Timeline



Jun 24, 2025:

2:20 PM Ticket #18069 (Crash in _get_polymer_spline) created by chimerax-bug-report@…
[…]
2:14 PM Ticket #18068 (Crash in glBufferSubData) created by chimerax-bug-report@…
[…]
2:07 PM Ticket #18059 (Remove volume smoothLines option since it is no longer supported by OpenGL) closed by Tom Goddard
fixed: Thanks!
10:53 AM Ticket #18067 (Toolshed hang) created by chimerax-bug-report@…
[…]
10:33 AM Ticket #18064 (Read .gro: 'Session' object has no attribute 'name') closed by pett
can't reproduce: I see no way for the 'element' variable to be anything but an Element, …
10:18 AM Ticket #18035 (PAE matrix mismatch) closed by Tom Goddard
fixed: Fixed in daily build, not in 1.10. I made the PAE code guess if the …
9:26 AM Ticket #18066 (Crash in garbage collection) closed by pett
duplicate
9:25 AM Ticket #18065 (Crash in garbage collection) closed by pett
duplicate
9:22 AM Ticket #18063 (Crash in event loop) closed by pett
can't reproduce: Seems basically the same as #17852
7:16 AM Ticket #18066 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
6:14 AM Ticket #18065 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
1:03 AM Ticket #18064 (Read .gro: 'Session' object has no attribute 'name') created by chimerax-bug-report@…
[…]

Jun 23, 2025:

11:26 PM Ticket #18063 (Crash in event loop) created by chimerax-bug-report@…
[…]
2:28 PM Ticket #18062 (Save dialog mmCIF option defaults differ from saving PDB.) created by goddard@…
[…]
12:36 PM Ticket #18061 (Allow ChimeraX to run Boltz-2 predictions on user's computer) created by Tom Goddard
Boltz 2 released on June 6, 2025 and includes new features over Boltz …
12:20 PM Ticket #18052 ('name' not in Surface session-restore data) closed by Tom Goddard
can't reproduce: User has a session 2-2.cxs that refers to an MRC file that has bad …
12:05 PM Ticket #18058 (H-Bonds: acc_phi_psi() bad number of arguments) closed by pett
can't reproduce: Works for standard 5oph entry
12:01 PM Ticket #18060 (Trajectory h-bonds problems) created by pett
[…]
11:53 AM Ticket #18057 (Crash on Mac waking from sleep) closed by pett
duplicate
11:52 AM Ticket #18056 (Crash on Mac waking from sleep) closed by pett
duplicate
11:49 AM Ticket #18053 (MemoryError opening mmCIF files) closed by pett
duplicate: Hi Filip, Thanks for reporting this problem. It has been fixed in …
11:46 AM Ticket #18051 (Unknown crash) closed by pett
can't reproduce
11:44 AM Ticket #18049 (Graphics hardware encountered an error and was reset) closed by Tom Goddard
limitation: This ChimeraX crash is caused by unstable Intel Mac graphics drivers. …
11:44 AM Ticket #18050 ('pip install pyKVFinder' fails with empty error message) closed by pett
duplicate: Duplicate of #17229
11:41 AM Ticket #18045 (Problem reading .cmm file) closed by Tom Goddard
limitation: This error is from opening a ChimeraX .cmm file that is empty. An …
11:38 AM Ticket #18043 (Crash in drawing after 'view matrix') closed by Tom Goddard
can't reproduce: There is no indication in this Linux ChimeraX crash report of what …
11:30 AM Ticket #18046 (Crash on Mac waking from sleep) closed by pett
duplicate
11:27 AM Ticket #18059 (Remove volume smoothLines option since it is no longer supported by OpenGL) created by Tom Goddard
The volume command has a smoothLines option that is not implemented …
11:26 AM Ticket #18044 (KVFinder: some how cavity model is closed but still in table) closed by pett
can't reproduce
10:06 AM Ticket #18058 (H-Bonds: acc_phi_psi() bad number of arguments) created by chimerax-bug-report@…
[…]
9:43 AM Ticket #18057 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
7:09 AM Ticket #18056 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
6:54 AM Ticket #18055 (Add full-screen SBS stereo for Samsung Odyssey 3D display) created by Tom Goddard
Add a separate full-screen side-by-side stereo window that is separate …
6:46 AM Ticket #18054 (ChimeraX mailing list archives have many blank messages) created by Tom Goddard
The ChimeraX mailing list archive web pages often include blank …
4:31 AM Ticket #18053 (MemoryError opening mmCIF files) created by filip_ilievski94@…
[…]
4:25 AM Ticket #18052 ('name' not in Surface session-restore data) created by chimerax-bug-report@…
[…]
1:46 AM Ticket #18051 (Unknown crash) created by chimerax-bug-report@…
[…]

Jun 22, 2025:

6:33 PM Ticket #18050 ('pip install pyKVFinder' fails with empty error message) created by chimerax-bug-report@…
[…]
6:04 AM Ticket #18049 (Graphics hardware encountered an error and was reset) created by noha.elhuseiny@…
[…]
5:47 AM Ticket #18048 (isolde sim start: OpenMMException: Error compiling kernel) created by 513367167@…
[…]
2:48 AM Ticket #18047 (SEQCROW: problem reading sqmout file) created by chimerax-bug-report@…
[…]

Jun 21, 2025:

8:49 PM Ticket #18046 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
5:07 PM Ticket #18045 (Problem reading .cmm file) created by horvath.peter.3@…
[…]
10:29 AM Ticket #18044 (KVFinder: some how cavity model is closed but still in table) created by chimerax-bug-report@…
[…]
7:09 AM Ticket #18037 (What happened to the windows version?) closed by pett
fixed
4:37 AM Ticket #18043 (Crash in drawing after 'view matrix') created by kananya@…
[…]

Jun 20, 2025:

6:12 PM ChangeLog edited by pett
(diff)
3:41 PM Ticket #18029 (Crash on Mac waking from sleep) closed by Tom Goddard
duplicate: The ChimeraX bug report panel that you used to submit this bug …
2:12 PM Ticket #18042 (isolde sim start: crash running on Linux) created by chimerax-bug-report@…
[…]
1:59 PM Ticket #18036 (MatchMaker: 'CategorizedOptionsPanel' object has no attribute ...) closed by pett
fixed: Fix: …
10:49 AM Ticket #18038 (Modeller: 'Sequence' object has no attribute 'match_maps') closed by pett
fixed: Fix: …
10:37 AM Ticket #18040 (Crash closing color key) closed by pett
duplicate: Hi Jean, Thanks for reporting this problem. It was fixed just after …
10:30 AM Ticket #18041 (Boltz installation failure) created by Elaine Meng
[…]
10:26 AM Ticket #18039 (Crash in event loop) closed by pett
can't reproduce
10:05 AM Ticket #18027 (Various problems creating/saving animations) closed by Zach Pearson
nonchimerax: This appears to be a Qt issue on some Linux systems. See …
9:55 AM Ticket #18034 (Crash showing volume dialog) closed by pett
can't reproduce: pre-1.7
9:52 AM Ticket #18033 (Crash using menu) closed by pett
can't reproduce
9:50 AM Ticket #18032 (Crash opening mmCIF) closed by pett
duplicate: 1.2.5
9:49 AM Ticket #18031 (Crash opening mmCIF) closed by pett
duplicate: 1.2.5
9:45 AM Ticket #18030 (Crash on Mac waking from sleep) closed by pett
duplicate
9:40 AM Ticket #18028 (Crash on Mac waking from sleep) closed by pett
duplicate
8:48 AM Ticket #18040 (Crash closing color key) created by jean.millet@…
[…]

Jun 19, 2025:

10:18 PM Ticket #18039 (Crash in event loop) created by chimerax-bug-report@…
[…]
10:07 PM Ticket #18038 (Modeller: 'Sequence' object has no attribute 'match_maps') created by chimerax-bug-report@…
[…]
12:08 PM Ticket #18021 (Graphics hardware encountered an error and was reset) closed by Tom Goddard
nonchimerax: This ChimeraX crash is a known problem with Apple's Intel graphics …
8:31 AM Ticket #18037 (What happened to the windows version?) created by nuhaalabbass@…
[…]
6:59 AM Ticket #18036 (MatchMaker: 'CategorizedOptionsPanel' object has no attribute ...) created by chimerax-bug-report@…
[…]
4:55 AM Ticket #18035 (PAE matrix mismatch) created by Tristan Croll
[…]

Jun 18, 2025:

11:52 PM Ticket #18034 (Crash showing volume dialog) created by chimerax-bug-report@…
[…]
9:17 PM Ticket #18033 (Crash using menu) created by chimerax-bug-report@…
[…]
8:06 PM Ticket #18032 (Crash opening mmCIF) created by chimerax-bug-report@…
[…]
8:00 PM Ticket #18031 (Crash opening mmCIF) created by chimerax-bug-report@…
[…]
7:28 PM Ticket #18030 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
7:10 PM Ticket #18029 (Crash on Mac waking from sleep) created by rslack@…
[…]
6:17 PM Ticket #18028 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
3:48 PM Ticket #18027 (Various problems creating/saving animations) created by mayerefaruk@…
[…]
2:08 PM Ticket #18017 (Non-chain-forming bond merges chains) closed by pett
fixed: Fixed in the next daily build. Not putting the fix into the …
12:02 PM Ticket #18026 (Crash in swap_buffers) closed by pett
limitation: Remote display
12:01 PM Ticket #18025 (Session restore: alignment sequences not same as original) closed by pett
can't reproduce
11:56 AM Ticket #18024 (Crash using open/save dialog) closed by pett
can't reproduce: Last stack involved molobject.py
11:55 AM Ticket #18023 (Crash on Mac waking from sleep) closed by pett
duplicate
11:37 AM Ticket #18019 (Crash on Mac waking from sleep) closed by pett
duplicate
7:30 AM Ticket #18026 (Crash in swap_buffers) created by chimerax-bug-report@…
[…]
7:12 AM Ticket #18025 (Session restore: alignment sequences not same as original) created by chimerax-bug-report@…
[…]
7:08 AM Ticket #18024 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
6:36 AM Ticket #18023 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
4:42 AM Ticket #18022 (QScore: model is None) created by chimerax-bug-report@…
[…]
1:42 AM Ticket #18021 (Graphics hardware encountered an error and was reset) created by nomin.bp@…
[…]

Jun 17, 2025:

9:03 PM Ticket #18020 (PICKLUSTER: list index out of range) created by chimerax-bug-report@…
[…]
7:51 PM Ticket #18019 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
5:27 PM Ticket #18018 (Ambiguous prefix chooses arbitrary command) created by psauer@…
[…]
4:09 PM Ticket #18017 (Non-chain-forming bond merges chains) created by psauer@…
[…] noIDB_MYC_model_refined_060_altconf-coot.cif
4:08 PM Ticket #18016 (crossfade: images do not match) created by jgrime@…
[…] Screenshot 2025-06-17 at 6.07.52 PM.png
2:30 PM Ticket #17853 (Remember render by attribute thresholds when multiple models chosen) closed by pett
fixed: Now fixed AFAICT. Fix available in next daily build. Fix: …
10:39 AM Ticket #18015 (Qt fatal error: Failed to initialize graphics backend for OpenGL) closed by pett
limitation: Remote display
10:38 AM Ticket #18014 (Crash at exit in Qt cleanup routines) closed by pett
duplicate
10:37 AM Ticket #18013 (Crash in garbage collection) closed by pett
duplicate
10:36 AM Ticket #18012 (Crash in event loop) closed by pett
can't reproduce
10:34 AM Ticket #18011 (Crash on Mac waking from sleep) closed by pett
duplicate
10:28 AM Ticket #18015 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by chimerax-bug-report@…
[…]
9:51 AM Ticket #18008 (Crash on Mac waking from sleep) closed by pett
duplicate
9:51 AM Ticket #18007 (Crash on Mac waking from sleep) closed by pett
duplicate
9:49 AM Ticket #18006 (Web services down) closed by pett
duplicate: Report from yesterday before the web services were restored
7:11 AM Ticket #18014 (Crash at exit in Qt cleanup routines) created by chimerax-bug-report@…
[…]
4:34 AM Ticket #18013 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
1:53 AM Ticket #18012 (Crash in event loop) created by chimerax-bug-report@…
[…]
1:47 AM Ticket #18011 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
12:46 AM Ticket #18010 (Crash in event loop) created by arshadkhanbaloch214@…
[…] 1.pdb

Jun 16, 2025:

7:35 PM Ticket #18009 (AllMetal3D: wrapped C/C++ object of type QLabel has been deleted) created by chimerax-bug-report@…
[…]
5:15 PM Ticket #18008 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
4:42 PM Ticket #18007 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
2:21 PM Ticket #18006 (Web services down) created by chimerax-bug-report@…
[…]
1:55 PM Ticket #17985 (AddH: type_info_for_atom KeyError) closed by pett
can't reproduce: Somehow an acceptor is not in type_info_for_atom. Would need the …
1:47 PM Ticket #18005 (Crash using color editor) created by teija.suhas@…
[…]
12:54 PM Ticket #17988 (Open output from ccp4-refmac refinement) closed by pett
not a bug
11:51 AM Ticket #18004 (Crash moving window between screens) closed by pett
duplicate
11:46 AM Ticket #18003 (Unable to open monitor interface to DISPLAY) closed by pett
can't reproduce: Mr. Google suggests this is a driver issue.
11:45 AM Ticket #18004 (Crash moving window between screens) created by chimerax-bug-report@…
[…]
11:44 AM Ticket #17986 (Crash in swap_buffers after label command) closed by Tom Goddard
nonchimerax: Probable buggy graphics driver. 2017 Intel graphics driver 20.19.15.4835.
11:42 AM Ticket #18002 ('ArrayGridData' object has no attribute 'dicom_data') closed by pett
duplicate
11:41 AM Ticket #18001 (Crash moving window between screens) closed by pett
duplicate
11:39 AM Ticket #18000 (KVFinder on old MacOS) closed by pett
limitation
11:37 AM Ticket #17999 (Graphics hardware encountered an error and was reset) closed by pett
duplicate
11:36 AM Ticket #17998 (Graphics hardware encountered an error and was reset) closed by pett
duplicate
11:33 AM Ticket #17997 ('ArrayGridData' object has no attribute 'dicom_data') closed by pett
duplicate
11:32 AM Ticket #17996 (Disk quota exceeded) closed by pett
nonchimerax
11:31 AM Ticket #17995 (Crash in event loop) closed by pett
can't reproduce: There was toolshed activity as well.
11:28 AM Ticket #17994 (Crash using open/save dialog) closed by pett
can't reproduce: Last stack has _update_graphics_if_needed
11:21 AM Ticket #18003 (Unable to open monitor interface to DISPLAY) created by chimerax-bug-report@…
[…]
11:20 AM Ticket #17993 (mshMIGPerform crash) closed by pett
can't reproduce: Very similar / same as #17777
11:12 AM Ticket #17992 (Remote display graphics failure) closed by pett
limitation
11:11 AM Ticket #17991 (Crash on Mac waking from sleep) closed by pett
duplicate
11:09 AM Ticket #17990 (Crash opening .gro file) closed by pett
can't reproduce
11:08 AM Ticket #17989 (viewer_option lambda returning None instead of option class) closed by pett
duplicate: Duplicate of #17895
11:00 AM Ticket #17987 (Crash on Mac waking from sleep) closed by pett
duplicate
10:37 AM Ticket #17982 (KVFinder on old MacOS) closed by pett
limitation: For ARM, has to be running MacOS 15 (for Intel, 14)
10:35 AM Ticket #18002 ('ArrayGridData' object has no attribute 'dicom_data') created by chimerax-bug-report@…
[…]
10:34 AM Ticket #17981 (Crash using open/save dialog) closed by pett
can't reproduce: Linux agains -- looks like the same system.
10:32 AM Ticket #17980 (Crash using open/save dialog) closed by pett
can't reproduce: On Linux this time
9:52 AM Ticket #18001 (Crash moving window between screens) created by chimerax-bug-report@…
[…]
9:22 AM Ticket #18000 (KVFinder on old MacOS) created by chimerax-bug-report@…
[…]
9:18 AM Ticket #17999 (Graphics hardware encountered an error and was reset) created by chimerax-bug-report@…
[…]
9:11 AM Ticket #17998 (Graphics hardware encountered an error and was reset) created by chimerax-bug-report@…
[…]
8:24 AM Ticket #17997 ('ArrayGridData' object has no attribute 'dicom_data') created by chimerax-bug-report@…
[…]
8:03 AM Ticket #17996 (Disk quota exceeded) created by chimerax-bug-report@…
[…]
6:58 AM Ticket #17995 (Crash in event loop) created by chimerax-bug-report@…
[…]
5:59 AM Ticket #17994 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
5:53 AM Ticket #17993 (mshMIGPerform crash) created by chimerax-bug-report@…
[…]
4:08 AM Ticket #17992 (Remote display graphics failure) created by chimerax-bug-report@…
[…]
2:30 AM Ticket #17991 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
2:27 AM Ticket #17990 (Crash opening .gro file) created by chimerax-bug-report@…
[…]

Jun 15, 2025:

7:48 PM Ticket #17989 (viewer_option lambda returning None instead of option class) created by chimerax-bug-report@…
[…]
3:58 PM Ticket #17988 (Open output from ccp4-refmac refinement) created by rkrishnan@…
[…]
9:24 AM Ticket #17987 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
3:52 AM Ticket #17986 (Crash in swap_buffers after label command) created by chimerax-bug-report@…
[…]

Jun 14, 2025:

1:50 PM Ticket #17985 (AddH: type_info_for_atom KeyError) created by chimerax-bug-report@…
[…]
4:15 AM Ticket #17984 (MemoryError saving session) created by chimerax-bug-report@…
[…]
12:05 AM Ticket #17983 (QScore: scores is None) created by chimerax-bug-report@…
[…]

Jun 13, 2025:

6:32 PM Ticket #17982 (KVFinder on old MacOS) created by chimerax-bug-report@…
[…]
3:28 PM Ticket #17877 (Crash opening mmCIF) closed by Greg Couch
can't reproduce: Unable to fix without the mmCIF file that triggers the bug. Please …
12:23 PM ChangeLog edited by Elaine Meng
(diff)
12:05 PM Ticket #17981 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
11:59 AM Ticket #17980 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
9:42 AM Ticket #17979 (alphafold contacts: Permission denied) closed by pett
nonchimerax
9:37 AM Ticket #17978 (Crash on Mac waking from sleep) closed by pett
duplicate
9:35 AM Ticket #17977 (Crash on Mac waking from sleep) closed by pett
duplicate
9:33 AM Ticket #17976 ('ArrayGridData' object has no attribute 'dicom_data') closed by pett
duplicate
7:40 AM Ticket #17979 (alphafold contacts: Permission denied) created by barnabas.williams@…
[…]
7:08 AM Ticket #17978 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
6:12 AM Ticket #17977 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
5:43 AM Ticket #17976 ('ArrayGridData' object has no attribute 'dicom_data') created by chimerax-bug-report@…
[…]

Jun 12, 2025:

7:29 PM Ticket #17975 (usage: 'int' object has no attribute 'split') closed by Greg Couch
fixed: Nevertheless, you shouldn't have had a traceback. And that traceback …
6:01 PM Ticket #17975 (usage: 'int' object has no attribute 'split') created by olibclarke@…
[…]
5:57 PM Ticket #17974 (AddH: more than 2 coplanar positions specified) closed by pett
not a bug: Likely a bad structure
5:54 PM Ticket #17973 (Add Charge: non-standard residue list is empty) closed by pett
can't reproduce: Eyeballing the code, I don't see how this could happen. Need the data.
4:19 PM Ticket #17974 (AddH: more than 2 coplanar positions specified) created by chimerax-bug-report@…
[…]
3:57 PM Ticket #8483 (Merging fragments issues) closed by pett
fixed
3:51 PM Ticket #17973 (Add Charge: non-standard residue list is empty) created by chimerax-bug-report@…
[…]
3:43 PM Ticket #2024 (Doc strings / optional arguments for aliases) closed by Greg Couch
fixed: Added "alias synopsis name text" that works for a previously …
3:05 PM Ticket #17972 (Crash on Mac waking from sleep) closed by pett
duplicate
2:12 PM Ticket #17972 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
10:38 AM Ticket #17971 ('pip install pyKVFinder' fails with empty error message) closed by pett
duplicate: Duplicate of #17229
10:35 AM Ticket #17969 (Crash moving window between screens) closed by pett
duplicate
10:33 AM Ticket #17968 ('pip install pyKVFinder' fails with empty error message) closed by pett
duplicate: Duplicate of #17229
10:27 AM Ticket #17967 (Crash using open/save dialog) closed by pett
can't reproduce: Last stack has _update_graphics_if_needed
8:34 AM Ticket #17971 ('pip install pyKVFinder' fails with empty error message) created by chimerax-bug-report@…
[…]
8:10 AM Ticket #17970 (Windows PyPi OpenMM: no CUDA) created by Tristan Croll
[…]
8:05 AM Ticket #17969 (Crash moving window between screens) created by chimerax-bug-report@…
[…]
6:34 AM Ticket #17968 ('pip install pyKVFinder' fails with empty error message) created by chimerax-bug-report@…
[…]

Jun 11, 2025:

10:59 PM Ticket #17967 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
12:00 PM Ticket #17966 (KVFinder on old MacOS) closed by pett
limitation: For ARM, has to be running MacOS 15 (for Intel, 14)
11:50 AM Ticket #17966 (KVFinder on old MacOS) created by chimerax-bug-report@…
[…]
11:21 AM Ticket #17915 (Boltz structures distorted) closed by Tom Goddard
can't reproduce: Glad you got it to work. Maybe there was a conflict between a …
11:17 AM Ticket #17964 (Crash in swap_buffers) closed by Tom Goddard
nonchimerax: Graphics driver crash. User was showing side view.
10:52 AM Ticket #17785 (Combine into existing ID) closed by pett
fixed: Fix: …
9:51 AM Ticket #17965 (Crash using open/save dialog) closed by pett
can't reproduce: Last stack involved _update_drawings
9:49 AM Ticket #17963 (Crash on Mac waking from sleep) closed by pett
duplicate
9:46 AM Ticket #17962 (AtomicShapeDrawing: AttributeError: 'list' object has no attribute ...) closed by pett
duplicate
9:43 AM Ticket #17961 (SEQCROW open .out: max() arg is an empty sequence) closed by pett
duplicate: Follow up to #17946 with attachment
9:43 AM Ticket #17960 (SEQCROW open .out: max() arg is an empty sequence) closed by pett
duplicate: Follow up to #17946 with attachment
9:41 AM Ticket #17959 (SEQCROW open .out: max() arg is an empty sequence) closed by pett
duplicate: Follow up to #17946 with attachment
8:03 AM Ticket #17965 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
5:10 AM Ticket #17964 (Crash in swap_buffers) created by chimerax-bug-report@…
[…]
3:03 AM Ticket #17963 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
2:30 AM Ticket #17962 (AtomicShapeDrawing: AttributeError: 'list' object has no attribute ...) created by chimerax-bug-report@…
[…]

Jun 10, 2025:

11:40 PM Ticket #17952 (Qt display issue with ChimeraX) closed by Greg Couch
limitation: Excellent! Thank you for telling us how the problem was fixed.
10:05 PM Ticket #17961 (SEQCROW open .out: max() arg is an empty sequence) created by tejalsawant.329@…
[…] molecule0.g98 (24).out
9:15 PM Ticket #17960 (SEQCROW open .out: max() arg is an empty sequence) created by tejalsawant.329@…
[…] molecule0.g98 (21).out
9:14 PM Ticket #17959 (SEQCROW open .out: max() arg is an empty sequence) created by tejalsawant.329@…
[…] molecule0.g98 (21).out
4:33 PM Ticket #9866 (Region/feature browsers need to react to non-self-generated region changes) closed by pett
fixed: Fix: …
11:56 AM Ticket #16654 (Session restore: ItemTable's selectionModel() is None (Parsing ...) closed by Zach Pearson
fixed: I am going to assume this was fixed.
11:55 AM Ticket #17925 (Could not find ffmpeg executable at ffmpeg) closed by Zach Pearson
fixed: Whoops. This problem had been fixed on the develop branch and I forgot …
11:42 AM Ticket #17958 (Add model id option to morph command) closed by Tom Goddard
fixed: Done. Added modelId option. If you try to use an existing model id …
11:40 AM Ticket #17958 (Add model id option to morph command) created by a.rohou@…
From: Alexis Rohou via ChimeraX-users <chimerax-users@…> …
11:25 AM Ticket #17957 (Intel/AMD graphics driver crash) closed by Tom Goddard
nonchimerax: This crash is from buggy Mac Intel graphics drivers. The bug report …
10:55 AM 2025-6-12 created by Tom Goddard
10:53 AM DeveloperMeetings edited by Tom Goddard
(diff)
10:38 AM Ticket #17957 (Intel/AMD graphics driver crash) created by decolibus@…
[…]
9:29 AM Ticket #17956 (Crash using open/save dialog) closed by pett
can't reproduce: Last stack involved molc.py
9:25 AM Ticket #17956 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
8:46 AM Ticket #17955 (Crash using open/save dialog) closed by pett
can't reproduce: 1.3; last stack had draw_new_frame
8:45 AM Ticket #17954 (Crash using open/save dialog) closed by pett
can't reproduce: 1.3; last stack had draw_new_frame
8:43 AM Ticket #17953 (Crash using open/save dialog) closed by pett
can't reproduce: Last stack involved graphics.py
8:41 AM Ticket #17951 (Crash on Mac waking from sleep) closed by pett
duplicate
8:37 AM Ticket #17949 (Crash using open/save dialog) closed by pett
can't reproduce: Last stack had _update_graphics_if_needed
7:55 AM Ticket #17955 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
7:55 AM Ticket #17954 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
7:27 AM Ticket #17953 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
5:00 AM Ticket #17952 (Qt display issue with ChimeraX) created by edouard.evangelisti@…
[…]
3:09 AM Ticket #17951 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]

Jun 9, 2025:

9:53 PM Ticket #17417 (Debug mode not working on Windows) closed by Greg Couch
fixed: Got --debug to work, but not all debug output goes to {{{stdout or …
7:36 PM Ticket #17950 (isolde sim start sel: OpenMMException: Error compiling kerne) created by chimerax-bug-report@…
[…]
6:49 PM Ticket #16201 (Crash opening .cif file) closed by Greg Couch
worksforme: No response. Likely fixed, but not possible to tell without original …
6:37 PM 2025-6-5 edited by Tom Goddard
(diff)
4:57 PM Dev2025-6-9 edited by Tom Goddard
(diff)
3:19 PM Dev2025-6-9 created by Tom Goddard
3:19 PM DeveloperMeetings edited by Tom Goddard
(diff)
1:10 PM Ticket #17949 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
12:04 PM Ticket #17947 (measure sasa: crash in spheres_surface_area) closed by Tom Goddard
can't reproduce: Looks like the measure sasa crash happened with this data file and …
11:56 AM Ticket #17944 (Crash hiding dust while drawing frame) closed by Tom Goddard
can't reproduce: Was computing connected triangles self.blist = …
11:49 AM Ticket #17943 (Crash in swap_buffers) closed by Tom Goddard
can't reproduce: Looks like a graphics driver crash. Could be a bug in the Nvidia …
10:04 AM Ticket #17948 (Crash using open/save dialog) closed by pett
can't reproduce: Last stack has _update_graphics_if_needed
9:55 AM Ticket #17945 (Crash on Mac waking from sleep) closed by pett
duplicate
9:46 AM Ticket #17941 ('CCP4Grid' object has no attribute 'dicom_data') closed by pett
duplicate
9:46 AM Ticket #17948 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
9:45 AM Ticket #17940 (Crash on Mac waking from sleep) closed by pett
duplicate
9:44 AM Ticket #17939 (Crash at exit) closed by pett
fixed: Since we no longer call ~QApplication on Mac at exit, this report is moot.
9:42 AM Ticket #17938 (Crash in garbage collection) closed by pett
duplicate
9:41 AM Ticket #17937 (Crash in garbage collection) closed by pett
duplicate: Hi Sana, Thanks for reporting this problem. It has been fixed in …
9:38 AM Ticket #17936 (Crash using open/save dialog) closed by pett
can't reproduce: No non-open/save stack trace in this one.
9:31 AM Ticket #17934 (Crash using open/save dialog) closed by pett
can't reproduce: Last stack involved molc.py
9:24 AM Ticket #17933 (Crash on Mac waking from sleep) closed by pett
duplicate
8:46 AM Ticket #17947 (measure sasa: crash in spheres_surface_area) created by miyovan@…
[…]
5:49 AM Ticket #17946 (SEQCROW open .out: max() arg is an empty sequence) created by tejalsawant.329@…
[…]
4:03 AM Ticket #17945 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
3:49 AM Ticket #17944 (Crash hiding dust while drawing frame) created by chimerax-bug-report@…
[…]
2:54 AM Ticket #17943 (Crash in swap_buffers) created by chimerax-bug-report@…
[…]
2:45 AM Ticket #17942 (RFE: looping animated PNGs) created by Tristan Croll
[…]
2:23 AM Ticket #17941 ('CCP4Grid' object has no attribute 'dicom_data') created by chimerax-bug-report@…
[…]
1:16 AM Ticket #17940 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]

Jun 8, 2025:

6:47 PM Ticket #17939 (Crash at exit) created by chimerax-bug-report@…
[…]

Jun 7, 2025:

11:25 PM Ticket #17938 (Crash in garbage collection) created by sana2000@…
[…]
7:52 PM Ticket #17937 (Crash in garbage collection) created by sana2000@…
[…]
7:34 PM Ticket #17936 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
1:24 PM Ticket #17935 (Sequence viewer preference: 'seqview' is not in list) created by chimerax-bug-report@…
[…]

Jun 6, 2025:

3:33 PM Ticket #17934 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
1:45 PM Ticket #17933 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
11:50 AM Ticket #17930 (Crash creating HtmlView profile) closed by Tom Goddard
duplicate: Probable Qt bug. Crashes in QWebEngineProfile(parent). We have 55 …
11:46 AM Ticket #17929 (Crash making status bar context current) closed by Tom Goddard
nonchimerax: There are 3 tracebacks all listing the same thread, all in different …
11:39 AM Ticket #17927 (Modified PAE) closed by Tom Goddard
not a bug: I don't understand. The predicted aligned error reflects confidence …
11:33 AM Ticket #17923 (Invalid texture upload) closed by Tom Goddard
can't reproduce: The error message "Invalid texture upload for 0x298dd5bc190 layer=0 …
11:15 AM Ticket #17932 (Boltz GUI expands to full window width if pasted sequence used) closed by Tom Goddard
fixed: Fixed in 1.10. The table for the predicted molecule assembly …
11:12 AM Ticket #17932 (Boltz GUI expands to full window width if pasted sequence used) created by goddard@…
[…]
10:11 AM Ticket #17931 (Accessing deleted widget) closed by pett
can't reproduce: But suspicious that there are consecutive loggings of "Closest …
9:33 AM Ticket #17928 (Cannot instantiate sseq.structure) closed by pett
can't reproduce: I have no idea how "ui mousemode right label" could try to instantiate …
9:02 AM Ticket #17924 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by pett
duplicate
8:43 AM Ticket #17931 (Accessing deleted widget) created by chimerax-bug-report@…
[…]
6:47 AM Ticket #17930 (Crash creating HtmlView profile) created by chimerax-bug-report@…
[…]
4:21 AM Ticket #17929 (Crash making status bar context current) created by chimerax-bug-report@…
[…]
2:52 AM Ticket #17928 (Cannot instantiate sseq.structure) created by chimerax-bug-report@…
[…]
2:26 AM Ticket #17927 (Modified PAE) created by florear@…
[…]
2:01 AM Ticket #17926 (SEQCROW: model.session is None while applying preset to morph) created by Tristan Croll
[…]

Jun 5, 2025:

9:40 PM Ticket #17925 (Could not find ffmpeg executable at ffmpeg) created by fcofas@…
[…]
7:29 PM Ticket #17924 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…
[…]
5:36 PM Ticket #17916 (Segger: maxnr is None) closed by Tom Goddard
wontfix: The user entered a non-numeric value in the Segger maximum number of …
5:30 PM Ticket #17917 (Crash in glBufferSubData changing volume level) closed by Tom Goddard
can't reproduce: ChimeraX crashed in OpenGL graphics call glBufferSubData(). The …
5:23 PM Ticket #17742 (Sequence association incomplete) closed by pett
fixed: Fixed -- in the daily build only since it's a fairly complex change. …
4:58 PM Dev2025-6-5 created by Tom Goddard
4:54 PM DeveloperMeetings edited by Tom Goddard
(diff)
4:39 PM Ticket #17923 (Invalid texture upload) created by chimerax-bug-report@…
[…]
4:31 PM Ticket #17716 (Toolshed installation of SEQCROW: subprocess.run("pip ..."): The ...) closed by Greg Couch
can't reproduce: Everything appears to work in the current release candidate.
4:07 PM Ticket #16830 (Toolshed not providing uninstalled info) closed by Greg Couch
fixed: The timeout for getting the available bundle information was too short.
4:01 PM Ticket #17009 (Registration page does not work) closed by Greg Couch
can't reproduce: Unable to reproduce
3:53 PM Ticket #17311 (ChimeraX startup messages: Failed to resolve 'webservices.rbvi.ucsf.edu') closed by Greg Couch
fixed: Put the check_for_updates call inside try/except
3:40 PM Ticket #16289 (Graduate Student Using ChimeraX - Encountering Issue w/ Downloading ...) closed by Greg Couch
fixed: Fixed in 1.11
2:31 PM Ticket #17922 (Q-score outputFile option gave traceback) created by Elaine Meng
[…] 4427_6i7o_AY.mrc
1:48 PM Ticket #17921 (Find Cavities table accessing dead cavity model) closed by pett
can't reproduce
1:36 PM Ticket #17920 (Crash moving window between screens) closed by pett
duplicate
1:34 PM Ticket #17919 (mshMIGPerform crash) closed by pett
duplicate: Duplicate of #17777
1:29 PM Ticket #17918 (Difference in secondary structure display between Mol* 3D and ChimeraX) closed by pett
not a bug: Hi Paul, The .cif file you provided lacks information about secondary …
1:18 PM Ticket #17921 (Find Cavities table accessing dead cavity model) created by chimerax-bug-report@…
[…]
12:59 PM Ticket #17914 (Crash using open/save dialog) closed by pett
duplicate: last stack trace had _update_graphics_if_needed
12:57 PM Ticket #17920 (Crash moving window between screens) created by chimerax-bug-report@…
[…]
10:53 AM Ticket #17919 (mshMIGPerform crash) created by chimerax-bug-report@…
[…]
10:51 AM Ticket #17912 (Crash on Mac waking from sleep) closed by pett
duplicate
10:47 AM Ticket #17889 (Device loss detected in Present()) closed by Tom Goddard
can't reproduce: Ok. We have several recent bug reports with "Device loss detected in …
10:45 AM Ticket #17910 (Crash in event loop) closed by pett
can't reproduce
10:38 AM Ticket #17909 ('MRCGrid' object has no attribute 'dicom_data') closed by pett
duplicate
10:33 AM Ticket #17908 ('MRCGrid' object has no attribute 'dicom_data') closed by pett
duplicate
10:33 AM Ticket #17907 ('MRCGrid' object has no attribute 'dicom_data') closed by pett
duplicate
10:32 AM Ticket #17906 ('MRCGrid' object has no attribute 'dicom_data') closed by pett
duplicate
10:31 AM Ticket #17905 (Crash on Mac waking from sleep) closed by pett
duplicate
8:49 AM Ticket #17918 (Difference in secondary structure display between Mol* 3D and ChimeraX) created by paul.kirchberger@…
[…] [[Image(...)]] [[Image(...)]] …
7:48 AM Ticket #17917 (Crash in glBufferSubData changing volume level) created by syedasfarul.haque@…
[…]
6:42 AM Ticket #17916 (Segger: maxnr is None) created by chimerax-bug-report@…
[…]
6:16 AM Ticket #17915 (Boltz structures distorted) created by dominik.oberthuer@…
[…]
2:44 AM Ticket #17914 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
2:23 AM Ticket #17913 (Problem installing XMAS) created by pascal.albanese@…
[…]
12:52 AM Ticket #17912 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
12:23 AM Ticket #17911 (EMalign: AssertionError: Downsample must be less than input volume size) created by chimerax-bug-report@…
[…]
12:18 AM Ticket #17910 (Crash in event loop) created by chimerax-bug-report@…
[…]

Jun 4, 2025:

11:52 PM Ticket #17909 ('MRCGrid' object has no attribute 'dicom_data') created by chimerax-bug-report@…
[…]
11:51 PM Ticket #17908 ('MRCGrid' object has no attribute 'dicom_data') created by chimerax-bug-report@…
[…]
11:51 PM Ticket #17907 ('MRCGrid' object has no attribute 'dicom_data') created by chimerax-bug-report@…
[…]
11:51 PM Ticket #17906 ('MRCGrid' object has no attribute 'dicom_data') created by chimerax-bug-report@…
[…]
10:24 PM Ticket #17905 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
5:42 PM Ticket #17903 (Session save: Similar Structures: 'NoneType' object has no attribute 'hits') closed by pett
duplicate: Duplicate of #16968
5:37 PM Ticket #17902 (Crash moving window between screens) closed by pett
duplicate
4:39 PM Ticket #17890 (Foldseek: index is out of bounds) closed by Tom Goddard
fixed: Fixed. I updated ChimeraX to assume new Foldseek server results …
3:22 PM Ticket #17904 (Logging out while ChimeraX is running on Windows causes a crash report) closed by Tom Goddard
limitation: Not sure there is any way we can detect that a Windows ChimeraX crash …
3:06 PM Ticket #17904 (Logging out while ChimeraX is running on Windows causes a crash report) created by goddard@…
[…]
2:43 PM Ticket #17903 (Session save: Similar Structures: 'NoneType' object has no attribute 'hits') created by chimerax-bug-report@…
[…]
1:53 PM Ticket #17902 (Crash moving window between screens) created by chimerax-bug-report@…
[…]
12:02 PM Ticket #17895 (viewer_option lambda returning None instead of option class) closed by pett
fixed: It's mystifying to me how this could occur (the setting value is not …
10:37 AM Ticket #17901 (Crash on exit in ~QAccessibleCache on Mac) closed by pett
can't reproduce
10:36 AM Ticket #17900 (Crash in _update_graphics_if_needed) closed by pett
can't reproduce: The tracebacks don't show the open/save dialogs being used here, …
10:05 AM Ticket #17898 (Crash in event loop) closed by pett
can't reproduce: at startup
9:59 AM Ticket #17896 (viewer_option lambda returning None instead of option class) closed by pett
duplicate
9:52 AM Ticket #17894 (Driver bug messes up UI) closed by pett
nonchimerax
9:50 AM Ticket #17893 (ISOLDE: ResidueStepper holding reference to dead model) closed by pett
duplicate
9:47 AM Ticket #17892 (Crash in event loop) closed by pett
can't reproduce: Crashed at startup
9:45 AM Ticket #17891 (Crash using open/save dialog) closed by pett
can't reproduce: Last stack involved graphics\clipping.py
9:20 AM Ticket #17901 (Crash on exit in ~QAccessibleCache on Mac) created by chimerax-bug-report@…
[…]
9:02 AM Ticket #17900 (Crash in _update_graphics_if_needed) created by chimerax-bug-report@…
[…]
8:38 AM Ticket #17899 (UniProt sequences should retain numbering) created by Tristan Croll
[…]
2:40 AM Ticket #17898 (Crash in event loop) created by chimerax-bug-report@…
[…]
12:09 AM Ticket #17897 (QScore: model is None) created by chimerax-bug-report@…
[…]

Jun 3, 2025:

11:35 PM Ticket #17896 (viewer_option lambda returning None instead of option class) created by chimerax-bug-report@…
[…]
10:44 PM Ticket #17895 (viewer_option lambda returning None instead of option class) created by chimerax-bug-report@…
[…]
10:36 PM Ticket #17894 (Driver bug messes up UI) created by chimerax-bug-report@…
[…]
10:29 PM Ticket #17893 (ISOLDE: ResidueStepper holding reference to dead model) created by chimerax-bug-report@…
[…]
10:06 PM Ticket #17892 (Crash in event loop) created by chimerax-bug-report@…
[…]
7:52 PM Ticket #17891 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
6:37 PM Ticket #17890 (Foldseek: index is out of bounds) created by michelle.christie@…
[…]
5:59 PM DeveloperMeetings edited by Tom Goddard
(diff)
5:58 PM 2025-6-5 edited by Tom Goddard
(diff)
5:56 PM Ticket #17888 (Test ChimeraX on Wayland) closed by Tom Goddard
not a bug: I see, we have specific environment variables that prevent ChimeraX …
4:31 PM Ticket #17889 (Device loss detected in Present()) created by gregdp@…
[…]
3:46 PM Ticket #17887 (Test ChimeraX on Wayland) closed by Tom Goddard
duplicate: Duplicate of #17888
3:38 PM Ticket #17888 (Test ChimeraX on Wayland) created by goddard@…
[…]
3:35 PM Ticket #17887 (Test ChimeraX on Wayland) created by goddard@…
[…]
2:45 PM Ticket #17885 (Meeting: can not serialize 'numpy.uint8' object) closed by Tom Goddard
fixed: Fixed in 1.10 and 1.11. The color option to the meeting start and …
1:55 PM Ticket #17886 (isolde sim start sel: OpenMMException: There is no registered Platform ...) created by rkrishnan@…
[…]
11:49 AM Ticket #17885 (Meeting: can not serialize 'numpy.uint8' object) created by chimerax-bug-report@…
[…]
11:18 AM Ticket #17884 (Testing linux crash report requires email address) closed by Tom Goddard
fixed
11:15 AM Ticket #17642 (Prevent reporting of useless bug reports) closed by Tom Goddard
fixed: Done. I made Linux crashes require email in ChimeraX 1.11 daily build.
11:08 AM Ticket #17884 (Testing linux crash report requires email address) created by goddard@…
[…]
10:33 AM Ticket #17883 (Crash on Mac waking from sleep) closed by pett
duplicate
10:21 AM Ticket #17879 (Similar Structures: save as TSV/CSV) closed by Tom Goddard
not a bug: The menu entry to save comma-separated values or tab-separated values …
10:17 AM 2025-6-5 created by Tom Goddard
10:16 AM DeveloperMeetings edited by Tom Goddard
(diff)
10:09 AM Ticket #17883 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
10:02 AM Ticket #17800 (Bond rotations need to respond to bond addition/deletion) closed by pett
can't reproduce: Actually, bond rotations do delete themselves when cycles are formed, …
9:40 AM Ticket #17882 (Crash accessing StructureSeq.structure) closed by pett
duplicate: Hi George, Thanks for reporting this problem. It is fixed in more …
9:13 AM Ticket #17882 (Crash accessing StructureSeq.structure) created by george.nyasha.chiduza@…
[…]
9:13 AM Ticket #17881 (Crash in garbage collection) closed by pett
duplicate
8:56 AM Ticket #17878 (Crash on Mac waking from sleep) closed by pett
duplicate
8:41 AM Ticket #17876 (Crash using open/save dialog) closed by pett
can't reproduce: Last stack had _update_graphics_if_needed
8:04 AM Ticket #17881 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
7:00 AM Ticket #17880 (RFE: position center of 2D label) created by Tristan Croll
[…]
5:45 AM Ticket #17879 (Similar Structures: save as TSV/CSV) created by michelle.christie@…
[…]
4:01 AM Ticket #17878 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
3:05 AM Ticket #17877 (Crash opening mmCIF) created by paula.schliebe@…
[…]
2:36 AM Ticket #17876 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]

Jun 2, 2025:

6:40 PM Ticket #17875 (Crash on Mac waking from sleep) closed by Tom Goddard
duplicate: This is a known crash and the ChimeraX Bug Report panel described what …
6:01 PM Ticket #17865 (Large number of structures → memory exhaustion) closed by pett
limitation: Glad you've almost gotten the script working. I'll probably have …
5:12 PM Ticket #17868 (AlphaFold: update best model) closed by Tom Goddard
fixed: Fixed in 1.11 daily builds, not in 1.10. I made ChimeraX put a second …
4:12 PM Dev2025-6-3 edited by Tom Goddard
(diff)
3:05 PM Dev2025-6-3 created by Tom Goddard
3:04 PM DeveloperMeetings edited by Tom Goddard
(diff)
1:57 PM Ticket #17875 (Crash on Mac waking from sleep) created by taic@…
[…]
1:11 PM Ticket #17874 (alphafold pae: KeyError: 'pae is not a file in the archive') closed by Tom Goddard
fixed: Added in ChimeraX 1.11 a user friendly error message explaining that …
12:04 PM Ticket #17869 (draw_elements: access violation) closed by Tom Goddard
nonchimerax: Looks like an Intel graphics driver bug. Intel graphics driver …
12:00 PM Ticket #17856 (The cached device pixel ratio value was stale on window expose) closed by pett
can't reproduce: Thanks for the additional info Sasha. I'm pretty sure the message is …
11:52 AM Ticket #17873 (Widget setFocus loop) closed by pett
can't reproduce
11:50 AM Ticket #17872 (Crash destroying OpenGL context on exit) closed by pett
duplicate: From before the fix
11:49 AM Ticket #17871 (glDrawBuffer: invalid operation) closed by pett
limitation: Looks like remote display
11:47 AM Ticket #17870 (Crash destroying OpenGL context on exit) closed by pett
duplicate: From before the fix
11:40 AM Ticket #17867 (Crash in swap_buffers) closed by pett
limitation: Probable remote display
11:39 AM Ticket #17866 (Crash using open/save dialog) closed by pett
can't reproduce: Last stack trace contained _update_graphics_if_needed
11:26 AM Ticket #17860 (Crash in compute_cap) closed by Tom Goddard
can't reproduce: Crashed in the C++ cap computation. Haven't seen this crash in the …
11:04 AM Dev2025-5-5 edited by pett
(diff)
9:45 AM Ticket #17874 (alphafold pae: KeyError: 'pae is not a file in the archive') created by o.bozkurt@…
[…]
9:45 AM Ticket #17873 (Widget setFocus loop) created by chimerax-bug-report@…
[…]
9:45 AM Ticket #17872 (Crash destroying OpenGL context on exit) created by chimerax-bug-report@…
[…]
9:45 AM Ticket #17871 (glDrawBuffer: invalid operation) created by chimerax-bug-report@…
[…]
9:45 AM Ticket #17870 (Crash destroying OpenGL context on exit) created by chimerax-bug-report@…
[…]
9:45 AM Ticket #17869 (draw_elements: access violation) created by chimerax-bug-report@…
[…]
9:45 AM Ticket #17868 (AlphaFold: update best model) created by hemmecl@…
[…]
9:43 AM Ticket #17867 (Crash in swap_buffers) created by chimerax-bug-report@…
[…]

May 31, 2025:

2:34 PM Ticket #17866 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
12:31 PM Ticket #17865 (Large number of structures → memory exhaustion) created by alexandra.zahradnikova@…
[…]
7:01 AM Ticket #17864 (Crash in event loop / toolshed load) created by 2023020518@…
[…]

May 30, 2025:

6:12 PM Ticket #17863 (Crash on Mac waking from sleep) closed by pett
duplicate
6:11 PM Ticket #17862 (Crash in StructureSeq.structure) closed by pett
can't reproduce
6:10 PM Ticket #17861 (Crash saving atomic session state) closed by pett
can't reproduce: Could be the garbage-collection bug that was fixed.
1:02 PM Ticket #17863 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
12:57 PM Ticket #17862 (Crash in StructureSeq.structure) created by chimerax-bug-report@…
[…]
12:48 PM Ticket #17861 (Crash saving atomic session state) created by chimerax-bug-report@…
[…]
12:04 PM Ticket #17860 (Crash in compute_cap) created by chimerax-bug-report@…
[…]
11:58 AM Ticket #17832 (LocScale-SURFER bundle development for Mac OS) closed by Tom Goddard
limitation
10:54 AM Ticket #17859 (Close request on destroyed tool window) closed by pett
can't reproduce
10:49 AM Ticket #17859 (Close request on destroyed tool window) created by chimerax-bug-report@…
[…]
10:41 AM Ticket #17803 (Crash in chem_group on Windows) closed by pett
can't reproduce
10:16 AM Ticket #17858 (Graphics hardware encountered an error and was reset) closed by pett
duplicate
10:01 AM Ticket #17857 (Cannot save command history: No space left on device) closed by pett
nonchimerax
9:49 AM Ticket #17855 (Crash in event loop) closed by pett
can't reproduce
9:44 AM Ticket #17854 (Crash in event loop) closed by pett
can't reproduce: Guessing this was run from the dmg because of all the …
9:41 AM Ticket #17858 (Graphics hardware encountered an error and was reset) created by chimerax-bug-report@…
[…]
8:12 AM Ticket #17857 (Cannot save command history: No space left on device) created by chimerax-bug-report@…
[…]
12:49 AM Ticket #17856 (The cached device pixel ratio value was stale on window expose) created by alexandra.zahradnikova@…
[…]
12:40 AM Ticket #17855 (Crash in event loop) created by chimerax-bug-report@…
[…]

May 29, 2025:

7:49 PM Ticket #17854 (Crash in event loop) created by chimerax-bug-report@…
[…]
4:51 PM Ticket #17853 (Remember render by attribute thresholds when multiple models chosen) created by Willow.Coyote-Maestas@…
Render by attribute remembers the thresholds and colors last used for …
3:05 PM Ticket #17778 (ChimeraX 1.9 SHA256 hash incorrrect) closed by Zach Pearson
fixed: Should be fixed.
2:36 PM Ticket #17851 (Toolbar→Molecule Display→Sequence does not handle blank chain ID) closed by pett
fixed: Fixed. Fix available in next daily build and release candidate, Fix: …
2:22 PM Ticket #17852 (Crash in event loop) closed by pett
can't reproduce
2:12 PM Ticket #17838 (vr roomCamera: AttributeError: 'NoneType' object has no attribute ...) closed by Tom Goddard
fixed: Fixed. User tried to enable VR room camera when VR had not been …
2:10 PM Ticket #17850 (Ticket Updated: INC-171399 - Possible bug on installation) closed by pett
not a bug
12:27 PM Ticket #17852 (Crash in event loop) created by chimerax-bug-report@…
[…]
11:16 AM Ticket #17851 (Toolbar→Molecule Display→Sequence does not handle blank chain ID) created by ddrichma@…
[…]
11:14 AM Ticket #17849 (Various OpenGL errors) closed by Tom Goddard
nonchimerax: Possibly remote display or graphic driver problem. Can't get driver …
11:11 AM Ticket #17846 (Crash on Mac waking from sleep) closed by Tom Goddard
duplicate: The ChimeraX Bug Reporter panel explains what we know about this crash …
11:11 AM Ticket #17850 (Ticket Updated: INC-171399 - Possible bug on installation) created by helpdesk@…
[…]
11:10 AM Ticket #17848 (Ticket Updated: INC-171399 - Possible bug on installation) closed by pett
not a bug
11:07 AM Ticket #17849 (Various OpenGL errors) created by chimerax-bug-report@…
[…]
11:04 AM Ticket #17848 (Ticket Updated: INC-171399 - Possible bug on installation) created by helpdesk@…
[…]
10:58 AM Ticket #17847 ('pip install pyKVFinder' fails with empty error message) closed by pett
duplicate: Duplicate of #17229; using two-month-old version
10:51 AM Ticket #17845 (Re: INC-171399 Possible bug on installation) closed by pett
not a bug: Actually a follow up to #17755; will add the info to that ticket
10:43 AM Ticket #17844 (FoldSeek: Permission denied writing temp file) closed by Tom Goddard
duplicate: This foldseek permission error is fixed in the ChimeraX 1.10 release …
10:36 AM Ticket #17843 ('pip install pyKVFinder' fails with empty error message) closed by pett
duplicate: Duplicate of #17229
10:30 AM Ticket #17842 (Crash in event loop) closed by pett
can't reproduce: After "toolshed show", though that might not be relevant
10:24 AM Ticket #17841 ('ArrayGridData' object has no attribute 'dicom_data') closed by pett
duplicate
10:21 AM Ticket #17840 (Crash in event loop) closed by pett
can't reproduce
10:18 AM Ticket #17839 (Maestro: KeyError: 'i_m_residue_number') closed by pett
duplicate: Duplicate of #9215
10:17 AM Ticket #15588 (Maestro: KeyError: 'i_m_residue_number') closed by pett
can't reproduce: No feedback received
10:06 AM Ticket #17837 (Crash at exit) closed by pett
duplicate: From before the fix went in
10:04 AM Ticket #17836 (Crash using open/save dialog) closed by pett
can't reproduce
9:48 AM Ticket #17847 ('pip install pyKVFinder' fails with empty error message) created by chimerax-bug-report@…
[…]
7:38 AM Ticket #17846 (Crash on Mac waking from sleep) created by guillermo.montoya@…
[…]
7:15 AM Ticket #17845 (Re: INC-171399 Possible bug on installation) created by helpdesk@…
[…]
7:04 AM Ticket #17844 (FoldSeek: Permission denied writing temp file) created by semihpehlivan@…
[…]
3:56 AM Ticket #17843 ('pip install pyKVFinder' fails with empty error message) created by chimerax-bug-report@…
[…]
3:55 AM Ticket #17842 (Crash in event loop) created by chimerax-bug-report@…
[…]
3:35 AM Ticket #17841 ('ArrayGridData' object has no attribute 'dicom_data') created by chimerax-bug-report@…
[…]
2:53 AM Ticket #17840 (Crash in event loop) created by chimerax-bug-report@…
[…]
2:19 AM Ticket #17839 (Maestro: KeyError: 'i_m_residue_number') created by chimerax-bug-report@…
[…]
1:11 AM Ticket #17838 (vr roomCamera: AttributeError: 'NoneType' object has no attribute ...) created by chimerax-bug-report@…
[…]
12:04 AM Ticket #17837 (Crash at exit) created by chimerax-bug-report@…
[…]

May 28, 2025:

6:36 PM Ticket #17836 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
12:03 PM Ticket #17835 (Crash in Qt event loop running AlphaFold prediction) closed by Tom Goddard
can't reproduce
11:54 AM Ticket #17835 (Crash in Qt event loop running AlphaFold prediction) created by chimerax-bug-report@…
[…]
11:47 AM Ticket #17834 (Session save: ItemTable's selectionModel() is None) closed by pett
duplicate: Duplicate of #16653
11:42 AM Ticket #17834 (Session save: ItemTable's selectionModel() is None) created by chimerax-bug-report@…
[…]
11:33 AM Ticket #17833 (Unknown error) closed by pett
can't reproduce: Maybe the tools panels were blank? Dunno.
11:29 AM Ticket #17833 (Unknown error) created by chimerax-bug-report@…
[…]
11:05 AM Ticket #2929 (ChimeraX header files not present in CentOS RPM) closed by Greg Couch
fixed: CString.h is in site-packages/chimerax/core/include/chutil/CString.h
10:42 AM Ticket #17825 (Read MRC: cannot convert float NaN to integer) closed by Tom Goddard
not a bug: I believe this ChimeraX error means the map file …
10:16 AM Ticket #17828 (Segger: invalid literal for int) closed by Tom Goddard
not a bug: User apparently pasted "6vop extract #1 region 0,360,0,360,0,360\n" …
10:14 AM Ticket #17827 (Various OpenGL errors) closed by Tom Goddard
nonchimerax: Graphics driver bug.
9:43 AM Ticket #17831 (Crash using open/save dialog) closed by pett
can't reproduce
9:40 AM Ticket #17830 (MemoryError opening mmCIF files) closed by pett
duplicate
9:23 AM Ticket #17826 (Crash using open/save dialog) closed by pett
can't reproduce: Last stack was in _update_graphics_if_needed
5:48 AM Ticket #17832 (LocScale-SURFER bundle development for Mac OS) created by A.Bharadwaj@…
[…]
4:07 AM Ticket #17831 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
3:39 AM Ticket #17830 (MemoryError opening mmCIF files) created by chimerax-bug-report@…
[…]
2:40 AM Ticket #17829 (Crash at startup) created by zhiling9921@…
[…]
1:37 AM Ticket #17828 (Segger: invalid literal for int) created by chimerax-bug-report@…
[…]
1:03 AM Ticket #17827 (Various OpenGL errors) created by chimerax-bug-report@…
[…]
12:31 AM Ticket #17826 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
12:13 AM Ticket #17825 (Read MRC: cannot convert float NaN to integer) created by basavraj.khanppnavar@…
[…]

May 27, 2025:

6:36 PM Ticket #17817 (Mutation Scores: NotImplementedError: cannot remove artist) closed by Tom Goddard
fixed: Fixed in ChimeraX 1.10 release candidates and daily builds dated May …
6:06 PM Ticket #17824 (Swapna and other operations slow) created by matthias.vorlaender@…
Dear ChimeraX team, I have noticed that on some structure I am …
5:28 PM Ticket #17823 (MemoryError opening mmCIF files) closed by pett
duplicate: Hi, This memory problem has been fixed in recent versions of …
4:57 PM Ticket #17823 (MemoryError opening mmCIF files) created by s3988903@…
[…]
4:00 PM Ticket #17820 ('MRCGrid' object has no attribute 'dicom_data') closed by pett
duplicate
3:59 PM Ticket #17819 (pyKVFinder: missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)) closed by pett
duplicate
3:06 PM Ticket #17822 (Allow installing experimental boltz branches for testing) closed by Tom Goddard
fixed: Fixed in 1.10. Added "branch" option to boltz install command.
3:05 PM Ticket #17822 (Allow installing experimental boltz branches for testing) created by Tom Goddard
Would be convenient to be able to specify a git branch of boltz to …
3:00 PM Ticket #17821 (Boltz GUI is ignoring new install location) closed by Tom Goddard
fixed: Fixed in 1.10. It was using the Boltz install location remembered in …
2:57 PM Ticket #17821 (Boltz GUI is ignoring new install location) created by goddard@…
[…]
2:53 PM Ticket #17813 (Building add_charge fails with metadata error) closed by Zach Pearson
fixed: Should be fixed
2:32 PM Ticket #17818 (Crash using open/save dialog) closed by pett
can't reproduce: Last stack trace was in molobject.py
2:21 PM Ticket #17814 (Crash in Qt event loop after opening/displaying MRC file) closed by Tom Goddard
can't reproduce: Crash was in Qt. Not enough info to tell what happened. Probably had …
2:14 PM Ticket #17815 (Many setGeometry errors → crash) closed by pett
can't reproduce: Maybe moving window to smaller display? Dunno.
2:09 PM Ticket #17812 (Crash at exit) closed by pett
duplicate
2:08 PM Ticket #17811 (Crash at exit) closed by pett
can't reproduce
2:05 PM Ticket #17810 (Crash on Mac waking from sleep) closed by pett
duplicate
2:02 PM Ticket #17806 (Crash moving window between screens) closed by Tom Goddard
can't reproduce: Seems to be a Qt bug moving window between screens on Windows, …
2:00 PM Ticket #17809 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by pett
can't reproduce
1:58 PM Ticket #17808 (Crash in graphics driver during Qt drawing) closed by pett
can't reproduce
1:56 PM Ticket #17807 (Crash in python_instances_of_class saving session) closed by pett
can't reproduce
1:52 PM Ticket #17805 (Crash destroying OpenGL context on exit) closed by pett
duplicate: From before the fix
1:50 PM Ticket #17804 (Crash in chem_group on Windows) closed by pett
can't reproduce
1:33 PM Ticket #17802 (Crash on Mac waking from sleep) closed by pett
duplicate
1:32 PM Ticket #17801 (Crash at exit in Qt cleanup routines) closed by pett
can't reproduce
1:24 PM Ticket #17799 (Dead model in Find Cavities table) closed by pett
can't reproduce
1:22 PM Ticket #17798 (Dead model in Find Cavities table) closed by pett
can't reproduce
1:14 PM Ticket #17797 (Crash using open/save dialog) closed by pett
can't reproduce: Last stack was in _update_graphics_if_needed
1:12 PM Ticket #17796 (AddH: More than 2 coplanar positions specified) closed by pett
not a bug: Bad PDB file
1:11 PM Ticket #17795 (Crash on Mac waking from sleep) closed by pett
duplicate
1:10 PM Ticket #17794 (Crash on exit) closed by pett
duplicate: From about 4 days before the fix went in.
1:07 PM Ticket #17793 (AtomicShapeDrawing: AttributeError: 'list' object has no attribute ...) closed by pett
duplicate: Hi, Thanks for reporting this problem. It was fixed about two days …
12:46 PM Ticket #17820 ('MRCGrid' object has no attribute 'dicom_data') created by chimerax-bug-report@…
[…]
12:34 PM Ticket #17819 (pyKVFinder: missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)) created by chimerax-bug-report@…
[…]
12:26 PM Ticket #17757 ("move": distance is None while undo is not None) closed by Tom Goddard
fixed: Fixed in 1.11. I made the move command not support undo if frames is …
12:02 PM Ticket #17791 (Crash in chem_group on Windows) closed by pett
can't reproduce
12:01 PM Ticket #17790 (Crash on Mac waking from sleep) closed by pett
duplicate
11:14 AM Ticket #17788 (Deep recursion in find_close_points_boxes) closed by Tom Goddard
limitation: Maybe this got around the PDB reader check for NaN/Inf because the …
11:13 AM Ticket #17789 (Bad PDB file) closed by pett
nonchimerax
11:08 AM DeveloperMeetings edited by Tom Goddard
(diff)
10:20 AM Ticket #17786 (pyKVFinder: missing LC_LOAD_DYLIB (must link with at least libSystem.dylib)) closed by pett
duplicate
9:40 AM Ticket #17818 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
8:05 AM Ticket #17817 (Mutation Scores: NotImplementedError: cannot remove artist) created by Ever.ODonnell@…
[…]
5:21 AM Ticket #17816 (Load MD atom subsets) created by Tristan Croll
[…]
2:39 AM Ticket #17815 (Many setGeometry errors → crash) created by chimerax-bug-report@…
[…]
12:12 AM Ticket #17814 (Crash in Qt event loop after opening/displaying MRC file) created by chimerax-bug-report@…
[…]

May 26, 2025:

9:41 PM Ticket #17813 (Building add_charge fails with metadata error) created by Greg Couch
Building the develop branch of ChimeraX from scratch fails with: […]
12:16 PM Ticket #17812 (Crash at exit) created by chimerax-bug-report@…
[…]
11:59 AM Ticket #17811 (Crash at exit) created by chimerax-bug-report@…
[…]
11:17 AM Ticket #17810 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]
11:01 AM Ticket #17809 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…
[…]
5:10 AM Ticket #17808 (Crash in graphics driver during Qt drawing) created by chimerax-bug-report@…
[…]
3:48 AM Ticket #17807 (Crash in python_instances_of_class saving session) created by chimerax-bug-report@…
[…]
2:43 AM Ticket #17806 (Crash moving window between screens) created by chimerax-bug-report@…
[…]
1:34 AM Ticket #17805 (Crash destroying OpenGL context on exit) created by chimerax-bug-report@…
[…]
1:32 AM Ticket #17804 (Crash in chem_group on Windows) created by chimerax-bug-report@…
[…]
1:24 AM Ticket #17803 (Crash in chem_group on Windows) created by chimerax-bug-report@…
[…]
12:28 AM Ticket #17802 (Crash on Mac waking from sleep) created by chimerax-bug-report@…
[…]

May 25, 2025:

7:10 PM Ticket #17801 (Crash at exit in Qt cleanup routines) created by chimerax-bug-report@…
[…]
6:59 PM Ticket #17800 (Bond rotations need to respond to bond addition/deletion) created by chimerax-bug-report@…
[…]
6:27 AM Ticket #17799 (Dead model in Find Cavities table) created by chimerax-bug-report@…
[…]
6:26 AM Ticket #17798 (Dead model in Find Cavities table) created by chimerax-bug-report@…
[…]
3:18 AM Ticket #17797 (Crash using open/save dialog) created by chimerax-bug-report@…
[…]
2:36 AM Ticket #17796 (AddH: More than 2 coplanar positions specified) created by chimerax-bug-report@…
[…]
Note: See TracTimeline for information about the timeline view.