Timeline



Feb 4, 2022:

6:28 PM Ticket #6088 (ISOLDE: add real-space map: structure is None) created by andrey.malyutin@…
[…]
6:27 PM Ticket #6087 (ISOLDE: swap equivalent atoms: Values array length 3 does not match ...) created by andrey.malyutin@…
[…]
3:19 PM Ticket #6086 (VR menus broken with Qt 6) created by goddard@…
[…]
2:59 PM Ticket #6085 (No QAbstractVideoSurface in Qt6) created by goddard@…
[…]
11:21 AM Ticket #6082 (Cannot save log session state: 'Log' object has no attribute 'page_source') closed by pett
duplicate: Fixing the log-start failure #6084 will fix this, so closing this ticket.
11:10 AM Ticket #6084 (Log fails to start: cannot import name 'ChimeraXHtmlView' from ...) created by gerwald_jogl@…
[…]
9:32 AM Ticket #6083 (CUDA/OpenCL errors: CUDA_ERROR_OUT_OF_MEMORY) created by zke@…
[…]
9:00 AM Ticket #6082 (Cannot save log session state: 'Log' object has no attribute 'page_source') created by gerwald_jogl@…
[…]
7:23 AM Ticket #6081 (Symmetry handler using dead structure) created by chimerax-bug-report@…
[…]
3:10 AM Ticket #6080 (Problem destroying status bar: wrapped C/C++ object of type QScreen ...) created by cristina.viola@…
[…]

Feb 3, 2022:

9:36 PM 2022-2-1 edited by Tom Goddard
(diff)
6:48 PM Ticket #6079 (Crash in event loop) created by pxxu@…
[…]
6:01 PM Ticket #6071 (Error in 'angle' command if atoms are linear) closed by pett
fixed: Hi Tony, Thanks for finding this. There was already code in there …
5:46 PM Ticket #6069 (Crash during surface calculation) closed by Tom Goddard
can't reproduce: Nothing in the crash report indicates what was going on. It shows …
5:21 PM Ticket #6074 (Crash reading HDF format) closed by Tom Goddard
can't reproduce: Crashed importing PyTables. The user had opened a PDB file 3j7h then …
4:24 PM Ticket #6073 (Crash adding "new frame" handler (enabling multitouch)) closed by Tom Goddard
can't reproduce: […] this is Python code registering a new frame handler to collect …
4:23 PM Ticket #6078 (Make crash reporting give better info when multiple ChimeraX instances ...) created by Tom Goddard
It seems that some crash reports have Python faulthandler logs showing …
3:55 PM Ticket #6077 (Crash removing dock widget from main window) created by gersede.maugars@…
[…]
2:38 PM Ticket #6076 (Crash during alphafold predict updating clip caps) created by chimerax-bug-report@…
[…]
2:26 PM Ticket #6075 ('None' in self.maps) created by jonny.flores12@…
[…]
2:21 PM NTTData edited by Elaine Meng
(diff)
2:17 PM NTTData edited by Elaine Meng
(diff)
2:13 PM NTTData edited by Elaine Meng
(diff)
1:56 PM NTTData edited by Elaine Meng
(diff)
1:19 PM NTTData edited by Elaine Meng
(diff)
11:20 AM DeveloperMeetings edited by Tom Ferrin
(diff)
10:59 AM Ticket #6068 (ISOLDE: cannot unpack non-iterable builtin_function_or_method object) closed by Tristan Croll
fixed: Fixed in 1.3.
10:45 AM Ticket #6072 ('DefaultApi' object has no attribute 'newer_versions') closed by Greg Couch
duplicate: Fixed by Zach
8:04 AM Ticket #6074 (Crash reading HDF format) created by chimerax-bug-report@…
[…]
5:57 AM Ticket #6073 (Crash adding "new frame" handler (enabling multitouch)) created by chimerax-bug-report@…
[…]
5:13 AM Ticket #6072 ('DefaultApi' object has no attribute 'newer_versions') created by chimerax-bug-report@…
[…]

Feb 2, 2022:

7:07 PM Ticket #6071 (Error in 'angle' command if atoms are linear) created by Tony Schaefer
[…]
5:33 PM Ticket #6070 (side view clip status not updated) closed by Tom Goddard
not a bug: The command "clip" creates a clip plane fixed in scene coordinates so …
5:29 PM Ticket #6070 (side view clip status not updated) created by pett
If I just do "clip", the the side view does not update the position …
4:14 PM Ticket #1704 (Implement full selection cascade) closed by pett
fixed: The "connected fragment" level of the selection hierarchy is …
2:50 PM ChangeLog edited by Elaine Meng
(diff)
2:49 PM ChangeLog edited by Elaine Meng
(diff)
1:27 PM Ticket #6069 (Crash during surface calculation) created by cesar.menor@…
[…]
1:14 PM Ticket #6068 (ISOLDE: cannot unpack non-iterable builtin_function_or_method object) created by chimerax-bug-report@…
[…]
12:18 PM Ticket #6066 ('DefaultApi' object has no attribute 'newer_versions') closed by Zach Pearson
fixed
11:28 AM Ticket #6065 (Crash in return statement) closed by Tom Goddard
can't reproduce: Appears to have crashed at startup, log contains no commands […] …
11:25 AM Ticket #6064 (Graphics errors after selection clear, macOS display scale confusion) closed by Tom Goddard
can't reproduce: OpenGL errors in glClear(). Mac laptop with Intel and AMD GPUs. …
11:20 AM Ticket #6061 (Crash in event loop / font machinery / saving session) closed by Tom Goddard
can't reproduce: Crash in native macOS font handling routines (CAImageQueuePing_). …
11:14 AM Ticket #6060 (Graphics driver crash, macOS 10.15.7, Intel Iris Graphics 540) closed by Tom Goddard
nonchimerax: Apple graphics driver crash.
11:02 AM Ticket #6067 (Update RCSB biounit fetch to new URLs if needed) created by Tom Goddard
The RCSB is updating their mmCIF assembly files and changing the ftp …
9:48 AM Ticket #6062 (Crash in event loop) closed by pett
can't reproduce
8:54 AM Ticket #6066 ('DefaultApi' object has no attribute 'newer_versions') created by Elaine Meng
[…]
6:40 AM Ticket #6065 (Crash in return statement) created by chimerax-bug-report@…
[…]
5:36 AM Ticket #6064 (Graphics errors after selection clear, macOS display scale confusion) created by chimerax-bug-report@…
[…]
2:07 AM Ticket #6063 (ISOLDE: various errors) created by jean-marc.jeckelmann@…
[…]

Feb 1, 2022:

11:38 PM Ticket #6062 (Crash in event loop) created by chimerax-bug-report@…
[…]
6:49 PM Ticket #6061 (Crash in event loop / font machinery / saving session) created by chimerax-bug-report@…
[…]
5:58 PM Ticket #5811 (Add Charge: handle UNK as templated if appropriate) closed by pett
fixed: Now treats polymeric UNK like ALA, and sets CB charge to 0.0
4:49 PM Ticket #2934 (Adding coord sets) closed by pett
fixed: add_coordsets() now check against previous coordinate set sizes (if …
3:44 PM Ticket #6060 (Graphics driver crash, macOS 10.15.7, Intel Iris Graphics 540) created by chimerax-bug-report@…
[…]
11:10 AM Ticket #6057 (Graphics driver crash, macOS 10.15.7, AMD Radeon Pro 560X) closed by Tom Goddard
nonchimerax: The Qt window toolkit that ChimeraX uses was trying to repaint part of …
10:05 AM 2022-2-1 created by Tom Goddard
10:04 AM DeveloperMeetings edited by Tom Goddard
(diff)
9:11 AM Ticket #6059 (Crash restoring a session in msgpack_deserialize()) closed by pett
can't reproduce: Probable garbage-collection crash
9:03 AM Ticket #6056 (Crash in garbage collection during new-object allocation) closed by pett
duplicate
9:02 AM Ticket #6055 (Unknown crash) closed by pett
can't reproduce
7:35 AM Ticket #6059 (Crash restoring a session in msgpack_deserialize()) created by chimerax-bug-report@…
[…]
7:05 AM Ticket #6058 (Session restore: invalid load key, '\x04') created by william.james@…
[…]
7:02 AM Ticket #6057 (Graphics driver crash, macOS 10.15.7, AMD Radeon Pro 560X) created by drorn@…
[…]
6:11 AM Ticket #6056 (Crash in garbage collection during new-object allocation) created by chimerax-bug-report@…
[…]
6:03 AM Ticket #6055 (Unknown crash) created by chimerax-bug-report@…
[…]

Jan 31, 2022:

10:53 PM Ticket #6054 (ChimeraX won't start on pre-installed Windows 11) created by kai.zhang.1@…
[…]
6:36 PM Ticket #6053 (MemoryError restoring session) created by chimerax-bug-report@…
[…]
1:59 PM Ticket #6049 (Clipping plane problem with multiple positions) closed by Tom Goddard
fixed: Fixed. There were 3 separate bugs with clip caps on instanced …
1:35 PM Ticket #6046 (Crash destroying open dialog (no Python log)) closed by pett
can't reproduce: Hi James, Thanks for the information. So it's an infrequent but not …
1:09 PM Ticket #6040 (Stack overflow in seq_canvas.py making SeqBlock instances) closed by pett
can't reproduce: Thought maybe I could reproduce it by making the viewer extremely …
11:11 AM Ticket #6052 (Crash in ssl at return statement at startup) closed by Tom Goddard
can't reproduce
11:05 AM Ticket #6048 (Crash in return statement) closed by Tom Goddard
can't reproduce: […] In Python code […] Have 4 crashes in return statements on …
11:02 AM Ticket #6047 (Crash in return statement) closed by Tom Goddard
can't reproduce: […] Python code […] where p is a QPoint. Seems likely to be …
10:53 AM Ticket #6044 (Crash in return statement) closed by Tom Goddard
can't reproduce: […] Python code at line 95 returns a boolean value […] Maybe …
10:46 AM Ticket #6051 (Cannot write PDB file) closed by pett
not a bug: Newer versions report OSErrors as messages rather than tracebacks
10:44 AM Ticket #6043 (Unknown crash after invalid "volume appearance") closed by Tom Goddard
can't reproduce: No useful stack trace info. Very likely not caused by any of the …
9:57 AM Ticket #6045 (Crash opening BILD file) closed by Greg Couch
can't reproduce: Need a reproducible case.
5:03 AM Ticket #6052 (Crash in ssl at return statement at startup) created by hamine.oliveira@…
[…]
4:04 AM Ticket #6051 (Cannot write PDB file) created by chimerax-bug-report@…
[…]
2:40 AM Ticket #6050 (ISOLDE vs. submodels) created by esa-pekka.kumpula@…
[…]
2:33 AM Ticket #6049 (Clipping plane problem with multiple positions) created by Tristan Croll
[…] mpro_crystal_7jkv.cxs

Jan 30, 2022:

6:37 AM Ticket #6048 (Crash in return statement) created by chimerax-bug-report@…
[…]

Jan 29, 2022:

6:51 PM Ticket #6047 (Crash in return statement) created by chimerax-bug-report@…
[…]
1:43 PM Ticket #6046 (Crash destroying open dialog (no Python log)) created by James.Chang@…
[…]
12:14 PM Ticket #6045 (Crash opening BILD file) created by chimerax-bug-report@…
[…]
10:05 AM Ticket #6044 (Crash in return statement) created by chimerax-bug-report@…
[…]

Jan 28, 2022:

10:38 PM Ticket #6043 (Unknown crash after invalid "volume appearance") created by chimerax-bug-report@…
[…]
8:12 PM Ticket #6042 (Unknown crash) created by rajib19@…
[…]
7:10 PM Ticket #6041 (Save TIFF stack: ImageJ hyperstack shape and axes do not match) closed by Tom Goddard
duplicate
6:33 PM Ticket #6039 (Modeller: 'target_name' referenced before assignment) closed by Tom Goddard
duplicate
5:59 PM Ticket #6037 (Crash at startup, no stack info, "VM - Object is not alive") closed by Tom Goddard
can't reproduce
5:51 PM Ticket #6036 (Crash in Qt event loop after "view sel" command, 10 year old graphics, ...) closed by Tom Goddard
can't reproduce: Maybe a graphics driver crash. Log was hundreds of commands long. No …
11:45 AM Ticket #6041 (Save TIFF stack: ImageJ hyperstack shape and axes do not match) created by chimerax-bug-report@…
[…]
7:00 AM Ticket #6040 (Stack overflow in seq_canvas.py making SeqBlock instances) created by chimerax-bug-report@…
[…]
6:58 AM Ticket #6039 (Modeller: 'target_name' referenced before assignment) created by isha.raj@…
[…]
5:22 AM Ticket #6038 (ChimeraX Log panel broken on Fedora) created by paulaj@…
[…]
4:55 AM Ticket #6037 (Crash at startup, no stack info, "VM - Object is not alive") created by zhangxiaofeng@…
[…]

Jan 27, 2022:

11:07 PM ChangeLog edited by Greg Couch
(diff)
8:46 PM Ticket #6036 (Crash in Qt event loop after "view sel" command, 10 year old graphics, ...) created by chimerax-bug-report@…
[…]
6:52 PM Ticket #6035 (OpenGL out of memory error, then crash several commands later on Windows) closed by Tom Goddard
can't reproduce: This error "Fatal Python error: Aborted" is not the usual "access …
5:14 PM Features edited by Tom Goddard
(diff)
3:35 PM 2022-1-27 edited by Tom Goddard
(diff)
3:26 PM Dev2022-1-27 edited by Tom Goddard
(diff)
3:26 PM Dev2022-2-10 created by Tom Goddard
3:25 PM DeveloperMeetings edited by Tom Goddard
(diff)
3:24 PM Dev2022-1-27 edited by Tom Goddard
(diff)
3:22 PM Dev2022-1-27 edited by Tom Goddard
(diff)
3:07 PM Ticket #6033 (Crash in show_surface_clip_caps()) closed by Tom Goddard
can't reproduce: […] which is code […] that is trying to recompute clip caps. …
3:01 PM Ticket #6030 (Crash in ctypes cast method or possibly garbage collection) closed by Tom Goddard
can't reproduce: […] which is a ctypes casting function […] This is calling …
2:06 PM Ticket #6035 (OpenGL out of memory error, then crash several commands later on Windows) created by chimerax-bug-report@…
[…]
1:54 PM Ticket #6034 (Jupyter notebooks) created by Tristan Croll
[…]
12:05 PM 2022-1-27 edited by Tom Ferrin
(diff)
9:41 AM Ticket #6031 (Modeller: local variable 'target_name' referenced before assignment) closed by pett
duplicate
9:22 AM Ticket #6033 (Crash in show_surface_clip_caps()) created by chimerax-bug-report@…
[…]
7:19 AM Ticket #6032 (Error restoring session: blastprotein: __init__() missing 1 required ...) created by chimerax-bug-report@…
[…]
3:56 AM Ticket #6031 (Modeller: local variable 'target_name' referenced before assignment) created by chimerax-bug-report@…
[…]

Jan 26, 2022:

11:52 PM Ticket #6030 (Crash in ctypes cast method or possibly garbage collection) created by chimerax-bug-report@…
[…]
5:47 PM Ticket #6028 (Define attribute: local variable 'lnum' referenced before assignment) closed by pett
fixed: Hi Gloria, Thanks for reporting this problem. Looking at the source …
4:44 PM Ticket #6029 (Allow alphafold sequences argument to handle subsequences from a ...) created by Tom Goddard
The SequencesArg in the atomic bundle can be specified with a …
4:16 PM Ticket #6026 (Incomplete retrieval of AlphaFold prediction) closed by Tom Goddard
nonchimerax: The error you report in ChimeraX running AlphaFold
4:08 PM Ticket #6028 (Define attribute: local variable 'lnum' referenced before assignment) created by gloglita@…
[…]
4:03 PM Ticket #6025 (Multiple graphics errors) closed by Tom Goddard
duplicate: Duplicate of #6024
4:00 PM Ticket #6024 (Multiple graphics errors) closed by Tom Goddard
nonchimerax: Intel OpenGL driver problem on Windows. Many OpenGL errors at startup …
3:57 PM Ticket #6023 (Crash running multiple AlphaFold predictions) closed by Tom Goddard
can't reproduce: Appears to be another QWebEngineView related crash. Crash looks like …
2:00 PM Ticket #6027 (Unknown crash) created by rruiz@…
[…]
1:34 PM Ticket #6026 (Incomplete retrieval of AlphaFold prediction) created by thomas.lenz@…
[…]
11:38 AM Ticket #6022 (Crash in 'return' statement (garbage collection?)) closed by Tom Goddard
can't reproduce: Thread 0x000041a0 (most recent call first): File "C:\Program …
11:32 AM Ticket #6019 (Crash in 'return' statement (garbage collection?)) closed by Tom Goddard
can't reproduce
11:14 AM Ticket #6020 (Graphics driver crash, macOS 10.15.7, Intel Iris Plus Graphics 645, ...) closed by Tom Goddard
nonchimerax: Apple graphics driver crash. Two displays.
11:12 AM Ticket #6018 (Graphics driver crash, macOS 11.6.2, Intel Iris Plus Graphics) closed by Tom Goddard
nonchimerax: Apple graphics driver crash. More details on the ChimeraX …
10:58 AM Ticket #6025 (Multiple graphics errors) created by chimerax-bug-report@…
[…]
10:27 AM Ticket #6024 (Multiple graphics errors) created by chimerax-bug-report@…
[…]
10:24 AM Ticket #6023 (Crash running multiple AlphaFold predictions) created by chimerax-bug-report@…
[…]
9:17 AM Ticket #6021 (Crash removing dock widget from main window) closed by pett
can't reproduce
5:42 AM Ticket #6022 (Crash in 'return' statement (garbage collection?)) created by chimerax-bug-report@…
[…]

Jan 25, 2022:

8:28 PM Ticket #6021 (Crash removing dock widget from main window) created by chimerax-bug-report@…
[…]
5:43 PM Ticket #6012 (Crash in rapid_access_shown at startup on Linux) closed by Tom Goddard
duplicate: The crash is the usual rapid_access_shown on Linux at startup. …
3:54 PM Ticket #6020 (Graphics driver crash, macOS 10.15.7, Intel Iris Plus Graphics 645, ...) created by chimerax-bug-report@…
[…]
3:41 PM Ticket #6019 (Crash in 'return' statement (garbage collection?)) created by chimerax-bug-report@…
[…]
1:55 PM Ticket #6018 (Graphics driver crash, macOS 11.6.2, Intel Iris Plus Graphics) created by benjamin.buchmuller@…
[…]
12:05 PM Ticket #6014 (Selection outline not rendered) closed by Tom Goddard
nonchimerax: I believe this is an Apple graphics driver bug specific to your …
11:36 AM Ticket #3889 (Select→Chain organization not preserved through session save/restore) closed by pett
fixed: Apparently fixed by other changes.
10:46 AM Ticket #6013 (Crash in event loop) closed by pett
can't reproduce
10:40 AM Ticket #5279 (Long running blastprotein job did not return) closed by Zach Pearson
fixed
1:45 AM Ticket #6017 (openmm.OpenMMException: Error initializing context: clCreateContext) created by cgalicia@…
[…]

Jan 24, 2022:

11:28 PM Ticket #6016 (Blast protein error: 'DefaultApi' object has no attribute 'job_id') closed by Zach Pearson
fixed
6:23 PM Ticket #5984 (Check for newer versions: 'DefaultApi' object has no attribute ...) closed by Zach Pearson
fixed: DefaultAPI error is no longer in toolshed but in BlastProtein.
6:13 PM Ticket #6016 (Blast protein error: 'DefaultApi' object has no attribute 'job_id') created by goddard@…
[…]
5:58 PM Ticket #6011 (Map fitting does not log command) closed by Tom Goddard
fixed: Fixed. Made Fit in Map panel log the equivalent fitmap command. …
5:50 PM Ticket #6015 (Old bundle installed) created by fred.mast@…
[…]
5:49 PM Ticket #5893 (Blast results problem: 'NoneType' object has no attribute 'split') closed by Zach Pearson
duplicate: Fixed by …
5:44 PM Ticket #5999 (Internal Server Error fetching Toolshed information) closed by Zach Pearson
fixed: Monkeypatch of backend caused unrecoverable error; this has been fixed …
5:43 PM Ticket #6000 (Internal Server Error fetching Toolshed information) closed by Zach Pearson
duplicate: Duplicates #5999.
5:41 PM Ticket #5995 (Error parsing Blast results) closed by Zach Pearson
fixed: Root cause was the same as #5998; apache could not write into the …
5:40 PM Ticket #5998 (Alphafold search broken: 500 Internal Server Error) closed by Zach Pearson
fixed: apache could not write into the directory it was set to use to store …
5:08 PM Ticket #6001 (Problems specifying AlphaFold arguments) closed by Tom Goddard
fixed: Fixed the other problem you asked about "." gap characters when using …
4:48 PM Ticket #6014 (Selection outline not rendered) created by info@…
[…]
4:01 PM Ticket #4899 (RFE: if "typed only" pref is off, command history should list ...) closed by pett
fixed: Okay, cxc file commands appear in history if "typed only" is false. …
3:22 PM Ticket #6013 (Crash in event loop) created by chimerax-bug-report@…
[…]
2:41 PM ChangeLog edited by Elaine Meng
(diff)
12:29 PM Ticket #6010 (Crash in numpy saving image) closed by Tom Goddard
can't reproduce: Thread 0x00004fb0 (most recent call first): File "C:\Program …
12:23 PM Ticket #6012 (Crash in rapid_access_shown at startup on Linux) created by chimerax-bug-report@…
[…]
12:22 PM Ticket #6008 (Problem opening DICOM data: object of type 'NoneType' has no len()) closed by Tom Goddard
fixed: Fixed. Code will now sort by TemporalPositionIdentifier instead of …
11:40 AM Ticket #6007 (Crash showing status after opening session) closed by Tom Goddard
nonchimerax: Crashed with "access violation" making opengl context in …
11:33 AM Ticket #6005 (Crash creating ribbon graphics, possibly during simulation) closed by Tom Goddard
can't reproduce: Duplicate of #6004. Appears to be graphics driver crash.
11:31 AM Ticket #6004 (Crash in graphics driver deleting ribbon graphics, possibly during ...) closed by Tom Goddard
nonchimerax: Crash in graphics driver while removing a ribbon in this ChimeraX …
11:26 AM Ticket #6002 (Graphics drive crash, macOS 10.15.5, Intel Iris Plus Graphics 640) closed by Tom Goddard
nonchimerax: Apple graphics driver crash. ChimeraX was using 25 GB of memory.
11:18 AM Ticket #6009 (Problem opening DICOM data: object of type 'NoneType' has no len()) closed by pett
duplicate
11:11 AM Ticket #6006 (Crash in event loop (bad memory access)) closed by pett
can't reproduce
10:50 AM Ticket #6011 (Map fitting does not log command) created by jaremko@…
[…]
10:39 AM Ticket #6003 (Qt crash during exit) closed by pett
duplicate
2:26 AM Ticket #6010 (Crash in numpy saving image) created by chimerax-bug-report@…
[…]

Jan 23, 2022:

2:56 PM Ticket #6009 (Problem opening DICOM data: object of type 'NoneType' has no len()) created by tskillman@…
[…]
2:55 PM Ticket #6008 (Problem opening DICOM data: object of type 'NoneType' has no len()) created by tskillman@…
[…]
7:31 AM Ticket #6007 (Crash showing status after opening session) created by chimerax-bug-report@…
[…]
1:07 AM Ticket #6006 (Crash in event loop (bad memory access)) created by chimerax-bug-report@…
[…]

Jan 22, 2022:

6:45 PM Ticket #6005 (Crash creating ribbon graphics, possibly during simulation) created by chimerax-bug-report@…
[…]
6:30 PM Ticket #6004 (Crash in graphics driver deleting ribbon graphics, possibly during ...) created by chimerax-bug-report@…
[…]
2:16 PM Ticket #6003 (Qt crash during exit) created by chimerax-bug-report@…
[…]
12:59 PM Ticket #6002 (Graphics drive crash, macOS 10.15.5, Intel Iris Plus Graphics 640) created by chimerax-bug-report@…
[…]
9:51 AM Ticket #6001 (Problems specifying AlphaFold arguments) created by martti.tolvanen@…
[…]
7:06 AM Ticket #6000 (Internal Server Error fetching Toolshed information) created by martti.tolvanen@…
[…]
5:27 AM Ticket #5999 (Internal Server Error fetching Toolshed information) created by paula_teeuwen@…
[…]

Jan 21, 2022:

4:18 PM Ticket #5989 (Error saving supersampled image after showing Side View) closed by Tom Goddard
can't reproduce: Bug report says user had just the retina display of this Mac laptop. …
4:11 PM Ticket #5990 (Qt crash during exit) closed by Tom Goddard
duplicate: ChimeraX crashed when it was quitting. This is a bug in the PyQt
4:08 PM Ticket #5994 (Crash during AlphaFold prediction) closed by Tom Goddard
duplicate: Thread 0x000023fc (most recent call first): File "C:\Program …
4:01 PM Ticket #5997 (Crazy silhouettes) closed by Tom Goddard
nonchimerax: This is probably a bug in your graphics driver. Your specific Mac …
3:49 PM Ticket #5993 (Crash updating clip caps) closed by Tom Goddard
can't reproduce: Made new ticket for earlier alphafold search error #5998
3:40 PM Ticket #5998 (Alphafold search broken: 500 Internal Server Error) created by goddard@…
[…]
3:34 PM Ticket #5996 (Crash getting ring information) closed by pett
duplicate: Hi Yen-Li, Unfortunately, the only way to avoid this crash for …
3:28 PM Ticket #5992 (Crash creating opengl context while loading toolshed info) closed by Tom Goddard
can't reproduce: There are two threads in this crash report and the "current" thread is …
3:08 PM Ticket #5997 (Crazy silhouettes) created by siyuchen2021@…
[…] Ku_1JEY.tif
2:51 PM Ticket #5996 (Crash getting ring information) created by yen-li.li@…
[…]
2:46 PM Ticket #5995 (Error parsing Blast results) created by dylancarman561@…
[…]
2:32 PM Ticket #5987 (AlphaFold prediction with Qt 6: 'QWebEngineDownloadRequest' object has ...) closed by Tom Goddard
fixed: Fixed. Made separate qt 5 and qt 6 download code for alphafold predict.
1:26 PM Ticket #5994 (Crash during AlphaFold prediction) created by chimerax-bug-report@…
[…]
12:15 PM Ticket #5993 (Crash updating clip caps) created by chimerax-bug-report@…
[…]
9:18 AM Ticket #5992 (Crash creating opengl context while loading toolshed info) created by chimerax-bug-report@…
[…]
9:16 AM Ticket #5988 (Crash showing main window) closed by pett
can't reproduce
9:07 AM Ticket #5983 (various errors) closed by pett
duplicate: Seems like all these errors are moot in 1.3
9:04 AM Ticket #5982 (Crash reading mmCIF file) closed by pett
can't reproduce
9:02 AM Ticket #5991 (cross-eyed stereo) created by hps@…
from Peter Speilmann registration comment: "cross-eyed stero would be …
8:10 AM Ticket #5990 (Qt crash during exit) created by jyassa@…
[…]
6:57 AM Ticket #5989 (Error saving supersampled image after showing Side View) created by chimerax-bug-report@…
[…]
5:12 AM Ticket #5988 (Crash showing main window) created by chimerax-bug-report@…
[…]

Jan 20, 2022:

10:58 PM Ticket #5986 (Bug reporter broken: error in new locale.getdefaultlocale() code) closed by Greg Couch
fixed: Fixed. See https://bugs.python.org/issue18378 for a discussion of …
10:32 PM Ticket #5987 (AlphaFold prediction with Qt 6: 'QWebEngineDownloadRequest' object has ...) created by Tom Goddard
Could not report this with bug reporter since it is broken. Bug on …
10:24 PM Ticket #5986 (Bug reporter broken: error in new locale.getdefaultlocale() code) created by Tom Goddard
Bug reporter has been broken on Mac for the last 16 days in daily …
10:23 PM Ticket #5985 (Download page Ubuntu install command is wrong) created by Tom Goddard
The ChimeraX daily build Ubuntu 20.04 install command listed on the …
10:14 PM Ticket #5984 (Check for newer versions: 'DefaultApi' object has no attribute ...) created by goddard@…
[…]
6:09 PM Dev2022-1-27 created by Tom Goddard
6:07 PM 2022-1-27 created by Tom Goddard
6:06 PM DeveloperMeetings edited by Tom Goddard
(diff)
6:05 PM 2022-1-20 edited by Tom Goddard
(diff)
5:53 PM Ticket #5972 (Crash setting window size during session restore) closed by Tom Goddard
can't reproduce: ChimeraX set the window size when opening a session and was then …
5:48 PM Ticket #5983 (various errors) created by chimerax-bug-report@…
[…]
5:38 PM Ticket #5978 (Crash in _mouse_buttons_down) closed by Tom Goddard
can't reproduce: […] Line 519 in mousemodes.py […] Opened a session with some …
3:10 PM Ticket #5982 (Crash reading mmCIF file) created by chimerax-bug-report@…
[…]
2:43 PM Ticket #5966 (Crash destroying open dialog) closed by pett
can't reproduce: Hi James, Thanks for getting back to me. Unfortunately, that's still …
2:23 PM Ticket #5977 (ISOLDE: KeyError in find_glycan_template_name_and_link) closed by Tristan Croll
fixed: Long-since fixed. Upshot is that the user has an …
2:21 PM NTTData edited by Tom Goddard
(diff)
2:17 PM Ticket #5976 (REST error contacting Toolshed) closed by pett
fixed: Hi Bharath, Thanks for reporting this problem. It was an issue with …
2:11 PM Ticket #5970 (REST error contacting Toolshed) closed by Greg Couch
duplicate
2:08 PM Ticket #5981 (Crash after X11 connection broke) created by chimerax-bug-report@…
[…]
2:02 PM NTTData edited by Elaine Meng
(diff)
2:02 PM NTTData edited by Elaine Meng
(diff)
1:57 PM NTTData edited by Elaine Meng
(diff)
1:54 PM Ticket #5973 (Check for new version: name '_getuser' is not defined) closed by Greg Couch
fixed: Fixed in the current daily build.
1:36 PM NTTData edited by Elaine Meng
(diff)
1:03 PM Ticket #5975 (REST error contacting Toolshed) closed by pett
duplicate
12:46 PM Ticket #5971 (REST error contacting Toolshed) closed by pett
duplicate
12:31 PM Ticket #5950 (Problem installing Chimera 1.3 on Ubuntu 18.04) closed by Greg Couch
can't reproduce: Sorry, I just tried this on Ubuntu 18.04, and it installed without any …
12:21 PM Ticket #5980 (Unknown crash) created by cuncun.qiao@…
[…]
12:20 PM Ticket #5979 (ChimeraX bug report submission) closed by Zach Pearson
fixed: Should now correctly fail with {{{{"title": "Missing parameter", …
12:17 PM 2022-1-20 edited by Tom Ferrin
(diff)
12:02 PM 2022-1-20 edited by Tom Ferrin
(diff)
11:59 AM Ticket #5979 (ChimeraX bug report submission) created by Greg Couch
[…]
11:58 AM 2022-1-20 edited by Tom Ferrin
(diff)
11:54 AM 2022-1-20 edited by Tom Ferrin
(diff)
11:28 AM 2022-1-20 edited by Tom Ferrin
(diff)
11:25 AM 2022-1-20 edited by Tom Ferrin
(diff)
11:22 AM 2022-1-20 edited by Tom Ferrin
(diff)
11:18 AM 2022-1-20 edited by Tom Ferrin
(diff)
10:35 AM Ticket #5978 (Crash in _mouse_buttons_down) created by chimerax-bug-report@…
[…]
9:23 AM Ticket #5977 (ISOLDE: KeyError in find_glycan_template_name_and_link) created by chimerax-bug-report@…
[…]
9:21 AM Ticket #5976 (REST error contacting Toolshed) created by bsakshib@…
[…]
9:11 AM Ticket #5975 (REST error contacting Toolshed) created by chimerax-bug-report@…
[…]
8:53 AM Ticket #5974 (REST error contacting Toolshed) created by chimerax-bug-report@…
[…]
5:21 AM Ticket #5973 (Check for new version: name '_getuser' is not defined) created by vijayalphafold@…
[…]
4:15 AM Ticket #5972 (Crash setting window size during session restore) created by kelvin.lau@…
[…]
3:44 AM Ticket #5971 (REST error contacting Toolshed) created by chimerax-bug-report@…
[…]
1:43 AM Ticket #5970 (REST error contacting Toolshed) created by Tristan Croll
[…]

Jan 19, 2022:

11:15 PM Ticket #5969 (Crash in event loop) created by cuncun.qiao@…
[…]
6:48 PM Ticket #5968 (Edwin Rojas-Unable to access toolbox to download) closed by pett
fixed: Hi Edwin, I'm not really sure how to do *just* minimization in ISOLDE …
5:59 PM Ticket #5968 (Edwin Rojas-Unable to access toolbox to download) created by emrojas@…
[…] Capture.PNG
5:44 PM Ticket #5965 (Crash in event loop after swapaa) closed by pett
can't reproduce
5:40 PM Ticket #5963 (Toolshed down) closed by pett
fixed: The Toolshed is back up now.
3:33 PM Ticket #5967 (add independent-rotation option to turn, roll commands) created by Elaine Meng
now that we have a "rotate independent" mouse mode, would be nice to …
3:22 PM ChangeLog edited by Elaine Meng
(diff)
2:12 PM Ticket #5966 (Crash destroying open dialog) created by James.Chang@…
[…]
2:07 PM Ticket #5925 (Swapaa: name 'critera' is not defined) closed by pett
fixed: 'criteria' was misspelled
12:01 PM Ticket #5965 (Crash in event loop after swapaa) created by chimerax-bug-report@…
[…]
11:42 AM Ticket #5962 (Graphics driver crash, macOS 11.5.2, Intel Iris Pro) closed by Tom Goddard
nonchimerax: Apple graphics driver crash. Many Gbyte size maps open, ChimeraX …
11:31 AM Ticket #5955 (Crash removing dock widget from main window during AlphaFold prediction) closed by Tom Goddard
can't reproduce: I put in some code to better protect against tool window dock widgets …
11:10 AM Ticket #5964 (Optimizing ISOLDE map zoning using JAX) created by Tristan Croll
[…]
10:32 AM Ticket #5960 (Qt crash during exit) closed by pett
duplicate
10:31 AM Ticket #5959 (Restoring session: invalid load key) closed by pett
duplicate
10:22 AM Ticket #5958 (Crash checking if change-tracker changed after 'save' command) closed by pett
can't reproduce: My thinking now is that it's ctypes temporarily being unable to access …
9:12 AM Ticket #5956 (Crash getting ring information for nucleotides) closed by pett
fixed: Hi Yen-Li, Thanks for reporting this problem. We have recently put …
9:01 AM Ticket #5953 (Crash after H-bonds shown) closed by pett
can't reproduce: Wasn't the first time the hbonds command was used in the session.
8:41 AM Ticket #5963 (Toolshed down) created by earias@…
[…]
8:25 AM Ticket #5962 (Graphics driver crash, macOS 11.5.2, Intel Iris Pro) created by chimerax-bug-report@…
[…]
3:48 AM Ticket #5961 (Crash in OpenMM getState) created by chimerax-bug-report@…
[…]
3:40 AM Ticket #5960 (Qt crash during exit) created by chimerax-bug-report@…
[…]
2:47 AM Ticket #5959 (Restoring session: invalid load key) created by chimerax-bug-report@…
[…]
2:07 AM Ticket #5958 (Crash checking if change-tracker changed after 'save' command) created by chimerax-bug-report@…
[…]
12:52 AM Ticket #5957 (Ramachandran plot accessing deleted widgets) created by DLMLEN001@…
[…]

Jan 18, 2022:

11:45 PM Ticket #5932 (Add independent center of rotation mouse mode) closed by Tom Goddard
fixed: I added an independent rotation mouse mode that is enabled by the tile …
11:42 PM Ticket #2495 (RFE: set independent) closed by Tom Goddard
fixed: Fixed. I made the tile command switch to a new independent rotation …
9:22 PM Ticket #5956 (Crash getting ring information for nucleotides) created by yen-li.li@…
[…]
7:52 PM Ticket #5955 (Crash removing dock widget from main window during AlphaFold prediction) created by sbodapati@…
[…]
7:27 PM Ticket #5954 (Add Phenix douse tool to add waters) created by Tom Goddard
As part of the Phenix R24 grant we will be allowing ChimeraX to call …
6:41 PM Ticket #5953 (Crash after H-bonds shown) created by chimerax-bug-report@…
[…]
6:41 PM Ticket #5952 (Render By Attribute tool) created by martti.tolvanen@…
Implement equivalent to Chimera's Render By Attribute tool.
5:41 PM Ticket #5951 (Put Qt fatal message output into bug reports) created by Tom Goddard
We see many crashes on Windows in the Qt event loop. Maybe we would …
5:27 PM Ticket #5944 (Crash updating clip caps) closed by Tom Goddard
can't reproduce: Hid and showed model in a multimodel PDB file. […] Was checking or …
5:19 PM Ticket #5943 (Crash after/during AlphaFold predict) closed by Tom Goddard
can't reproduce: The AlphaFold prediction had not finished -- it logs a message when it …
4:53 PM Ticket #5941 (Crash checking if clip planes changed after 'select' command) closed by Tom Goddard
can't reproduce: Maybe it is a graphics driver crash. On Windows the Python …
4:44 PM Ticket #5949 (Cannot open new session) closed by pett
not a bug: Hi Chitra, For the most part you cannot open a session made by a …
4:41 PM ChangeLog edited by pett
(diff)
4:31 PM Ticket #5938 (Graphics driver crash, macOS 10.15.7, Intel Iris Graphics 6100) closed by Tom Goddard
nonchimerax: Apple graphics driver crash. Graphics window had just been resized.
4:30 PM Ticket #5950 (Problem installing Chimera 1.3 on Ubuntu 18.04) created by man6ny@…
[…]
4:15 PM Ticket #5945 (Crash parsing atom spec) closed by pett
duplicate
2:25 PM Ticket #5949 (Cannot open new session) created by chariharan@…
[…]
1:54 PM Ticket #5936 (Crash after volume level command) closed by Tom Goddard
can't reproduce: Crash appears to be in Qt event loop. But actually there are about 15 …
1:49 PM Ticket #5942 (Crash checking change tracking after closing models) closed by pett
can't reproduce
12:12 PM Ticket #5939 ("Fake" attribute state manager lacks some methods) closed by pett
duplicate
11:59 AM Ticket #5934 (Crash updating volume drawings after models close) closed by Tom Goddard
can't reproduce: Thread 0x00002f34 (most recent call first): File "C:\Program …
11:42 AM Ticket #5931 (Graphics driver crash, macOS 11.6.1, Intel UHD Graphics 630) closed by Tom Goddard
duplicate: Duplicate of #5930. MacBook Pro using ultrawide external display, …
11:39 AM Ticket #5930 (Graphics driver crash, macOS 11.6.1, Intel UHD Graphics 630) closed by Tom Goddard
nonchimerax: Apple graphics driver crash.
11:32 AM Ticket #5948 (Make zoom command move clip planes) closed by Tom Goddard
fixed: Fixed. Made zoom command move near/far clip planes if they are enabled.
11:30 AM Ticket #5948 (Make zoom command move clip planes) created by meng@…
From: Elaine Meng Subject: view/zoom bug? Date: January 16, 2022 at …
11:11 AM Ticket #5937 (Crash in garbage collection during new-object allocation) closed by pett
duplicate
11:08 AM Ticket #5935 (Crash showing Rapid Access at startup) closed by pett
can't reproduce
11:02 AM Ticket #5933 (Check for new version: name '_getuser' is not defined) closed by pett
duplicate
10:17 AM 2022-1-20 created by Tom Goddard
10:15 AM DeveloperMeetings edited by Tom Goddard
(diff)
9:20 AM Ticket #5947 (Crash in GL.glUniform1f) created by nxb318@…
[…]
9:06 AM Ticket #5946 (Crash after opening session containing volumes) created by nxb318@…
[…]
8:03 AM Ticket #5945 (Crash parsing atom spec) created by chimerax-bug-report@…
[…]
6:02 AM Ticket #5944 (Crash updating clip caps) created by chimerax-bug-report@…
[…]
4:38 AM Ticket #5943 (Crash after/during AlphaFold predict) created by hamine.oliveira@…
[…]
2:55 AM Ticket #5942 (Crash checking change tracking after closing models) created by chimerax-bug-report@…
[…]

Jan 17, 2022:

10:40 PM Ticket #5743 (Quick Start Guide: Linux Python missing bz2 module) closed by Greg Couch
fixed: This is fixed in the post 1.3 daily build. Our CentOS build …
7:56 PM Ticket #5941 (Crash checking if clip planes changed after 'select' command) created by chimerax-bug-report@…
[…]
7:44 PM Ticket #5940 (SMILES server-connection failure) created by cyeow1@…
[…]
2:21 PM Ticket #5939 ("Fake" attribute state manager lacks some methods) created by chimerax-bug-report@…
[…]
12:55 PM Ticket #5938 (Graphics driver crash, macOS 10.15.7, Intel Iris Graphics 6100) created by chimerax-bug-report@…
[…]
11:08 AM Ticket #5937 (Crash in garbage collection during new-object allocation) created by chimerax-bug-report@…
[…]
8:33 AM Ticket #5936 (Crash after volume level command) created by chimerax-bug-report@…
[…]
2:38 AM Ticket #5935 (Crash showing Rapid Access at startup) created by chimerax-bug-report@…
[…]
2:17 AM Ticket #5934 (Crash updating volume drawings after models close) created by chimerax-bug-report@…
[…]

Jan 15, 2022:

4:10 AM Ticket #5933 (Check for new version: name '_getuser' is not defined) created by chimerax-bug-report@…
[…]

Jan 14, 2022:

6:25 PM Ticket #5932 (Add independent center of rotation mouse mode) created by juliannahan@…
[…]
5:20 PM Ticket #5931 (Graphics driver crash, macOS 11.6.1, Intel UHD Graphics 630) created by chimerax-bug-report@…
[…]
5:08 PM Ticket #5930 (Graphics driver crash, macOS 11.6.1, Intel UHD Graphics 630) created by chimerax-bug-report@…
[…]
4:38 PM Ticket #5929 (Crash in event loop) created by chimerax-bug-report@…
[…]
3:54 PM Ticket #5928 ("name 'stream' is not defined" opening model positions file) closed by Tom Goddard
fixed: There is a mistake in the ChimeraX code that is trying to print an …
3:34 PM Ticket #5926 (ChimeraX 1.3 won't start (Windows 10)) closed by Tom Goddard
nonchimerax: The most common reason ChimeraX fails to start is your system graphics …
3:29 PM Ticket #5928 ("name 'stream' is not defined" opening model positions file) created by jribeiro@…
[…]
2:46 PM Ticket #5927 (Attempt to use either positions or matrix file) closed by Tom Goddard
not a bug: I don't understand what you are trying to do. If you are trying to …
1:10 PM Ticket #5924 (Crash in event loop) closed by pett
can't reproduce
1:09 PM Ticket #5923 (Crash in Clashes GUI generating command) closed by pett
can't reproduce
1:06 PM Ticket #5922 (Crash fetching Ring's "aromatic" property) closed by pett
duplicate: Hi Yen-Li, Thanks for reporting this problem. It was fixed about 3 …
10:06 AM Ticket #5927 (Attempt to use either positions or matrix file) created by jribeiro@…
[…] model.cmx
9:04 AM Ticket #5926 (ChimeraX 1.3 won't start (Windows 10)) created by sitb@…
[…]
8:16 AM Ticket #5925 (Swapaa: name 'critera' is not defined) created by chimerax-bug-report@…
[…]
8:07 AM Ticket #5924 (Crash in event loop) created by chimerax-bug-report@…
[…]
3:40 AM Ticket #5923 (Crash in Clashes GUI generating command) created by chimerax-bug-report@…
[…]
1:38 AM Ticket #5918 (ISOLDE: implicit solvent applied twice if CUDA fails and falls back to ...) closed by Tristan Croll
fixed: SBGRID are fixing the CUDA library error, and the bug in ISOLDE's …

Jan 13, 2022:

11:41 PM Ticket #5922 (Crash fetching Ring's "aromatic" property) created by yen-li.li@…
[…]
5:32 PM Ticket #4902 ("key" command does not show color key if Color Key graphical interface ...) closed by pett
fixed
5:22 PM 2022-1-13 edited by Tom Goddard
(diff)
5:18 PM 2022-1-13 edited by Tom Goddard
(diff)
5:04 PM Dev2022-1-13 edited by Tom Goddard
(diff)
4:47 PM Ticket #5911 (Problem with realsense command: Couldn't resolve requests) closed by Tom Goddard
can't reproduce: Glad someone is trying the realsense depth camera with VR. But they …
4:35 PM Ticket #5913 (Crash in ctypes crash after session opened) closed by Tom Goddard
can't reproduce: All the user did was open a session file […] which appears to …
3:58 PM Ticket #5919 (Problem reading cube file: could not convert string to float) closed by Tom Goddard
can't reproduce: All I can guess is the user overwrote the file so it was no longer in …
3:57 PM Ticket #5921 (Crash after running MatchMaker) closed by pett
can't reproduce
12:33 PM Ticket #5916 (Crash after running MatchMaker) closed by pett
can't reproduce
12:18 PM Ticket #5921 (Crash after running MatchMaker) created by chimerax-bug-report@…
[…]
11:11 AM 2022-1-13 edited by Tom Ferrin
(diff)
11:09 AM 2022-1-13 edited by Tom Ferrin
(diff)
10:55 AM Ticket #5915 (Swapaa failure setting stick size) closed by pett
duplicate: Hi Yen-Li, Thanks for reporting this problem. It was fixed 3 days …
10:52 AM Ticket #5914 (Fatal Qt error during app initialization) closed by pett
can't reproduce
9:57 AM Ticket #5920 (Restoring session with volume not found leads to errors) created by Tom Goddard
If when restoring a session a volume is not found and the user does …
9:53 AM Ticket #5910 (Multiple volume/session failures followed by out of memory opening ...) closed by Tom Goddard
nonchimerax: The error says "MemoryError: not enough memory" after opening a …
9:46 AM Ticket #5907 (Better starting directory when ChimeraX launched by file association) reopened by Tom Goddard
Should test if same behavior in Windows 11.
9:45 AM Ticket #5909 (Crash during/after AlphaFold prediction) closed by Tom Goddard
can't reproduce: Crash in Qt event loop. My best guess is that the Qt html panel for …
9:41 AM Ticket #5919 (Problem reading cube file: could not convert string to float) created by chimerax-bug-report@…
[…]
6:55 AM Ticket #5918 (ISOLDE: implicit solvent applied twice if CUDA fails and falls back to ...) created by richard_walsh@…
[…]
3:35 AM Ticket #5916 (Crash after running MatchMaker) created by chimerax-bug-report@…
[…]
3:31 AM Ticket #5890 (openmm.OpenMMException: Error launching CUDA compiler) closed by Tristan Croll
fixed: Great! To my knowledge the first instance of ISOLDE running under WSL2 …
2:21 AM Ticket #5915 (Swapaa failure setting stick size) created by yen-li.li@…
[…]

Jan 12, 2022:

11:11 PM Ticket #5914 (Fatal Qt error during app initialization) created by chimerax-bug-report@…
[…]
10:09 PM Ticket #5913 (Crash in ctypes crash after session opened) created by chimerax-bug-report@…
[…]
9:06 PM Ticket #5912 (Crash handling tool window closeEvent after AlphaFold prediction finishes) created by chimerax-bug-report@…
[…]
9:03 PM Ticket #5911 (Problem with realsense command: Couldn't resolve requests) created by chimerax-bug-report@…
[…]
6:59 PM Ticket #5910 (Multiple volume/session failures followed by out of memory opening ...) created by xupeiyu3@…
[…]
6:20 PM NTTData edited by Elaine Meng
(diff)
6:20 PM NTTData edited by Elaine Meng
(diff)
5:46 PM Ticket #5442 (multiple columns of options) closed by pett
fixed: Changed the suggested parts of the Clashes interface to use multiple …
2:45 PM Ticket #5907 (Better starting directory when ChimeraX launched by file association) closed by Tom Goddard
nonchimerax: After rebooting Windows 10 I observe the same behavior that double …
10:38 AM Ticket #5909 (Crash during/after AlphaFold prediction) created by chimerax-bug-report@…
[…]
10:09 AM Ticket #5908 (Crash in event loop after hiding models) closed by pett
can't reproduce
10:05 AM Ticket #5906 (Calling windowShouldClose: on the delegate for the QNSPanel) closed by pett
can't reproduce
9:41 AM Ticket #5908 (Crash in event loop after hiding models) created by chimerax-bug-report@…
[…]
4:47 AM Ticket #5907 (Better starting directory when ChimeraX launched by file association) created by Tristan Croll
[…]
12:30 AM Ticket #5905 (Linux: No module named '_bz2') closed by Greg Couch
fixed: Added bzip2 development libraries to the CentOS 7 and CentOS 8 images …

Jan 11, 2022:

8:55 PM Ticket #5906 (Calling windowShouldClose: on the delegate for the QNSPanel) created by chimerax-bug-report@…
[…]
8:23 PM Ticket #5904 (Graphics driver crash, macOS 10.14.6, Intel Iris Pro) closed by Tom Goddard
nonchimerax: Apple graphics driver crash.
5:55 PM Ticket #5903 (Crash showing Rapid Access at startup) closed by pett
can't reproduce
2:36 PM Ticket #5905 (Linux: No module named '_bz2') created by chimerax-bug-report@…
[…]
1:38 PM Ticket #5904 (Graphics driver crash, macOS 10.14.6, Intel Iris Pro) created by chimerax-bug-report@…
[…]
11:47 AM Ticket #5903 (Crash showing Rapid Access at startup) created by chimerax-bug-report@…
[…]
11:27 AM Ticket #5183 (Features covers image on download page for some versions of Chrome) closed by Zach Pearson
can't reproduce: Newer versions of browsers don't seem to have this issue.
10:53 AM Ticket #5902 (OpenMM: RuntimeError: Release Object) closed by Tristan Croll
can't reproduce: Yeah... chances are this is already fixed, but if not will have to …
10:47 AM Ticket #5889 (openmm.OpenMMException: Error compiling kernel) closed by Tristan Croll
limitation: The error message itself doesn't give much to go on, but I think the …
10:18 AM Ticket #5902 (OpenMM: RuntimeError: Release Object) created by chimerax-bug-report@…
[…]
9:58 AM 2022-1-13 created by Tom Goddard
9:57 AM DeveloperMeetings edited by Tom Goddard
(diff)
9:56 AM DeveloperMeetings edited by Tom Goddard
(diff)
9:44 AM Ticket #5901 (Unknown crash with unformatted stack trace) closed by pett
can't reproduce: Even more uninformative than usual.
9:36 AM Ticket #5898 (Crash opening mmCIF) closed by pett
can't reproduce
9:31 AM Ticket #5901 (Unknown crash with unformatted stack trace) created by chimerax-bug-report@…
[…]
7:14 AM Ticket #5900 (ISOLDE: add real-space map: structure is None) created by leonardotrosa@…
[…]
7:13 AM Ticket #5899 (ISOLDE: swap equivalent atoms: Values array length 3 does not match ...) created by leonardotrosa@…
[…]
5:30 AM Ticket #5898 (Crash opening mmCIF) created by chimerax-bug-report@…
[…]

Jan 10, 2022:

4:52 PM Ticket #5897 (Add per-residue correlation calculation like Phenix) created by yumeng.yan@…
On Jan 10, 2022, at 3:48 PM, Yumeng Yan wrote: Hi Tom, ... Another …
4:38 PM Ticket #5896 (Add measure correlation command) closed by Tom Goddard
fixed: Added measure correlation command to measure the correlation between …
3:41 PM Ticket #5896 (Add measure correlation command) created by yumeng.yan@…
Yumeng Yan was using fitmap with shift false and rotate false options …
3:15 PM Ticket #5892 (Failure reading IMOD file) closed by Tom Goddard
fixed: Fixed in tonight's ChimeraX daily builds. ChimeraX was not correctly …
2:08 PM Ticket #5878 (Crash on redraw with Rapid Access still showing) closed by pett
can't reproduce: Line 21 of changes.py is also a 'return' statement. This whole ticket …
10:57 AM Ticket #5894 (Linux: ImportError: libGLU.so.1: cannot open shared object file: No ...) closed by Greg Couch
worksforme: User needs to install mesa libGLU package. On Ubuntu 20.04, that is …
10:55 AM Ticket #5895 (Add volume surface and mesh gui panel) created by kelvin.kclau@…
On Jan 10, 2022, at 4:47 AM, Kelvin Lau via ChimeraX-users wrote: …
10:10 AM Ticket #5885 (Error checking for new version: NameError: name '_getuser' is not defined) closed by Greg Couch
fixed: Fixed in the daily build.
9:34 AM Ticket #5886 (Crash in garbage collection during new-object allocation) closed by pett
duplicate
9:30 AM Ticket #5884 (Crash in trigger handler after saving image) closed by pett
can't reproduce
7:07 AM Ticket #5894 (Linux: ImportError: libGLU.so.1: cannot open shared object file: No ...) created by chimerax-bug-report@…
[…]
6:26 AM Ticket #5893 (Blast results problem: 'NoneType' object has no attribute 'split') created by shabir.najmudin@…
[…]
4:18 AM Ticket #5892 (Failure reading IMOD file) created by wanda.kukulski@…
[…] test3.mod
2:29 AM Ticket #5891 (Crash in change-tracking after 'cd' command) created by vijayalphafold@…
[…]

Jan 9, 2022:

9:32 AM Ticket #5890 (openmm.OpenMMException: Error launching CUDA compiler) created by jmkrieger@…
[…]

Jan 8, 2022:

12:19 PM Ticket #5888 (Time out error checking for new ChimeraX version) closed by Greg Couch
fixed: Ignore network/server errors when checking for new version.
12:17 PM Ticket #5889 (openmm.OpenMMException: Error compiling kernel) created by Alexandrea.Rizo@…
[…]

Jan 7, 2022:

8:10 PM Ticket #5828 (Crash drawing frame) closed by Tom Goddard
can't reproduce: We have seen many crashes on Windows in draw_new_frame() which is …
7:55 PM Ticket #5881 (Save TIFF stack: ImageJ hyperstack shape and axes do not match) closed by Tom Goddard
fixed: Fixed. The call to tifffile.py imwrite() specified axis order …
7:44 PM Ticket #5888 (Time out error checking for new ChimeraX version) created by goddard@…
[…]
11:53 AM Ticket #5887 (swapna) created by anton.vila@…
Implement swapna command.
7:28 AM Ticket #5886 (Crash in garbage collection during new-object allocation) created by chimerax-bug-report@…
[…]

Jan 6, 2022:

11:36 PM Ticket #5885 (Error checking for new version: NameError: name '_getuser' is not defined) created by chimerax-bug-report@…
[…]
10:38 PM Ticket #5884 (Crash in trigger handler after saving image) created by chimerax-bug-report@…
[…]
8:49 PM Ticket #5883 (MemoryError saving map in session) closed by Tom Goddard
limitation: Out of memory error saving a session trying to convert to a byte …
8:21 PM Ticket #5880 (Crash after restoring session with Segger session restore error) closed by Tom Goddard
can't reproduce: ChimeraX crashed after opening a session when trying to draw Thread …
8:11 PM Ticket #5879 (Could not find virtual screen for QCocoaScreen) closed by Tom Goddard
duplicate: ChimeraX startup failure due to a Qt bug Could not find virtual …
8:05 PM Training edited by Tom Goddard
(diff)
8:01 PM 2022-1-6 edited by Tom Goddard
(diff)
8:00 PM 2022-1-6 edited by Tom Goddard
(diff)
7:59 PM 2022-1-6 edited by Tom Goddard
(diff)
2:06 PM NTTData edited by Elaine Meng
(diff)
2:03 PM NTTData edited by Elaine Meng
(diff)
1:23 PM NTTData edited by Elaine Meng
(diff)
11:29 AM 2022-1-6 edited by Scooter Morris
(diff)
11:28 AM 2022-1-6 edited by Scooter Morris
(diff)
11:09 AM 2022-1-6 edited by Greg Couch
(diff)
11:08 AM 2022-1-6 edited by Greg Couch
(diff)
11:01 AM 2022-1-6 edited by Scooter Morris
(diff)
10:59 AM 2022-1-6 edited by Scooter Morris
(diff)
10:37 AM Ticket #5882 (Qt crash during exit) closed by pett
can't reproduce: Hi, Thanks for reporting this problem. We recommend that you …
10:35 AM Ticket #5701 ("Remind me later" false on new version check keeps reminding) closed by Greg Couch
fixed: Fixed on 30 Nov 2021, 86d23b00f0caf436f38e89534da9cffc6882b8ba. The …
1:14 AM Ticket #5883 (MemoryError saving map in session) created by chimerax-bug-report@…
[…]
12:57 AM Ticket #5882 (Qt crash during exit) created by zgx2015@…
[…]

Jan 5, 2022:

4:06 PM Ticket #5796 (Stack overflow, possibly due to screen locking) closed by pett
can't reproduce: Leaving ChimeraX running overnight also did not produce a crash. I …
4:03 PM Ticket #5881 (Save TIFF stack: ImageJ hyperstack shape and axes do not match) created by kimsk@…
[…]
3:15 PM Ticket #5880 (Crash after restoring session with Segger session restore error) created by chimerax-bug-report@…
[…]
1:29 PM Ticket #5879 (Could not find virtual screen for QCocoaScreen) created by chimerax-bug-report@…
[…]
11:23 AM Ticket #5878 (Crash on redraw with Rapid Access still showing) created by chimerax-bug-report@…
[…]
10:07 AM Ticket #5875 (Crash during or after session close, possibly in check_for_changes) closed by pett
can't reproduce
8:16 AM Ticket #5877 (Notes with markers/blobs) created by Tristan Croll
[…]
7:32 AM Ticket #5876 (Crash recording spin movie) created by charlotte12brown@…
[…]
7:31 AM Ticket #5875 (Crash during or after session close, possibly in check_for_changes) created by chimerax-bug-report@…
[…]
Note: See TracTimeline for information about the timeline view.