![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Nov 6, 2023:
- 10:15 PM Ticket #10104 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 9:09 PM Ticket #10103 (Crash setting clip parameters) created by
- […]
- 9:03 PM Ticket #10102 (Crash showing scale bar) created by
- […]
- 6:53 PM Ticket #10101 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 5:17 PM Ticket #10087 (Crash closing volume viewer window) closed by
- can't reproduce: Hi Gillian, If it happens again, try the ChimeraX daily build (or the …
- 5:08 PM ChangeLog edited by
- (diff)
- 4:57 PM Ticket #10100 (Open forEachFile fails if file names contain spaces) closed by
- fixed: Fixed. The option opened the file by running the user command open …
- 4:54 PM Ticket #10100 (Open forEachFile fails if file names contain spaces) created by
- […]
- 4:40 PM Ticket #10099 (Unable to restore objects of NewerVersionQuery class) closed by
- duplicate: Duplicate of #9924
- 4:34 PM Ticket #10098 (DockPrep not catching ChargeError) closed by
- duplicate: Duplicate of #9960
- 4:04 PM Ticket #10097 (Crash loading toolshed) closed by
- can't reproduce
- 3:44 PM Ticket #10099 (Unable to restore objects of NewerVersionQuery class) created by
- […]
- 3:33 PM Dev2023-11-6 edited by
- (diff)
- 3:11 PM Dev2023-11-6 edited by
- (diff)
- 3:01 PM Ticket #8798 (ChimeraX hangs at startup checking for updates) closed by
- fixed: Fixed. ChimeraX was hanging checking for newer versions. Which it …
- 2:46 PM Ticket #10090 (QKeyEvent in drag/drop code) closed by
- duplicate: This appears to be a Qt bug. It has been reported twice before #9712 …
- 2:41 PM Ticket #10091 (Crash swapping buffers after 'clip' command) closed by
- can't reproduce: Probably Mesa graphics crash.
- 2:36 PM Ticket #10094 (Cannot download AlphaFold model) closed by
- fixed: Fixed. Since jaxlib depends on CUDA and the CUDA version gets updated …
- 1:13 PM Ticket #10095 (Restore new session in old ChimeraX) closed by
- limitation
- 1:11 PM Ticket #10093 (Crash in event loop) closed by
- can't reproduce
- 1:10 PM Ticket #10092 (Crash showing Rapid Access at startup) closed by
- can't reproduce
- 1:07 PM Ticket #10098 (DockPrep not catching ChargeError) created by
- […]
- 1:07 PM 2023-11-9 created by
- 1:06 PM 2023-11-2 created by
- 1:02 PM DeveloperMeetings edited by
- (diff)
- 1:01 PM Dev2023-11-6 created by
- 1:00 PM Dev2023-10-30 edited by
- (diff)
- 12:58 PM DeveloperMeetings edited by
- (diff)
- 12:57 PM Ticket #10089 (Crash using File→Open dialog on Windows and/or returning from function) closed by
- can't reproduce: 1.3
- 12:43 PM Ticket #10096 (Allow setting initial volume colors) closed by
- fixed: Done. I added the initialColors option to the volume command and the …
- 12:40 PM Ticket #10097 (Crash loading toolshed) created by
- […]
- 12:39 PM Ticket #10096 (Allow setting initial volume colors) created by
- From: James Hooker via ChimeraX-users <chimerax-users@…> …
- 11:49 AM Ticket #10088 (color by conservation problem) closed by
- duplicate: Asked and answered on the chimerax-users list.
- 8:27 AM Ticket #10095 (Restore new session in old ChimeraX) created by
- […]
- 8:03 AM Ticket #10094 (Cannot download AlphaFold model) created by
- […]
- 4:19 AM Ticket #10093 (Crash in event loop) created by
- […]
- 2:51 AM Ticket #10092 (Crash showing Rapid Access at startup) created by
- […]
- 2:15 AM Ticket #10091 (Crash swapping buffers after 'clip' command) created by
- […]
- 1:30 AM Ticket #10090 (QKeyEvent in drag/drop code) created by
- […]
Nov 5, 2023:
- 2:58 PM Ticket #10089 (Crash using File→Open dialog on Windows and/or returning from function) created by
- […]
- 8:12 AM Ticket #10088 (color by conservation problem) created by
- […] [[Image(...)]]
Nov 3, 2023:
- 8:36 PM Ticket #10087 (Crash closing volume viewer window) created by
- […]
- 7:34 PM Ticket #10086 (fly command does not interpolate clip planes) created by
- On Nov 3, 2023, at 7:43 AM, Sean Connell via ChimeraX-users …
- 7:33 PM Ticket #4551 (Weird shadows during 'fly') closed by
- fixed
- 7:29 PM Ticket #10085 (mseries with negative step: NameError: name 'models' is not defined) closed by
- fixed: Fixed. The mseries code was clearly intended to work with negative …
- 7:17 PM Ticket #10085 (mseries with negative step: NameError: name 'models' is not defined) created by
- […]
- 6:55 PM Ticket #10084 (Allow surface zone command to hide surface near atoms) created by
- From: Rayees Mattoo via ChimeraX-users <chimerax-users@…> …
- 6:29 PM Ticket #10081 (Qt panels not displaying) closed by
- nonchimerax: None of the Qt window toolkit buttons or menus are showing. That is a …
- 5:16 PM Ticket #10082 (About ChimeraX-Toolshed) closed by
- fixed: Hi, Until a couple of hours ago, our compute cluster was down and …
- 5:01 PM Ticket #10083 (Crash at startup) created by
- […]
- 4:17 PM Ticket #10082 (About ChimeraX-Toolshed) created by
- […]
- 4:17 PM Ticket #10081 (Qt panels not displaying) created by
- […] ChimeraX Error.png
- 4:17 PM Ticket #10080 (ChimeraX ToolShed doesn't open) created by
- […]
Oct 27, 2023:
- 1:05 PM Ticket #10078 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate: Hi David, Thanks for reporting this problem. This is a bug in the Qt …
- 1:01 PM Ticket #10077 (Crash after rmf readtraj) closed by
- duplicate: Probable duplicate of #8614
- 12:40 PM Ticket #10079 (Colors of exported GLTF models don't match ChimeraX colors) created by
- […]
- 12:17 PM Ticket #10078 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 12:14 PM Ticket #10077 (Crash after rmf readtraj) created by
- […]
- 12:05 PM Ticket #10076 (VRML output for 3D color printers) created by
- […] [[Image(...)]]
- 11:59 AM Ticket #10075 (Add center or translate mouse mode) closed by
- fixed
- 11:56 AM Ticket #10075 (Add center or translate mouse mode) created by
- From: Daniel Larsson via ChimeraX-users <chimerax-users@…> …
- 11:31 AM Ticket #10072 ('StrandPlank' object has no attribute '_straight_tilt') closed by
- not a bug: Not sure how you found this modeStrand option of the cartoon style …
- 11:23 AM Ticket #10070 (ESMFold: SSL: CERTIFICATE_VERIFY_FAILED unable to get local issuer ...) closed by
- duplicate: ESMFold server problem is already reported and we will remove ESMFold …
- 11:22 AM Ticket #10074 (Updating list of available bundles failed: [SSL: ...) created by
- Copied from ticket #10070: The following bug report has been …
- 11:11 AM Ticket #10073 (Graphics crash, macOS 12.5.1, Intel Iris Plus Graphics 645) closed by
- nonchimerax: Apple Intel graphics driver crash. Unfortunately Apple Intel graphics …
- 11:03 AM Ticket #10071 (Graphics crash, macOS 11.7.6, Intel UHD Graphics 617) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 5:45 AM Ticket #10073 (Graphics crash, macOS 12.5.1, Intel Iris Plus Graphics 645) created by
- […]
- 3:57 AM Ticket #10072 ('StrandPlank' object has no attribute '_straight_tilt') created by
- […]
Oct 26, 2023:
- 4:14 PM Ticket #9861 (Clipper installation) closed by
- duplicate: I believe this is essentially a duplicate of #9877. And is resolved …
- 4:10 PM 2023-10-26 edited by
- (diff)
- 3:59 PM Ticket #10052 (Plugin install / uninstall problems) closed by
- fixed: This should be fixed in the next daily build (Oct 27 or later).
- 3:58 PM Ticket #9877 (Cannot uninstall bundle) closed by
- fixed: Stopped using "python -I" and instead fix up environment so …
- 3:54 PM NIAID2023 edited by
- (diff)
- 3:48 PM Ticket #9255 (Installing bundle nukes Tools menu) closed by
- fixed: Used to update the Tools menu by creating a new menu and replacing the …
- 3:48 PM Ticket #9873 (Installed version number not updated) closed by
- duplicate: I think this is a duplicate of #9877. Since uninstalls were not …
- 3:07 PM Ticket #9255 (Installing bundle nukes Tools menu) reopened by
- I can still reproduce this behavior. The Tools menu is entirely …
- 3:00 PM Ticket #9985 (Computing sequence conservation: OSError: [Errno 12] Cannot allocate memory) closed by
- can't reproduce: I can't reproduce this on an Ubuntu 22.04 system. I guess I suggest …
- 2:24 PM Ticket #10067 (AlphaFold: Downloaded prediction file not found) closed by
- fixed: Fixed. It appears Google Colab updated CUDA from version 11.x to …
- 2:09 PM NIAID2023 edited by
- (diff)
- 1:55 PM NIAID2023 edited by
- (diff)
- 1:26 PM Ticket #10071 (Graphics crash, macOS 11.7.6, Intel UHD Graphics 617) created by
- […]
- 11:08 AM Ticket #10070 (ESMFold: SSL: CERTIFICATE_VERIFY_FAILED unable to get local issuer ...) created by
- […]
- 10:30 AM Ticket #10069 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 10:28 AM Ticket #10068 (Qt fatal error) closed by
- can't reproduce: Hi Deepak, Thanks for reporting this problem. Try upgrading to the …
- 3:28 AM Ticket #10069 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 3:07 AM Ticket #10068 (Qt fatal error) created by
- […]
- 2:07 AM Ticket #10067 (AlphaFold: Downloaded prediction file not found) created by
- […]
Oct 25, 2023:
- 11:06 PM Ticket #9876 (Installing a bundle reports "No bundles were installed") closed by
- fixed: Removing the warning, that pip was out of date, also removed the …
- 6:46 PM Ticket #9255 (Installing bundle nukes Tools menu) closed by
- can't reproduce: Can't reproduce on Windows with daily build. Please confirm on macOS.
- 2:16 PM Ticket #10063 (Unknown crash) closed by
- can't reproduce: Thanks for letting us know. --Eric
- 11:43 AM Ticket #10066 (ISOLDE: stop sim: 'AdaptiveDistanceRestraintMgr' object has no ...) created by
- […]
- 11:40 AM Ticket #10065 (Dependencies wrong to bundles with multiple architectures) created by
- […] Just noticed what looks like a bug in the Tool Shed while …
- 11:39 AM Ticket #10064 (Toolshed cannot delete distribution if another toolshed tool depends on it) created by
- Tristan noted that he cannot delete the Clipper 0.15 linux …
- 11:32 AM Ticket #10055 (Graphics crash, macOS 12.6.2, Intel Iris Graphics 550) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 10:51 AM Ticket #10062 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate: Hi Esther, Thanks for reporting this problem. This is a bug in the Qt …
- 10:44 AM Ticket #10060 (save_pdb() call fails) closed by
- nonchimerax: Hi Dominik, The error you are getting implies that the second …
- 10:34 AM Ticket #10059 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 10:33 AM Ticket #10058 (Crash in atom-spec parsing) closed by
- can't reproduce: Probable duplicate of #4842
- 10:31 AM Ticket #10057 (Crash in atom-spec parsing) closed by
- can't reproduce: Probable duplicate of #4842
- 10:16 AM Ticket #10063 (Unknown crash) created by
- […]
- 7:32 AM Ticket #10062 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 7:31 AM Ticket #10061 (XMAS: could not convert string to float) created by
- […]
- 6:15 AM Ticket #10060 (save_pdb() call fails) created by
- […]
- 2:10 AM Ticket #10059 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
Oct 24, 2023:
- 8:30 PM Ticket #10058 (Crash in atom-spec parsing) created by
- […]
- 7:45 PM Ticket #10057 (Crash in atom-spec parsing) created by
- […]
- 3:06 PM Dev2023-10-24 created by
- 3:03 PM DeveloperMeetings edited by
- (diff)
- 1:50 PM Ticket #9993 (Crash in coulombic in assign_charges()) closed by
- can't reproduce: Crash is in "for o_a, c_a in zip(struct.atoms, charged_struct.atoms):" …
- 1:26 PM Ticket #10056 (ESMFold: unable to get local issuer certificate) created by
- […]
- 12:53 PM Ticket #10055 (Graphics crash, macOS 12.6.2, Intel Iris Graphics 550) created by
- […]
- 11:31 AM Dev2023-10-30 created by
- 11:31 AM Ticket #10004 (Reading SDF file: atoms[index].charge = charge IndexError: list ...) closed by
- fixed: Yes, the charge section of the file has indices for atoms that don't …
- 11:30 AM 2023-10-26 created by
- 11:29 AM 2023-10-19 edited by
- (diff)
- 11:20 AM DeveloperMeetings edited by
- (diff)
- 9:59 AM Ticket #10054 ("turn" arguments) closed by
- not a bug: Hi Kirill, "turn x 1 45" means turn around the X axis by 1 degree for …
- 9:54 AM Ticket #10053 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 7:39 AM Ticket #10054 ("turn" arguments) created by
- […]
- 1:22 AM Ticket #10053 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
Oct 23, 2023:
- 5:50 PM Ticket #10007 (Session files get larger on each save) closed by
- fixed: Hi Dror, Though that second session doesn't get anywhere near 400 MB …
- 4:16 PM Dev2023-10-23 edited by
- (diff)
- 2:58 PM Ticket #10052 (Plugin install / uninstall problems) created by
- […]
- 1:47 PM Ticket #9332 (Support multimask segmentations) closed by
- fixed: Added some code to the SeriesFile class to try and detect multimask …
- 12:00 PM ChangeLog edited by
- (diff)
- 11:53 AM Ticket #10047 (Dead volume model (self.session is None) in session.selection) closed by
- fixed: Fixed. Made the code that remembers selection promotions and …
- 11:53 AM ChangeLog edited by
- (diff)
- 11:39 AM Ticket #10046 (glDrawBuffer(GL_BACK): invalid operation, Linux) closed by
- can't reproduce: Have seen this many times, only on Linux. Maybe it invalidates the …
- 11:30 AM Ticket #10051 (Add PDB-REDO to fetch by id to get x-ray maps) created by
- From: Oliver Clarke via ChimeraX-users <chimerax-users@…> …
- 11:27 AM Ticket #10050 (Allow specifying that a map is a difference map when opening) closed by
- fixed: Done. Added the "difference" option when opening map files to the …
- 11:26 AM Ticket #10050 (Allow specifying that a map is a difference map when opening) created by
- From: Francisco Murphy Pérez via ChimeraX-users …
- 11:22 AM Ticket #10049 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 11:06 AM Ticket #10044 (No space left on device) closed by
- duplicate
- 11:06 AM Ticket #10043 (No space left on device) closed by
- duplicate
- 11:05 AM Ticket #10042 (No space left on device) closed by
- nonchimerax: Hi Ruchi, All these problems you've reported saving sessions and …
- 10:40 AM Ticket #10041 ('PickedPseudobond' object has no attribute 'group') closed by
- duplicate
- 10:37 AM Ticket #10040 (Basic Actions: 'QEventLoop' object has no attribute 'exec_') closed by
- duplicate
- 10:33 AM Ticket #10039 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 10:30 AM Ticket #10037 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 10:10 AM Ticket #10049 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 6:58 AM Ticket #10048 (ArtiaX: session save: Unknown class name 'Tomogram') created by
- […]
- 5:50 AM Ticket #10047 (Dead volume model (self.session is None) in session.selection) created by
- […]
- 4:26 AM Ticket #10046 (glDrawBuffer(GL_BACK): invalid operation, Linux) created by
- […]
- 3:06 AM Ticket #10045 (MemoryError opening mmCIF) created by
- […]
Oct 22, 2023:
- 11:02 PM Ticket #10044 (No space left on device) created by
- […]
- 10:54 PM Ticket #10043 (No space left on device) created by
- […]
- 10:51 PM Ticket #10042 (No space left on device) created by
- […]
- 2:09 PM Ticket #10041 ('PickedPseudobond' object has no attribute 'group') created by
- […]
- 8:05 AM Ticket #10040 (Basic Actions: 'QEventLoop' object has no attribute 'exec_') created by
- […]
- 1:17 AM Ticket #10039 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
Oct 21, 2023:
- 2:33 PM Ticket #10038 (MemoryError opening mmCIF) created by
- […]
- 2:21 AM Ticket #10037 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
Oct 20, 2023:
- 4:36 PM Ticket #10036 (Add programming documentation on how to include PyPi dependencies in a ...) created by
- On Oct 20, 2023, at 4:58 AM, Vincent Mallet via ChimeraX-users …
- 4:12 PM Ticket #10034 (Graphics crash, macOS 13.3.1, Intel Iris Plus Graphics) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 2:28 PM Ticket #10008 (Reading PDB file: UnicodeDecodeError: 'utf-8' codec can't decode byte ...) closed by
- can't reproduce: Yeah, ChimeraX already tries UTF-8, -16, and -32 automatically, so …
- 12:37 PM Ticket #10035 (Add tests to DICOM) created by
- I had to revert two commits recently that fixed some TCIA datasets so …
- 12:25 PM Ticket #10034 (Graphics crash, macOS 13.3.1, Intel Iris Plus Graphics) created by
- […]
- 11:44 AM Ticket #10030 (Graphics crash, macOS 13.0.1, Intel Iris Plus Graphics 655) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 11:40 AM Ticket #10029 (Map filter: Cannot cast ufunc 'clip' output) closed by
- fixed: Fixed. The volume scale command produces a float32 array and then …
- 11:16 AM Dev2023-10-23 edited by
- (diff)
- 11:14 AM Ticket #10033 (Sequence feature browser: invalid result from ...) closed by
- duplicate
- 10:11 AM Ticket #10032 (MatchMaker: 'NoneType' object has no attribute 'setChecked') closed by
- duplicate
- 10:07 AM Ticket #10033 (Sequence feature browser: invalid result from ...) created by
- […]
- 10:00 AM Ticket #10028 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 7:44 AM Ticket #10032 (MatchMaker: 'NoneType' object has no attribute 'setChecked') created by
- […]
- 4:35 AM Ticket #10031 (XMAS 1.1.2: this version of pandas is incompatible with numpy < 1.22.4) created by
- […]
- 1:28 AM Ticket #10030 (Graphics crash, macOS 13.0.1, Intel Iris Plus Graphics 655) created by
- […]
- 12:54 AM Ticket #10029 (Map filter: Cannot cast ufunc 'clip' output) created by
- […]
Oct 19, 2023:
- 5:16 PM Ticket #10028 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 5:15 PM Ticket #8522 (Crash opening mmCIF on Linux) closed by
- duplicate: I believe this is the memory bug in the mmCIF reader that is fixed in …
- 4:37 PM Ticket #9897 (bundle_tutorial.zip broken) closed by
- fixed: Fixed. Need to update script to Python 3.
- 4:27 PM Ticket #3684 (mmCIF memory leak) closed by
- fixed: Duplicate of #8815.
- 4:26 PM Ticket #9034 (MemoryError open mmCIF) closed by
- duplicate: Duplicate of #8815.
- 4:12 PM Tickets #8847,8851,8897,8935,9014,9113,9132,9137,9150,9159,9163,9165,9181,9182,9201,9202,9203,9250,9251,9264,9285,9293,9335,9436,9444,9472,9476,9520,9531,9667,9670,9768,9777,9809,9888,9895,9899,10020 batch updated by
- duplicate: Duplicated of #8815.
- 3:59 PM Ticket #9924 (Unable to restore objects of NewerVersionQuery class) closed by
- fixed: Starting in daily builds from today and in the release, ChimeraX will …
- 3:23 PM Ticket #10023 (Crash calculating contour surface) closed by
- can't reproduce: This ChimeraX bug report says "Python aborted". That usually is …
- 3:07 PM Ticket #10027 (Installing a python module at plugin start/load) created by
- This might not be a bug but it is definitely an email for the …
- 10:08 AM Ticket #9995 (TOML documentation out of date) closed by
- fixed: Fixed the …
- 9:45 AM Ticket #10022 (RFE: coulombic option to force charge recalculation) reopened by
- Nonetheless, there probably should be an option for these rare use cases.
- 9:42 AM Ticket #10026 (Restore new session in old ChimeraX) closed by
- limitation: Hi Pradip, Although you can restore old sessions in newer versions of …
- 9:38 AM Ticket #10025 (Unknown problem) closed by
- can't reproduce
- 9:35 AM Ticket #10024 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 9:32 AM Ticket #10022 (RFE: coulombic option to force charge recalculation) closed by
- not a bug: Hi Tristan, If coulombic sees that all relevant atoms have a 'charge' …
- 9:18 AM Ticket #10021 (ISOLDE: swap_equivalent_atoms: different number of atoms being swapped) closed by
- duplicate: This should be fixed if you upgrade to ISOLDE 1.6 (by updating …
- 9:06 AM Ticket #10019 (MemoryError opening mmCIF files) closed by
- duplicate
- 9:04 AM Ticket #10016 (Restore new session in old ChimeraX) closed by
- limitation
- 8:22 AM Ticket #10026 (Restore new session in old ChimeraX) created by
- […]
- 7:54 AM Ticket #10025 (Unknown problem) created by
- […]
- 7:21 AM Ticket #10024 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 5:25 AM Ticket #10023 (Crash calculating contour surface) created by
- […]
- 4:52 AM Ticket #10022 (RFE: coulombic option to force charge recalculation) created by
- […]
- 2:09 AM Ticket #10021 (ISOLDE: swap_equivalent_atoms: different number of atoms being swapped) created by
- […]
- 12:49 AM Ticket #10020 (MemoryError opening mmCIF files) created by
- […]
- 12:42 AM Ticket #10019 (MemoryError opening mmCIF files) created by
- […]
Oct 18, 2023:
- 3:45 PM Ticket #10018 (Improve AlphaFold Error Plot guessing the PAE file to use) closed by
- fixed: Done. Allowed names shorter than 6 characters to match and names that …
- 3:42 PM Ticket #10018 (Improve AlphaFold Error Plot guessing the PAE file to use) created by
- […]
- 2:39 PM Ticket #10015 (Saving DICOM orthoplane display as GLTF fails) closed by
- fixed: Fixed. PIL.Image.fromarray() does not work with a numpy array of …
- 2:37 PM Ticket #10014 (Saving DICOM plane as GLTF produces black rectangle) closed by
- fixed: Fixed. The GLTF code was using the data value texture and ignoring …
- 1:48 PM Ticket #10017 (Better separation between BLAST jobs and the GUI) created by
- From Tom: I was trying to BLAST 31 protein sequences today using some …
- 1:38 PM Ticket #9720 (Segmentations: slice view drawings should be unrelated to 3D view drawings) closed by
- fixed: Made the slice viewers use different drawings than the main view that …
- 1:37 PM Ticket #10009 (ValueError: error processing: 'tasks' -> : Unable to restore objects ...) closed by
- duplicate: Duplicates #9924
- 1:08 PM Ticket #10016 (Restore new session in old ChimeraX) created by
- […]
- 12:25 PM Ticket #10015 (Saving DICOM orthoplane display as GLTF fails) created by
- […]
- 12:23 PM Ticket #10014 (Saving DICOM plane as GLTF produces black rectangle) created by
- […]
- 12:10 PM Ticket #10013 (Crash in Qt event loop: QPainter::begin: Paint device returned engine ...) closed by
- duplicate
- 12:03 PM Ticket #10010 (Failed opening session: H5F_open unable to read superblock) closed by
- can't reproduce: It's not clear why the HDF5 library failed reading an hdf5 file …
- 11:36 AM Ticket #10006 (Crash in Qt event loop after opening AlphaFold model, Linux possible ...) closed by
- can't reproduce: Not any info to diagnose problem. DISPLAY=:1 instead of :0 so maybe …
- 11:33 AM Ticket #10013 (Crash in Qt event loop: QPainter::begin: Paint device returned engine ...) created by
- […]
- 11:33 AM Ticket #9980 (ChimeraX will not start on Mac Studio 2022 in Sonoma) closed by
- fixed: Fixed. The problem was the ui-1 setting file which says the last …
- 11:32 AM Ticket #10012 (Startup crash on macOS Sonoma) closed by
- fixed: Fixed. I put in some safety code to limit the initial window width …
- 10:57 AM Ticket #10012 (Startup crash on macOS Sonoma) created by
- […]
- 9:39 AM Ticket #10011 (Crash opening MTZ file: clipper/maps/xmapset.py", line 450 in ...) created by
- […]
- 7:40 AM Ticket #10010 (Failed opening session: H5F_open unable to read superblock) created by
- […]
Oct 17, 2023:
- 2:01 PM Ticket #10009 (ValueError: error processing: 'tasks' -> : Unable to restore objects ...) created by
- […]
- 1:38 PM Ticket #10001 (Clip plane motion problem) closed by
- fixed
- 1:38 PM Ticket #10001 (Clip plane motion problem) reopened by
- Fixed. Thanks for the detailed steps. The rotation between the two …
- 1:27 PM Ticket #10008 (Reading PDB file: UnicodeDecodeError: 'utf-8' codec can't decode byte ...) created by
- […]
- 1:14 PM Ticket #10007 (Session files get larger on each save) created by
- […] LH2 5HB for design.cxs
- 12:57 PM Ticket #10006 (Crash in Qt event loop after opening AlphaFold model, Linux possible ...) created by
- […]
- 12:51 PM Dev2023-10-23 created by
- 12:50 PM 2023-10-19 created by
- 12:48 PM DeveloperMeetings edited by
- (diff)
- 12:24 PM Ticket #10003 (Give better error message when AlphaFold prediction download fails) closed by
- fixed: Done. Gave error message suggesting how to recover the results.zip file.
- 12:22 PM Ticket #10005 (Render by attribute: TypeError: object of type 'function' has no len()) closed by
- duplicate
- 12:20 PM Ticket #9984 (Render by attribute histogram error: TypeError: object of type ...) closed by
- duplicate: Fixed 3 months ago #9328
- 12:10 PM Ticket #10002 (Crash in QTabBar::paintEvent(QPaintEvent*)) closed by
- duplicate
- 12:09 PM Ticket #10001 (Clip plane motion problem) closed by
- worksforme: I set the near plane with the side view, then "view name p1", then …
- 12:02 PM Ticket #10005 (Render by attribute: TypeError: object of type 'function' has no len()) created by
- […]
- 12:02 PM Ticket #10000 (Clip planes don't move smoothly between named views) closed by
- worksforme: Elaine, maybe it is worth adding to the documentation that when …
- 11:42 AM Ticket #10004 (Reading SDF file: atoms[index].charge = charge IndexError: list ...) created by
- […] rank1_confidence-0.69.sdf
- 11:39 AM Ticket #10003 (Give better error message when AlphaFold prediction download fails) created by
- […]
- 12:48 AM Ticket #9557 (Registration server unavailable) closed by
- can't reproduce: My guess is that this is an issue with the NIH's firewall. Or maybe a …
- 12:22 AM Ticket #9178 (Accepting a new Toolshed bundle appears to hang with circling arrows icon) closed by
- fixed: Bug was due to incomplete switch to Django 4. Replaced …
- 12:19 AM Ticket #8815 (mmCIF reading causing "not enough memory" error) closed by
- fixed: There was a memory leak in the code that read CIF tables as text …
- 12:15 AM Ticket #8827 (Out of memory after opening small mmCIF 7phr on Mac. Also ssl ...) closed by
- duplicate: The out of memory bug is a duplicate of #8815 and is fixed in the …
Oct 16, 2023:
- 10:53 PM Ticket #10002 (Crash in QTabBar::paintEvent(QPaintEvent*)) created by
- […]
- 4:27 PM Dev2023-10-16 edited by
- (diff)
- 4:21 PM Ticket #8818 (Read mmCIF: not enough memory) closed by
- duplicate: We believe this bug the same as #8815 and is fixed in the daily build.
- 3:41 PM ChangeLog edited by
- (diff)
- 2:06 PM Ticket #10001 (Clip plane motion problem) created by
- […]
- 1:57 PM Ticket #10000 (Clip planes don't move smoothly between named views) created by
- […]
- 1:08 PM Ticket #9999 (BlastProtein returns more results than the 100 maximum requested) created by
- […]
- 11:54 AM Ticket #9991 (ChimeraX hangs saving file on macOS Sonoma) closed by
- duplicate: Reporter provided more details in #9994.
- 11:51 AM Ticket #9998 (AlphFold Error Plot: TypeError: expected str, bytes or os.PathLike ...) closed by
- fixed: Fixed. The AlphaFold Error Plot Browse button was trying to set the …
- 11:45 AM Ticket #9997 (Crashed in QTabBar::paintEvent()) closed by
- duplicate
- 11:40 AM Ticket #9996 (view command not doing smooth zoom) closed by
- not a bug
- 11:26 AM Ticket #9992 (ChimeraX bug report submission) closed by
- nonchimerax
- 11:15 AM Ticket #9989 (Movie recording failed: OSError: [Errno 28] No space left on device) closed by
- nonchimerax
- 11:12 AM Ticket #9988 (Graphics crash, macOS 13.4, Intel Iris Plus Graphics 655) closed by
- nonchimerax
- 11:11 AM Ticket #9987 (ChimeraX bug report submission) closed by
- not a bug
- 11:06 AM Ticket #9986 (Render by attribute: TypeError: object of type 'function' has no len()) closed by
- duplicate: Same report as #9984.
- 10:56 AM Ticket #9998 (AlphFold Error Plot: TypeError: expected str, bytes or os.PathLike ...) created by
- […]
- 9:16 AM Ticket #9997 (Crashed in QTabBar::paintEvent()) created by
- […]
- 8:26 AM Ticket #9996 (view command not doing smooth zoom) created by
- […]
- 7:23 AM Ticket #9995 (TOML documentation out of date) created by
- […]
- 6:50 AM Ticket #9994 (ChimeraX hangs saving a session, macOS Sonoma) created by
- […]
- 12:30 AM Ticket #9993 (Crash in coulombic in assign_charges()) created by
- […]
Oct 15, 2023:
- 8:30 PM Ticket #9992 (ChimeraX bug report submission) created by
- […]
- 12:43 PM Ticket #9991 (ChimeraX hangs saving file on macOS Sonoma) created by
- […]
- 12:41 PM Ticket #9990 (Error opening zero-length session file in DropBox) created by
- […]
- 5:23 AM Ticket #9989 (Movie recording failed: OSError: [Errno 28] No space left on device) created by
- […]
- 4:19 AM Ticket #9988 (Graphics crash, macOS 13.4, Intel Iris Plus Graphics 655) created by
- […]
Oct 14, 2023:
- 11:17 PM Ticket #9987 (ChimeraX bug report submission) created by
- […]
- 10:30 AM Ticket #9986 (Render by attribute: TypeError: object of type 'function' has no len()) created by
- […]
- 10:26 AM Ticket #9985 (Computing sequence conservation: OSError: [Errno 12] Cannot allocate memory) created by
- […]
- 10:16 AM Ticket #9984 (Render by attribute histogram error: TypeError: object of type ...) created by
- […]
- 9:43 AM Ticket #9983 (ISOLDE: openmm.OpenMMException: Error initializing context: ...) created by
- […]
Oct 13, 2023:
- 11:16 PM 2023-10-12 edited by
- (diff)
- 2:12 PM Ticket #9597 (Antechamber doesn't like blank residue name) closed by
- fixed: The residue name isn't "0" -- the residue name is blank. The residue …
- 12:41 PM Ticket #9977 (Didn't find section 'Peptide bond' in tab 'ISOLDE') closed by
- not a bug: This is why, at the end of installation, ISOLDE pops up a dialog …
- 12:29 PM Ticket #9981 (Graphics crash, macOS 14.0, Intel Iris Plus Graphics) closed by
- nonchimerax
- 11:47 AM Ticket #9982 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 11:39 AM Ticket #9979 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 11:38 AM Ticket #9978 (QXcbConnection: XCB error: 9 (BadDrawable)) closed by
- can't reproduce: Version 0.91
- 11:20 AM Ticket #9982 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 11:02 AM Ticket #9974 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 10:50 AM Ticket #9981 (Graphics crash, macOS 14.0, Intel Iris Plus Graphics) created by
- […]
- 10:32 AM Ticket #9980 (ChimeraX will not start on Mac Studio 2022 in Sonoma) created by
- […]
- 7:07 AM Ticket #9979 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 3:59 AM Ticket #9978 (QXcbConnection: XCB error: 9 (BadDrawable)) created by
- […]
- 2:49 AM Ticket #9977 (Didn't find section 'Peptide bond' in tab 'ISOLDE') created by
- […]
Oct 12, 2023:
- 7:31 PM Ticket #9976 (Fetching PDB biounit shows error in status line) closed by
- fixed: Fixed. As suspected, ChimeraX does not know how many bioassemblies …
- 7:23 PM Ticket #9976 (Fetching PDB biounit shows error in status line) created by
- […]
- 7:19 PM Ticket #9971 (AlphaFold error plot: Operation not permitted) closed by
- limitation: User didn't have permission to list files in a mail download directory …
- 7:17 PM Ticket #9972 (Graphics crash, macOS 14.0, Intel Iris Plus Graphics) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 6:52 PM Ticket #9975 (ISOLDE sim start: OpenMMException: Error compiling kernel: Compile ...) created by
- […]
- 3:14 PM Ticket #9974 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 2:43 PM ChangeLog edited by
- (diff)
- 2:42 PM ChangeLog edited by
- (diff)
- 2:06 PM Ticket #9970 (Crash using open/save dialog) closed by
- can't reproduce
- 2:05 PM Ticket #9969 (Crash using open/save dialog) closed by
- can't reproduce
- 10:06 AM Ticket #8913 (Crash showing Rapid Access at startup) closed by
- worksforme
- 9:56 AM NIAID2023 edited by
- (diff)
- 9:43 AM Ticket #9973 (Models panel automatically resizes column widths when it shouldn't) created by
- […]
- 9:16 AM Ticket #9972 (Graphics crash, macOS 14.0, Intel Iris Plus Graphics) created by
- […]
- 8:31 AM Ticket #9971 (AlphaFold error plot: Operation not permitted) created by
- […]
- 3:58 AM Ticket #9970 (Crash using open/save dialog) created by
- […]
- 3:44 AM Ticket #9969 (Crash using open/save dialog) created by
- […]
Oct 11, 2023:
- 5:59 PM Ticket #9946 (SwissDock: chlorines treated as carbons) closed by
- fixed: Fixed. The fix will be in the next daily build. Fix: …
- 5:50 PM Ticket #9966 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 5:06 PM Ticket #9968 (Save image of sequence/alignment) created by
- Save an image or possibly an SVG of a sequence/alignment
- 12:57 PM Ticket #9967 (3D segmentation cursor doesn't always spawn near the 3D model) created by
- The 3D segmentation cursor always starts at (0,0,0), but 3D models of …
- 12:22 PM Ticket #9945 (QThread: Destroyed while thread is still running) closed by
- duplicate: Same as #9956
- 12:22 PM Ticket #9728 (DICOM: QThread: Destroyed while thread is still running) closed by
- duplicate: Same as #9956
- 12:16 PM Ticket #9966 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 11:58 AM Ticket #9801 (LookSee meeting file transfer very slow, 20 seconds) closed by
- fixed: Using GZipStream took 2.3 seconds to compress 22 Mbytes which would …
- 11:47 AM Ticket #9962 (Syntax error reading marker file) closed by
- can't reproduce: Bad marker file, maybe it is empty (syntax error at column 0 of line …
- 11:46 AM Ticket #9965 (Segmentations opened from files give traceback on edit) created by
- 11:43 AM Ticket #9955 (Movie creation: No space left on device) closed by
- nonchimerax: No disk space when encoding movie. Error writing trailer of …
- 11:40 AM Ticket #9953 (Graphics crash, macOS 13.4.1, Intel Iris Plus Graphics 645) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 10:54 AM Ticket #9956 (Download Dicom tool: QThread: Destroyed while thread is still running) closed by
- fixed: OK, starting another thread while the previous one is active should be …
- 10:41 AM Ticket #9964 (TCIA 1.3.6.1.4.1.14519.5.2.1.234132074440664539509159575625111026305 ...) created by
- 10:38 AM Ticket #9961 (Crash at startup) closed by
- limitation: Hello, it looks like you are trying to run ChimeraX remotely. …
- 9:31 AM Ticket #9963 (ChargeError during dockprep) closed by
- duplicate
- 9:22 AM Ticket #9959 (Session restore: invalid load key) closed by
- duplicate: Restoring new session in old ChimeraX
- 9:20 AM Ticket #9958 (MemoryError opening mmCIF files) closed by
- duplicate
- 9:19 AM Ticket #9957 (Crash in QTabBar::paintEvent) closed by
- duplicate
- 9:19 AM Ticket #9963 (ChargeError during dockprep) created by
- […]
- 9:15 AM Ticket #9954 (MemoryError opening mmCIF files) closed by
- duplicate
- 9:09 AM Ticket #9952 (MemoryError opening mmCIF files) closed by
- duplicate
- 9:06 AM Ticket #9951 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate: Hi Huixia, Thanks for reporting this problem. This is a bug in the Qt …
- 8:39 AM Ticket #9962 (Syntax error reading marker file) created by
- […]
- 8:07 AM Ticket #9961 (Crash at startup) created by
- […]
- 3:56 AM Ticket #9960 (ChargeError during dockprep) created by
- […]
- 3:10 AM Ticket #9959 (Session restore: invalid load key) created by
- […]
- 2:50 AM Ticket #9958 (MemoryError opening mmCIF files) created by
- […]
- 1:19 AM Ticket #9957 (Crash in QTabBar::paintEvent) created by
- […]
Oct 10, 2023:
- 6:34 PM Ticket #9956 (Download Dicom tool: QThread: Destroyed while thread is still running) created by
- […]
- 3:39 PM Ticket #9955 (Movie creation: No space left on device) created by
- […]
- 1:54 PM Ticket #9954 (MemoryError opening mmCIF files) created by
- […]
- 1:38 PM Ticket #9953 (Graphics crash, macOS 13.4.1, Intel Iris Plus Graphics 645) created by
- […]
- 11:55 AM Ticket #9952 (MemoryError opening mmCIF files) created by
- […]
- 11:53 AM 2023-10-12 edited by
- (diff)
- 11:47 AM Dev2023-10-16 created by
- 11:46 AM 2023-10-12 created by
- 11:44 AM DeveloperMeetings edited by
- (diff)
- 11:14 AM Ticket #9950 (PDBimages: No module named 'chimerax.atomic.mmcif') closed by
- fixed: Fixed by new PDBImages bundle in Toolshed. Use menu Tools / More …
- 10:34 AM Ticket #9951 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 10:28 AM Ticket #9944 (MRC header value nsymbt is invalid) closed by
- invalid: Not clear what the error was they were trying to report. They opened …
- 9:32 AM Ticket #9949 (QRhiGles2: Failed to make context current) closed by
- can't reproduce
- 9:30 AM Ticket #9948 (UnicodeDecodeError opening PDB file) closed by
- can't reproduce: 1.6.1 also tries UTF-16 and UTF-32, so what encoding is this file?
- 9:23 AM Ticket #9947 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate: Hi Duc, Thanks for reporting this problem. This is a bug in the Qt …
- 9:08 AM Ticket #9943 (Unknown crash) closed by
- can't reproduce
- 8:04 AM Ticket #9950 (PDBimages: No module named 'chimerax.atomic.mmcif') created by
- […]
- 7:33 AM Ticket #9949 (QRhiGles2: Failed to make context current) created by
- […]
- 6:11 AM Ticket #9948 (UnicodeDecodeError opening PDB file) created by
- […]
- 2:44 AM Ticket #9947 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 1:13 AM Ticket #9946 (SwissDock: chlorines treated as carbons) created by
- […] clusters.dock4.pdb
Oct 9, 2023:
- 8:27 PM Ticket #9945 (QThread: Destroyed while thread is still running) created by
- […]
- 7:33 PM Ticket #9922 (LookSee meeting does not handle two models with same name) closed by
- can't reproduce: I'm not able to reproduce this. There is support for multiple copies …
- 7:12 PM Ticket #9944 (MRC header value nsymbt is invalid) created by
- […]
- 6:14 PM Ticket #9905 (LookSee meeting does not remove hand controllers when participant leaves) closed by
- fixed: Fixed. Now send a participant left message and the others delete the …
- 5:44 PM Ticket #9943 (Unknown crash) created by
- […]
- 5:11 PM Ticket #9923 (LookSee meeting incompatible version warning not shown) closed by
- fixed: Fixed. Made the code wait for the first message which must be the …
- 4:18 PM Dev2023-10-9 edited by
- (diff)
- 3:04 PM Dev2023-10-9 edited by
- (diff)
- 1:58 PM Dev2023-10-9 edited by
- (diff)
- 1:57 PM Ticket #9942 (Implement ribbon worms) created by
- Some users have requested ribbon worms (tubes of varying radius), most …
- 1:36 PM Dev2023-10-9 edited by
- (diff)
- 1:06 PM Ticket #9941 (Crash using File→Open dialog on Windows and/or returning from function) closed by
- can't reproduce
- 1:04 PM Ticket #9941 (Crash using File→Open dialog on Windows and/or returning from function) created by
- […]
- 11:33 AM Ticket #9940 (Save mmCIF: 'SaveOptionsWidget' object has no attribute 'compute_sheets') closed by
- duplicate
- 11:29 AM Ticket #9928 (Graphics crash, macOS 13.0.1, Intel Iris Plus Graphics 655) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 11:28 AM Ticket #9939 (Histogram: `bins` must be positive, when an integer) closed by
- can't reproduce
- 11:04 AM Ticket #9937 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 11:02 AM Ticket #9936 (name 'api_call_headers' is not defined) closed by
- duplicate
- 10:59 AM Ticket #9935 (MemoryError opening mmCIF) closed by
- duplicate
- 10:58 AM Ticket #9934 (Crash while asking to register) closed by
- can't reproduce
- 10:55 AM Ticket #9933 (MemoryError opening mmCIF) closed by
- duplicate
- 10:52 AM Ticket #9931 (Blast: self.job.model_name is None) closed by
- duplicate: Duplicate of #9070
- 10:48 AM Ticket #9930 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 10:35 AM Ticket #9929 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate: Hi Tianyi, Thanks for reporting this problem. This is a bug in the Qt …
- 10:30 AM Ticket #9927 (MemoryError opening mmCIF) closed by
- duplicate: May not _actually_ be a duplicate -- for some reason this user opened …
- 10:12 AM Ticket #9926 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 10:06 AM Ticket #9925 (Restore new session in old ChimeraX) closed by
- limitation
- 7:07 AM Ticket #9940 (Save mmCIF: 'SaveOptionsWidget' object has no attribute 'compute_sheets') created by
- […]
- 6:58 AM Ticket #9939 (Histogram: `bins` must be positive, when an integer) created by
- […]
- 6:23 AM Ticket #9938 (PICKLUSTER: KeyError: 'chain1') created by
- […]
- 1:31 AM Ticket #9937 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
Oct 8, 2023:
- 11:06 PM Ticket #9936 (name 'api_call_headers' is not defined) created by
- […]
- 8:14 PM Ticket #9935 (MemoryError opening mmCIF) created by
- […]
- 8:10 PM Ticket #9934 (Crash while asking to register) created by
- […]
- 8:01 PM Ticket #9933 (MemoryError opening mmCIF) created by
- […]
- 8:01 PM Ticket #9932 (MemoryError saving session) created by
- […]
- 6:47 PM Ticket #9931 (Blast: self.job.model_name is None) created by
- […]
- 3:21 PM Ticket #9930 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 7:45 AM Ticket #9929 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 7:13 AM Ticket #9928 (Graphics crash, macOS 13.0.1, Intel Iris Plus Graphics 655) created by
- […]
- 5:36 AM Ticket #9927 (MemoryError opening mmCIF) created by
- […]
Oct 7, 2023:
- 5:03 AM Ticket #9926 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 4:21 AM Ticket #9925 (Restore new session in old ChimeraX) created by
- […]
Note:
See TracTimeline
for information about the timeline view.
