Timeline



Dec 4, 2024:

10:35 PM Ticket #16421 (FoldSeek: Permission denied writing temp file) created by 23036745r@…
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5:58 PM Ticket #16420 (Combine: Cannot set polymeric chain ID directly from Residue) created by chimerax-bug-report@…
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4:58 PM Ticket #16419 (Crash running save dialog) created by chimerax-bug-report@…
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4:46 PM Ticket #16418 (Crash opening mmCIF) created by chimerax-bug-report@…
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3:37 PM Ticket #16417 (Crash opening mmCIF) created by chimerax-bug-report@…
[…]
3:19 PM Ticket #16416 (Crash opening mmCIF) created by chimerax-bug-report@…
[…]
11:42 AM Ticket #16408 (Clipper: ArrayMemoryError creating NXmapHandler) closed by Tom Goddard
limitation: I suspect this memory error is not caused by ISOLDE. There is a …
11:39 AM Ticket #16405 (MemoryError saving map in session) closed by Tom Goddard
limitation: The user ran out of memory. It happened to be while saving a session …
11:05 AM Ticket #16415 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
10:58 AM Ticket #16414 (ISOLDE install failed in Mac ChimeraX 1.8 due to Clipper version) created by goddard@…
[…]
10:02 AM Ticket #16412 (H-bonds: acc_phi_psi() number of arguments) closed by Eric Pettersen
not a bug: Bad connectivity
10:01 AM Ticket #16411 (MemoryError opening mmCIF file) closed by Eric Pettersen
duplicate
9:59 AM Ticket #16410 (Non-ASCII character in PDB file) closed by Eric Pettersen
can't reproduce: Looking at the log, it seems there's a pretty fair chance the user …
9:51 AM Ticket #16407 (Crash handling text input in save dialog) closed by Eric Pettersen
can't reproduce
9:50 AM Ticket #16406 ('ObjectLabels' object has no attribute '_structure_change_handler') closed by Eric Pettersen
fixed: The changes to handle pseudobond-deletion-while-unopened moved the …
8:54 AM Ticket #16413 (Crash checking for changes during "lighting soft") created by fengzr1028@…
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8:22 AM Ticket #16412 (H-bonds: acc_phi_psi() number of arguments) created by chimerax-bug-report@…
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7:53 AM Ticket #16411 (MemoryError opening mmCIF file) created by chimerax-bug-report@…
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7:09 AM Ticket #16410 (Non-ASCII character in PDB file) created by chimerax-bug-report@…
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5:57 AM Ticket #16409 (Failure importing clipper_python) created by chimerax-bug-report@…
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4:08 AM Ticket #16408 (Clipper: ArrayMemoryError creating NXmapHandler) created by chimerax-bug-report@…
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2:19 AM Ticket #16407 (Crash handling text input in save dialog) created by chimerax-bug-report@…
[…]

Dec 3, 2024:

7:53 PM Ticket #16406 ('ObjectLabels' object has no attribute '_structure_change_handler') created by chimerax-bug-report@…
[…]
7:31 PM Ticket #16405 (MemoryError saving map in session) created by chimerax-bug-report@…
[…]
2:55 PM Ticket #16403 (Graphics crash, macOS 14.7.1, AMD Radeon Pro 5500M) closed by Tom Goddard
nonchimerax: Apple AMD graphics driver crash.
2:53 PM Ticket #16404 (Make bug reporter give advice for common crashes) closed by Tom Goddard
fixed
2:50 PM Ticket #16404 (Make bug reporter give advice for common crashes) created by Tom Goddard
Would like to have Bug Reporter detect common crashes that we cannot …
1:05 PM Dev2024-12-9 created by Tom Goddard
1:04 PM 2024-12-5 created by Tom Goddard
1:02 PM DeveloperMeetings edited by Tom Goddard
(diff)
10:52 AM Ticket #16398 (Graphics crash, macOS 14.7.1, AMD Radeon Pro 5500M, starting ISOLDE ...) closed by Tom Goddard
nonchimerax
10:21 AM Ticket #16374 (KVFinder "nearby" value not valid) closed by Eric Pettersen
fixed: Hi Thibault, This is fixed in the daily build now. Since the fix …
8:42 AM Ticket #16401 (Add Charge failure) closed by Eric Pettersen
limitation
8:39 AM Ticket #16399 (Crash in graphics driver during Qt drawing) closed by Eric Pettersen
can't reproduce: Crashed in 1.6.1; Reported in 1.8
7:56 AM Ticket #16403 (Graphics crash, macOS 14.7.1, AMD Radeon Pro 5500M) created by chimerax-bug-report@…
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7:55 AM Ticket #16402 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by chimerax-bug-report@…
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7:31 AM Ticket #16401 (Add Charge failure) created by chimerax-bug-report@…
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12:27 AM Ticket #16400 (Save trajectory in session: bytes object is too large) created by rsramirezorozc@…
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12:03 AM Ticket #16399 (Crash in graphics driver during Qt drawing) created by chimerax-bug-report@…
[…]

Dec 2, 2024:

8:41 PM Ticket #16398 (Graphics crash, macOS 14.7.1, AMD Radeon Pro 5500M, starting ISOLDE ...) created by chimerax-bug-report@…
[…]
5:17 PM Ticket #16385 (Attempt to save 3D label for dead pseudobond in session) closed by Eric Pettersen
fixed: Morph was deleting atoms (and therefore pseudobonds connected to them, …
4:00 PM Dev2024-12-2 edited by Tom Goddard
(diff)
12:36 PM Ticket #16396 (glClear: invalid framebuffer operation) closed by Tom Goddard
can't reproduce: Error in glClear() trying to draw the status line after an expose …
12:32 PM Ticket #16394 (Invalid texture upload) closed by Tom Goddard
nonchimerax: Appears to be an opengl driver error in glBufferData() creating a …
12:27 PM Ticket #16393 (Attempt to retrieve context when no valid context) closed by Tom Goddard
nonchimerax: ChimeraX failed to start because of OpenGL problems. The Qt window …
12:23 PM Ticket #16392 (vop gaussian: ArrayMemoryError) closed by Tom Goddard
limitation: User trying to smooth a 150 Gbyte map file.
12:09 PM Ticket #16397 (Crash on Mac waking from sleep) closed by Eric Pettersen
duplicate
12:07 PM Ticket #16395 (Find H-bonds: More than 2 coplanar positions specified) closed by Eric Pettersen
not a bug: Hi Jitendra, This error typically occurs because there are …
11:47 AM Ticket #16391 (Crash on Mac waking from sleep) closed by Eric Pettersen
duplicate
11:46 AM Ticket #16390 (Find Cavities crash) closed by Eric Pettersen
duplicate: Hi Adiana, As per ticket #16387, if you could provide any examples …
11:40 AM Ticket #16389 (Crash on Mac waking from sleep) closed by Eric Pettersen
duplicate
11:38 AM Ticket #16388 (Viewing Gromacs output) closed by Eric Pettersen
not a bug
6:48 AM Ticket #16397 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
6:11 AM Ticket #16396 (glClear: invalid framebuffer operation) created by chimerax-bug-report@…
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6:05 AM Ticket #16395 (Find H-bonds: More than 2 coplanar positions specified) created by jitued@…
[…]

Dec 1, 2024:

11:10 PM Ticket #16394 (Invalid texture upload) created by chimerax-bug-report@…
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7:57 AM Ticket #16393 (Attempt to retrieve context when no valid context) created by ae4781@…
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1:41 AM Ticket #16392 (vop gaussian: ArrayMemoryError) created by chimerax-bug-report@…
[…]

Nov 29, 2024:

10:40 AM Ticket #16391 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
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2:52 AM Ticket #16390 (Find Cavities crash) created by a.gargano@…
[…]

Nov 28, 2024:

7:41 AM Ticket #16389 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
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6:44 AM Ticket #16388 (Viewing Gromacs output) created by jhmvangils@…
[…] 1ao7.pdb​
6:12 AM Ticket #16387 (Find Cavities crash) created by a.gargano@…
[…]
4:17 AM Ticket #16386 (Coulombic: 'Atom' object has no attribute 'charge') created by vmruano@…
[…]

Nov 27, 2024:

7:02 PM Ticket #16384 (Graphics crash, macOS 11.7, Intel HD Graphics 6000) closed by Tom Goddard
nonchimerax: Apple Intel graphics driver crash.
2:53 PM Ticket #16383 (Crash showing sequence viewer) closed by Eric Pettersen
limitation: If the "AL123456.3.fasta" file in this report is the same as the one …
2:11 PM Ticket #16385 (Attempt to save 3D label for dead pseudobond in session) created by martzeric@…
[…]
2:08 PM Ticket #16382 (Crash as MatchMaker tool closes) closed by Eric Pettersen
can't reproduce
12:41 PM Ticket #16384 (Graphics crash, macOS 11.7, Intel HD Graphics 6000) created by chimerax-bug-report@…
[…]
12:18 PM Ticket #16377 (Save map fits: m.filename is None) closed by Tom Goddard
fixed: Fixed in 1.9 and 1.10. User used "fit search" to fit an atomic model …
11:46 AM Ticket #16379 (Crash showing tool window) closed by Eric Pettersen
can't reproduce: Hi Dewight, Thanks for reporting this problem. I would recommend …
11:41 AM Ticket #16378 (Save map fits: m.filename is None) closed by Eric Pettersen
duplicate
10:26 AM Ticket #16383 (Crash showing sequence viewer) created by chimerax-bug-report@…
[…]
1:19 AM Ticket #16382 (Crash as MatchMaker tool closes) created by chimerax-bug-report@…
[…]

Nov 26, 2024:

4:24 PM Ticket #16221 (Read CHAI-1 PAE .npy files) closed by Tom Goddard
fixed: Done in ChimeraX 1.9 and 1.10. I made the AlphaFold Error Plot tool …
3:55 PM Ticket #16381 (Recognize AlphaFold 3 PAE json file name automatically) closed by Tom Goddard
fixed: Fixed in 1.9 and 1.10. AlphaFold 3 local run produces model and PAE …
3:50 PM Ticket #16381 (Recognize AlphaFold 3 PAE json file name automatically) created by goddard@…
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3:29 PM Ticket #16380 (Make crosseye and walleye camera start with good initial geometry) closed by Tom Goddard
fixed: Done in ChimeraX 1.10 daily builds, not in 1.9. The cross-eye …
3:23 PM Ticket #16380 (Make crosseye and walleye camera start with good initial geometry) created by Tom Goddard
I tried helping Bob Stroud make a cross-eye stereo pair image …
2:17 PM Ticket #16379 (Crash showing tool window) created by dewight.wiiliams@…
[…]
12:31 PM Ticket #16372 (Problematic Fragment shader source code) closed by Tom Goddard
nonchimerax: The error is complaining about Qt a window toolkit OpenGL shader …
12:27 PM Ticket #16378 (Save map fits: m.filename is None) created by chimerax-bug-report@…
[…]
12:26 PM Ticket #16377 (Save map fits: m.filename is None) created by chimerax-bug-report@…
[…]
12:26 PM Dev2024-12-2 created by Tom Goddard
12:24 PM DeveloperMeetings edited by Tom Goddard
(diff)
11:39 AM Ticket #16376 (Crash in garbage collection) closed by Eric Pettersen
duplicate
11:37 AM Ticket #16376 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
9:29 AM Ticket #16373 (Crash in Sequence::rname3to1 drawing ribbons after restoring session) closed by Eric Pettersen
can't reproduce
4:16 AM Ticket #16375 ('Segmentation' object has no attribute 'data') created by chimerax-bug-report@…
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2:27 AM Ticket #16374 (KVFinder "nearby" value not valid) created by thibault.tubiana@…
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2:19 AM Ticket #16373 (Crash in Sequence::rname3to1 drawing ribbons after restoring session) created by chimerax-bug-report@…
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12:07 AM Ticket #16372 (Problematic Fragment shader source code) created by devbrat.phd@…
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Nov 25, 2024:

7:01 PM Dev2024-11-25 edited by Tom Goddard
(diff)
2:43 PM Ticket #16368 (Save movie: ArrayMemoryError) closed by Tom Goddard
can't reproduce: Could not allocate 34 Mbytes for a framebuffer image (3000 x 3000 x 4) …
2:29 PM Ticket #16367 (Save surface in session: ArrayMemoryError) closed by Tom Goddard
duplicate: Duplicate of #16365
2:27 PM Ticket #16365 (volume splitbyzone: ArrayMemoryError) closed by Tom Goddard
limitation: Out of memory with volume split by zone on Windows 10 with only 8 GB …
2:26 PM Ticket #16361 (Crash in find_close_points_boxes recursion) closed by Tom Goddard
limitation: find_close_points() crashed due to an infinite recursion and stack …
2:05 PM Ticket #16371 (BLAST needs to deal with missing AlphaFold v1-3) created by Zach Pearson
11:32 AM Ticket #16370 (Qt fatal error: Failed to initialize graphics backend for OpenGL) closed by Eric Pettersen
can't reproduce
11:31 AM Ticket #16369 (Crash in Metal driver drawing Qt widget) closed by Eric Pettersen
can't reproduce
11:15 AM Ticket #16364 (Crash in open/save dialog on Windows) closed by Eric Pettersen
can't reproduce
11:14 AM Ticket #16363 ('MarkedHistogram' object has no attribute '_min_val') closed by Eric Pettersen
duplicate
11:10 AM Ticket #16362 (Error setting cavity color) closed by Eric Pettersen
fixed: This is fixed, but the fix is in the upcoming changes to Find …
7:36 AM Ticket #16370 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by chimerax-bug-report@…
[…]

Nov 24, 2024:

8:23 PM Ticket #16369 (Crash in Metal driver drawing Qt widget) created by chimerax-bug-report@…
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4:27 PM Ticket #16368 (Save movie: ArrayMemoryError) created by chimerax-bug-report@…
[…]
1:50 AM Ticket #16367 (Save surface in session: ArrayMemoryError) created by chimerax-bug-report@…
[…]

Nov 23, 2024:

2:11 AM Ticket #16366 (segmentations mouse mode: list index out of range) created by chimerax-bug-report@…
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Nov 22, 2024:

10:56 PM Ticket #16365 (volume splitbyzone: ArrayMemoryError) created by chimerax-bug-report@…
[…]
10:20 PM Ticket #16364 (Crash in open/save dialog on Windows) created by chimerax-bug-report@…
[…]
8:31 PM Ticket #16363 ('MarkedHistogram' object has no attribute '_min_val') created by chimerax-bug-report@…
[…]
6:51 PM Ticket #16362 (Error setting cavity color) created by Elaine Meng
[…]
6:08 PM Ticket #16361 (Crash in find_close_points_boxes recursion) created by chimerax-bug-report@…
[…]
2:09 PM Ticket #16359 (Crash on Mac waking from sleep) closed by Tom Goddard
duplicate: ChimeraX crashed in the Qt window toolkit. This is a bug in Qt which …
2:03 PM Ticket #16352 (vop add: ArrayMemoryError) closed by Tom Goddard
limitation: Out of memory allocating a volume from volume add command. Working …
1:47 PM Ticket #16348 (Graphics crash, macOS 13.2.1, Intel Iris Plus Graphics) closed by Tom Goddard
nonchimerax: Apple Intel graphics driver crash.
10:59 AM NIAID2024 edited by Tom Goddard
(diff)
10:51 AM NIAID2024 edited by Tom Goddard
(diff)
10:50 AM NIAID2024 edited by Tom Goddard
(diff)
10:49 AM NIAID2024 edited by Tom Goddard
(diff)
10:48 AM NIAID2024 edited by Tom Goddard
(diff)
10:22 AM Ticket #16360 (Crash in garbage collection) closed by Eric Pettersen
duplicate
10:14 AM Ticket #16360 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
8:48 AM Ticket #16358 (ui view fourup: ZeroDivisionError) closed by Eric Pettersen
duplicate
8:45 AM Ticket #16356 (Crash drawing widget) closed by Eric Pettersen
can't reproduce: Hi Nicolas, The version of ChimeraX you are using (0.91) is five …
4:24 AM Ticket #16359 (Crash on Mac waking from sleep) created by helen.duyvesteyn@…
[…]
1:56 AM Ticket #16358 (ui view fourup: ZeroDivisionError) created by chimerax-bug-report@…
[…]
1:56 AM Ticket #16357 (ui view fourup: ZeroDivisionError) created by chimerax-bug-report@…
[…]
1:53 AM Ticket #16356 (Crash drawing widget) created by nicolas.biteau@…
[…]

Nov 21, 2024:

4:35 PM Ticket #16354 (Cannot save preferences file: No space left on device) closed by Eric Pettersen
nonchimerax
4:32 PM Ticket #16353 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by Eric Pettersen
duplicate: Hi Muralikrishna, Thanks for reporting this problem. It is fixed in …
4:27 PM Ticket #16351 (Color byattr: min() arg is an empty sequence) closed by Eric Pettersen
can't reproduce
4:26 PM Ticket #16350 (Crash running open-file dialog) closed by Eric Pettersen
can't reproduce
4:21 PM Ticket #16347 (Crash on Mac waking from sleep) closed by Eric Pettersen
duplicate
3:44 PM Ticket #16346 (Bug with the user-defined selector) closed by Eric Pettersen
can't reproduce: Hi Suli-Anne, Thanks for reporting this problem. Since "name frozen" …
1:33 PM 2024-11-21 edited by Tom Goddard
(diff)
12:41 PM Ticket #16355 (help matchmaker: 'NoneType' object has no attribute 'split') created by chimerax-bug-report@…
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11:57 AM Ticket #16354 (Cannot save preferences file: No space left on device) created by chimerax-bug-report@…
[…]
8:45 AM Ticket #16353 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by muralikrishna.lella@…
[…]
5:37 AM Ticket #16352 (vop add: ArrayMemoryError) created by chimerax-bug-report@…
[…]
1:02 AM Ticket #16351 (Color byattr: min() arg is an empty sequence) created by chimerax-bug-report@…
[…]
12:07 AM Ticket #16350 (Crash running open-file dialog) created by chimerax-bug-report@…
[…]

Nov 20, 2024:

10:16 PM 2024-11-21 edited by Tom Goddard
(diff)
10:15 PM 2024-11-21 edited by Tom Goddard
(diff)
5:05 PM Ticket #16061 (Support chains in "color byattribute") closed by Eric Pettersen
fixed: Implemented chain attributes in the "color byattribute" command. The …
3:54 PM Ticket #16349 (Session save: Unable to restore objects of IHMModel class in ...) created by ccaffalett@…
[…]
1:43 PM Ticket #16348 (Graphics crash, macOS 13.2.1, Intel Iris Plus Graphics) created by chimerax-bug-report@…
[…]
1:19 PM Ticket #16347 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
12:27 PM Ticket #16346 (Bug with the user-defined selector) created by Suli-Anne.Laurin@…
[…]
11:40 AM Ticket #16333 (Render by Attribute: cannot create weak reference to 'NoneType' object) closed by Eric Pettersen
fixed: Fix: …
11:39 AM ChangeLog edited by Elaine Meng
(diff)
10:25 AM Ticket #16344 (Segger: bounding_grid() missing 1 required positional argument: 'cube') closed by Tom Goddard
duplicate: Fixed months ago. This bug was only in a few daily builds.
9:58 AM Ticket #16345 (Segger: bounding_grid() missing 1 required positional argument: 'cube') closed by Eric Pettersen
duplicate
9:52 AM Ticket #16342 (Crash moving window between screens) closed by Eric Pettersen
can't reproduce
9:49 AM Ticket #16341 (Crash on exit) closed by Eric Pettersen
can't reproduce
8:31 AM Ticket #16345 (Segger: bounding_grid() missing 1 required positional argument: 'cube') created by chimerax-bug-report@…
[…]
8:30 AM Ticket #16344 (Segger: bounding_grid() missing 1 required positional argument: 'cube') created by chimerax-bug-report@…
[…]
7:41 AM Ticket #16343 (SEQCROW: 'Session' object has no attribute 'log') created by chimerax-bug-report@…
[…]
4:37 AM Ticket #16342 (Crash moving window between screens) created by chimerax-bug-report@…
[…]
3:32 AM Ticket #16341 (Crash on exit) created by chimerax-bug-report@…
[…]

Nov 19, 2024:

6:44 PM Ticket #16339 (Crash on Mac waking from sleep) closed by Tom Goddard
duplicate: ChimeraX crashed due to a bug in the Qt window toolkit. It seems to …
5:36 PM Ticket #16338 (Crash on Mac waking from sleep) closed by Eric Pettersen
duplicate
5:34 PM Ticket #16337 (Crash on Mac waking from sleep) closed by Eric Pettersen
duplicate
5:33 PM Ticket #16336 (Crash closing models) closed by Eric Pettersen
can't reproduce: Some were combinations, but that's not enough to go on.
4:52 PM Dev2024-11-25 edited by Eric Pettersen
(diff)
1:56 PM Ticket #16340 (ISOLDER: Scipy symbol not found while registering command) created by jean-marc.jeckelmann@…
[…]
1:55 PM Ticket #16339 (Crash on Mac waking from sleep) created by ccaffalett@…
[…]
1:37 PM Ticket #16338 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
12:03 PM Ticket #16337 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
11:55 AM Dev2024-11-25 edited by Tom Goddard
(diff)
11:54 AM Dev2024-11-25 created by Tom Goddard
11:53 AM 2024-11-21 created by Tom Goddard
11:37 AM Ticket #16336 (Crash closing models) created by chimerax-bug-report@…
[…]
11:36 AM DeveloperMeetings edited by Tom Goddard
(diff)
11:25 AM Ticket #16335 (Segmentations: KeyError deleting VolumeImage) created by chimerax-bug-report@…
[…]
11:25 AM Ticket #16334 (DICOM: index is out of bounds) created by chimerax-bug-report@…
[…]
10:59 AM Ticket #16331 (Crash on Mac waking from sleep) closed by Eric Pettersen
duplicate
10:58 AM Ticket #16327 (Session tries to add same model twice) closed by Tom Goddard
can't reproduce: They are using Segger and opened some .seg segmentations from Segger. …
10:58 AM Ticket #16330 (ArtiaX: superqt slider: float division by zero) closed by Eric Pettersen
duplicate
10:49 AM Ticket #16328 (Crash on Mac waking from sleep) closed by Eric Pettersen
duplicate
10:45 AM Ticket #16326 (Crash running open/save dialog) closed by Eric Pettersen
can't reproduce
10:37 AM Ticket #16332 (Covalent vs. coordination bonds) closed by Eric Pettersen
fixed: In the 1.8 build they are covalent, but in the daily build from 10/29 …
10:12 AM Ticket #16333 (Render by Attribute: cannot create weak reference to 'NoneType' object) created by chimerax-bug-report@…
[…]
9:48 AM Ticket #16332 (Covalent vs. coordination bonds) created by Eric Pettersen
The heme iron bonds in mmCIF 6fqf are covalent when they should be …
3:35 AM Ticket #16331 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
2:45 AM Ticket #16330 (ArtiaX: superqt slider: float division by zero) created by chimerax-bug-report@…
[…]
1:33 AM Ticket #16329 (ArtiaX: superqt slider: float division by zero) created by chimerax-bug-report@…
[…]

Nov 18, 2024:

8:47 PM Ticket #16328 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
5:03 PM Ticket #16327 (Session tries to add same model twice) created by chimerax-bug-report@…
[…]
4:30 PM Dev2024-11-18 edited by Tom Goddard
(diff)