergräber<[email protected]>
*Sent:* Saturday, August 22, 2026 6:12 pm
*To:* Matthew Snee<[email protected]>;
[email protected] <[email protected]>
*Subject:* Re: [ccp4bb] Quartz/Coot 0.9.8.96
Dear Matthew,
For me, using Tahoe 26.6.2 and XQuartz 2.8.6, Coot 0.9 starts up with a
partly corrupted workspace.
Are you maybe referring to XQuartz 2.8.7beta?
Best,
Oliver
On 21.08.26 18:27, Matthew Snee wrote:
Hi All
Just to let everyone know, but the latest Xquartz or Tahoe update
appears to have fixed the (OpenGL) issue in Xquartz that broke
Coot 0.9
versions for mac.
*Matthew Snee, PhD*
Post-doctoral Research Associate
The Baldock Lab | Michael Smith Building C3.214 | Wellcome Trust
Centre
for Cell-Matrix Research |Division of Cell Matrix Biology &
Regenerative
Medicine| School of Biological Sciences| Faculty of Biology, Medicine
and Health, University of Manchester, Oxford Road, Manchester M13 9PT
Lab Tel: +44 (0)161 306 2869
cell-matrix-research
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End of CCP4BB Digest - 22 Aug 2026 to 23 Aug 2026 (#2026-203)
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