Timeline



Apr 5, 2022:

11:22 PM Ticket #6548 (MatchMaker: wrapped C/C++ object of type QPushButton has been deleted) created by chimerax-bug-report@…
[…]
7:20 PM Ticket #6547 (Crash creating QWebEngineProfile) created by chimerax-bug-report@…
[…]
11:03 AM Ticket #6168 (Demoted sequence in match_maps after residue deletion) closed by pett
fixed: Fixed. Fix will be in tomorrow's daily build.
10:03 AM Ticket #6527 (RFE: option to always draw a specific model on top) closed by Tom Goddard
not a bug: Seems the problem here was that Mauricio did not know that beta strand …
10:00 AM Ticket #6545 (Crash recording spin movie) closed by Tom Goddard
can't reproduce: ffmpeg encoding failed. ffmpeg does not give any sensible error …
9:54 AM Ticket #6539 (Hang during redraw?) closed by Tom Goddard
can't reproduce: The user typed ctrl-C at the shell (Linux) to interrupt ChimeraX. No …
9:44 AM 2022-4-7 created by Tom Goddard
9:42 AM DeveloperMeetings edited by Tom Goddard
(diff)
9:05 AM Ticket #6546 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
9:01 AM Ticket #6544 (Crash getting Windows version) closed by pett
can't reproduce
8:56 AM Ticket #6541 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
6:58 AM Ticket #6546 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
2:52 AM Ticket #6545 (Crash recording spin movie) created by chimerax-bug-report@…
[…]
12:41 AM Ticket #6544 (Crash getting Windows version) created by chimerax-bug-report@…
[…]

Apr 4, 2022:

8:08 PM Ticket #6543 (Update to AlphaFold 2.2.0) closed by Tom Goddard
fixed: Done.
5:20 PM Ticket #6524 (Loss of occupancy/bfactor) closed by pett
duplicate: Hi Moritz, Update your version of ChimeraX. There was a period of 11 …
5:19 PM Ticket #6543 (Update to AlphaFold 2.2.0) created by Tom Goddard
Update ChimeraX structure prediction from AlphaFold 2.1.0 to 2.2.0. …
4:00 PM Ticket #6542 (Errors checking for newer version) created by mscheung1@…
[…]
3:39 PM Ticket #6541 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
3:24 PM Ticket #6540 (OpenMM crash) created by chimerax-bug-report@…
[…]
3:08 PM Ticket #6539 (Hang during redraw?) created by chimerax-bug-report@…
[…]
12:21 PM Ticket #5164 (Include reference documentation) closed by Zach Pearson
fixed: [https://github.com/RBVI/ChimeraX/commit/932517bbe42f676154f4ece51fb902
12:06 PM Ticket #6538 (Add biomtSet option the sym command) created by jacob_r_anderson@…
Begin forwarded message: From: "Anderson, Jacob via ChimeraX-users" …
11:47 AM Ticket #6531 (Read pseudobonds: syntax error should not produce traceback) closed by Tom Goddard
fixed: Fixed. If atoms are not found give error message but no traceback.
11:35 AM Ticket #6530 (Infinite recursion in find_close_points_boxes) closed by Tom Goddard
duplicate: This bug was fixed 4 months ago, bug #5800. Fix is in daily build. …
11:34 AM Ticket #6496 (Blast failure during AlphaFold search) closed by Zach Pearson
fixed: After reconfiguring the way that the BLAST gui works for another …
11:24 AM Ticket #6537 (Graphics driver crash, macOS 10.13.6, Intel HD Graphics 6000) closed by Tom Goddard
nonchimerax: Apple graphics driver crash. Unfortunately Intel Mac graphics drivers …
11:19 AM Ticket #6536 (Crash in removeDockWidget()) closed by pett
can't reproduce
11:15 AM Ticket #6534 (Traceback with non-numeric seq_conservation attribute) closed by pett
duplicate
10:58 AM Ticket #6533 (Crash attempting to download sequence conservation from ConSurf ...) closed by pett
can't reproduce: I have little idea what the user actually means by their description. …
10:49 AM Ticket #6532 (Crash in event loop) closed by pett
can't reproduce
10:42 AM Ticket #6529 (Problem restoring session: invalid load key) closed by pett
duplicate
10:28 AM Ticket #6526 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
10:28 AM Ticket #6522 (Graphics driver crash, macOS 11.6.4, Intel Iris Plus Graphics 655, ...) closed by Tom Goddard
nonchimerax
10:26 AM Ticket #6525 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
9:33 AM Ticket #6521 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: Given that the user had done nothing else (according to the Python …
9:30 AM Ticket #6520 (Crash emitting signal) closed by pett
can't reproduce
9:28 AM Ticket #6519 (Crash running coulombic) closed by pett
can't reproduce
9:24 AM Ticket #6516 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
9:14 AM Ticket #6537 (Graphics driver crash, macOS 10.13.6, Intel HD Graphics 6000) created by islamnae@…
[…]
6:02 AM Ticket #6536 (Crash in removeDockWidget()) created by chimerax-bug-report@…
[…]

Apr 3, 2022:

8:20 PM Ticket #6535 (Crash using File→Open on Windows and/or in return statement) created by x6207220@…
[…]
3:03 PM Ticket #6534 (Traceback with non-numeric seq_conservation attribute) created by chimerax-bug-report@…
[…]
2:58 PM Ticket #6533 (Crash attempting to download sequence conservation from ConSurf ...) created by chimerax-bug-report@…
[…]
2:46 PM Ticket #6532 (Crash in event loop) created by chimerax-bug-report@…
[…]
2:44 PM Ticket #6531 (Read pseudobonds: syntax error should not produce traceback) created by chimerax-bug-report@…
[…]
9:54 AM Ticket #6530 (Infinite recursion in find_close_points_boxes) created by islamnae@…
[…]
8:33 AM Ticket #6529 (Problem restoring session: invalid load key) created by chimerax-bug-report@…
[…]

Apr 2, 2022:

6:01 PM Ticket #6528 (Crash opening mmCIF file) created by chimerax-bug-report@…
[…]
4:58 AM Ticket #6263 (Molecular Dynamics Viewer: Values array length does not match objects ...) closed by Kyle Diller
fixed: Fixed in version 1.3
4:57 AM Ticket #6383 (MD Viewer: could not broadcast input array from shape (0) into shape (0,3)) closed by Kyle Diller
fixed: Fixed in version 1.4

Apr 1, 2022:

3:46 PM Ticket #6527 (RFE: option to always draw a specific model on top) created by Elaine Meng
Mauricio Losilla would like an option to draw a specific model on top, …
2:51 PM Ticket #6526 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
12:27 PM Ticket #6525 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
8:32 AM Ticket #6524 (Loss of occupancy/bfactor) created by mhunkeler@…
[…]
6:33 AM Ticket #6523 (Matplotlib bug) created by Tristan Croll
[…]
4:52 AM Ticket #6522 (Graphics driver crash, macOS 11.6.4, Intel Iris Plus Graphics 655, ...) created by chimerax-bug-report@…
[…]
1:06 AM Ticket #6521 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]

Mar 31, 2022:

8:51 PM Ticket #6520 (Crash emitting signal) created by chimerax-bug-report@…
[…]
8:49 PM Ticket #6519 (Crash running coulombic) created by chimerax-bug-report@…
[…]
7:31 PM Ticket #6518 (Update OpenMM from version 7.6.0 to 7.7.0) closed by Tom Goddard
fixed: Update to 7.7.0 complete. Tested on all platforms with tug mouse mode …
6:38 PM Ticket #6518 (Update OpenMM from version 7.6.0 to 7.7.0) created by Tom Goddard
Want to update OpenMM because the latest version 7.7.0 has a Mac ARM64 …
4:19 PM Ticket #6286 (Give a good error message if RBVI resources unavailable) closed by Zach Pearson
fixed: Should be fixed by the same NewConnectionError catch that fixed …
4:13 PM Ticket #6497 (Crash showing bug reporter) closed by Tom Goddard
nonchimerax: ChimeraX crashed when it was trying to show the bug reporter dialog …
4:04 PM Ticket #6500 (Close PAE plot with structure) closed by Tom Goddard
fixed: Done.
3:41 PM Ticket #6517 (BLAST results should not show an empty table) closed by Zach Pearson
fixed: [https://github.com/RBVI/ChimeraX/commit/c25142a3c442bd8bc0c8a628c3a273
2:56 PM Ticket #6517 (BLAST results should not show an empty table) created by goddard@…
[…]
2:53 PM Ticket #6516 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
2:25 PM 2022-3-31 edited by Tom Goddard
(diff)
2:25 PM Ticket #6476 (Blast error while web services down) closed by Zach Pearson
fixed
2:24 PM Ticket #6501 (Session restore problem: Chain ID cannot be the empty string) closed by pett
can't reproduce: Hi Irina, I'm glad you found something that works for you. What I …
2:10 PM 2022-3-31 edited by Zach Pearson
(diff)
2:10 PM CZI Grant Status (1).pdf attached to 2022-3-31 by Zach Pearson
Zach's presentation with speaker notes
2:03 PM NTTData edited by Tom Goddard
(diff)
1:58 PM NTTData edited by Elaine Meng
(diff)
1:57 PM NTTData edited by Elaine Meng
(diff)
1:50 PM NTTData edited by Elaine Meng
(diff)
12:34 PM Ticket #6514 (Crash creating QWebEngineProfile) closed by Tom Goddard
nonchimerax: This Windows ChimeraX crash on startup is a bug in the Qt window …
10:54 AM Ticket #6513 (Crash using File→Open dialog on Windows and/or returning from function) closed by pett
can't reproduce
10:46 AM Ticket #6512 (Calling _cpp_modified failed) closed by pett
duplicate: Hi Barrett, Thanks for reporting this problem. I believe it is a …
9:54 AM Ticket #6509 (Crash using File→Open dialog on Windows and/or returning from function) closed by pett
can't reproduce
9:47 AM Ticket #6507 (Crash at startup) closed by pett
can't reproduce
9:43 AM Ticket #6506 (Crash using File→Open dialog on Windows and/or returning from function) closed by pett
can't reproduce
9:41 AM Ticket #6515 (Crash after swapaa) created by adrian.young@…
[…]
7:56 AM Ticket #6514 (Crash creating QWebEngineProfile) created by jeebakdeoghuria13@…
[…]
5:42 AM Ticket #6513 (Crash using File→Open dialog on Windows and/or returning from function) created by chimerax-bug-report@…
[…]
4:16 AM Ticket #6512 (Calling _cpp_modified failed) created by davis797@…
[…]
3:39 AM Ticket #6511 (Focus on sequence selection) created by Tristan Croll
[…]
3:38 AM Ticket #6510 (Zoom/recenter with mouse) created by Tristan Croll
[…]
1:51 AM Ticket #6509 (Crash using File→Open dialog on Windows and/or returning from function) created by chimerax-bug-report@…
[…]

Mar 30, 2022:

11:41 PM Ticket #6508 (Error getting mmCIF templates: URL can't contain control characters) created by chimerax-bug-report@…
[…]
11:40 PM Ticket #6507 (Crash at startup) created by chimerax-bug-report@…
[…]
8:20 PM Ticket #6506 (Crash using File→Open dialog on Windows and/or returning from function) created by chimerax-bug-report@…
[…]
11:32 AM Ticket #6505 (Chimera→ChimeraX session converter) created by Zach Pearson
This is a meta-ticket to track the effort to support Chimera sessions …
11:26 AM Ticket #6503 (Volume Viewer histogram: cannot convert float NaN to integer) closed by Tom Goddard
not a bug: Map file contained not-a-number NaN values. Bad file.
10:40 AM Ticket #6504 (Crash in QScreen::virtualGeometry()) closed by pett
can't reproduce: Probably somehow related to the dual displays
10:35 AM Ticket #6504 (Crash in QScreen::virtualGeometry()) created by chimerax-bug-report@…
[…]
10:26 AM Ticket #6502 (Problem saving blast table info in session) closed by pett
duplicate: Duplicate of #5453
9:39 AM Ticket #6499 (Error in toolshed error message) closed by pett
duplicate
8:55 AM Ticket #6503 (Volume Viewer histogram: cannot convert float NaN to integer) created by chimerax-bug-report@…
[…]
7:38 AM Ticket #6502 (Problem saving blast table info in session) created by chimerax-bug-report@…
[…]
2:36 AM Ticket #6501 (Session restore problem: Chain ID cannot be the empty string) created by i.ihnatenko@…
[…]
2:27 AM Ticket #6500 (Close PAE plot with structure) created by Tristan Croll
[…]

Mar 29, 2022:

10:14 PM Ticket #6499 (Error in toolshed error message) created by chimerax-bug-report@…
[…]
6:05 PM Ticket #5035 (Report sequence identity from MAV) closed by pett
fixed: "seq id" command and "Percent Identity..." context menu entry.
5:53 PM Ticket #6479 (Read EMAN HDF: could not broadcast input array from shape) closed by Tom Goddard
can't reproduce: The user opened an EMAN hdf5 map of size 1960 by 1024 by 60 initially …
5:53 PM Ticket #6491 (Crash opening session) closed by pett
fixed: Again, thanks for reporting this. It will be fixed in tomorrow's …
5:31 PM Ticket #6466 (Failure opening entries 51 and 94 from PDBDev) closed by Tom Goddard
fixed: I fixed the ChimeraX code causing the error opening PDBDev 94. It was …
4:07 PM Ticket #6498 (Reinstalling a bundle gives a traceback, should just give clear error ...) created by goddard@…
[…]
3:57 PM 2022-3-31 created by Tom Goddard
3:56 PM DeveloperMeetings edited by Tom Goddard
(diff)
1:48 PM Ticket #6497 (Crash showing bug reporter) created by moonapakdel@…
[…] clusters.dock4.pdb
11:43 AM Training edited by Tom Goddard
(diff)
10:37 AM Ticket #6494 (Graphics driver crash, macOS 11.4, Radeon Pro 570, dual display) closed by Tom Goddard
nonchimerax: Apple graphics driver crash while Qt was redrawing user interface.
10:21 AM Ticket #6495 (XMAS: 'tuple' object is not callable) closed by pett
nonchimerax
10:18 AM Ticket #6489 (glUniformMatrix4fv: invalid operation) closed by Tom Goddard
nonchimerax: Likely graphics driver error, Windows, GeForce GTX 1650, driver 456.71 …
10:16 AM Ticket #6482 (Crash in swap_buffers) closed by Tom Goddard
nonchimerax: Probably graphics driver crash, Windows, GTX 1050 MaxQ (laptop), May …
9:56 AM Ticket #6492 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
9:38 AM Ticket #6490 (Too many atoms bonded to C) closed by pett
can't reproduce: Probable bad PDB file.
9:38 AM Ticket #6496 (Blast failure during AlphaFold search) created by Elaine Meng
[…]
9:30 AM Ticket #6495 (XMAS: 'tuple' object is not callable) created by chimerax-bug-report@…
[…]
9:25 AM Ticket #6488 (Calling _cpp_modified failed) closed by pett
can't reproduce: Seems like it may be a duplicate of #6168 (Chain getting demoted to …
9:22 AM Ticket #6494 (Graphics driver crash, macOS 11.4, Radeon Pro 570, dual display) created by chimerax-bug-report@…
[…]
9:09 AM Ticket #6493 (Matchmaker: 'NoneType' object has no attribute 'setChecked') created by chimerax-bug-report@…
[…]
9:05 AM Ticket #6486 (Crash reading PDB file) closed by pett
duplicate
9:05 AM Ticket #6485 (Crash reading PDB file) closed by pett
duplicate
9:01 AM Ticket #6484 (Crash reading PDB file) closed by pett
can't reproduce: Hi Mauricio, Thanks for reporting this problem. You should upgrade …
8:47 AM Ticket #6481 (Crash closing tool) closed by pett
can't reproduce
7:53 AM Ticket #6492 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
7:41 AM Ticket #6491 (Crash opening session) created by carmen@…
[…]
7:40 AM Ticket #6490 (Too many atoms bonded to C) created by chimerax-bug-report@…
[…]
7:36 AM Ticket #6489 (glUniformMatrix4fv: invalid operation) created by chimerax-bug-report@…
[…]
2:51 AM Ticket #6488 (Calling _cpp_modified failed) created by chimerax-bug-report@…
[…]

Mar 28, 2022:

8:33 PM Ticket #6451 (ChimeraX 1.3 start up error) closed by Tom Goddard
nonchimerax: Glad it is working now.
5:07 PM Ticket #6487 (Mac multitouch sometimes broken with Qt 6) created by goddard@…
[…]
5:07 PM Ticket #6483 (Blast alphafold search fails: invalid literal for int() with base 10) closed by Zach Pearson
fixed: Should be fixed by …
4:19 PM Ticket #6486 (Crash reading PDB file) created by m.valdivia.delgado@…
[…]
4:17 PM Ticket #6485 (Crash reading PDB file) created by m.valdivia.delgado@…
[…]
4:15 PM Ticket #6484 (Crash reading PDB file) created by m.valdivia.delgado@…
[…]
3:48 PM Ticket #6483 (Blast alphafold search fails: invalid literal for int() with base 10) created by goddard@…
[…]
3:13 PM DeveloperMeetings edited by Zach Pearson
(diff)
3:12 PM Dev2022-4-07 created by Zach Pearson
2:33 PM Ticket #6471 (BLAST sequence search is hung) closed by Zach Pearson
fixed
2:23 PM Ticket #6482 (Crash in swap_buffers) created by sreemantula.arun@…
[…]
2:05 PM Ticket #6481 (Crash closing tool) created by chimerax-bug-report@…
[…]
1:52 PM Ticket #6480 (Closing already-dead tool window?) closed by pett
can't reproduce
1:42 PM Ticket #6480 (Closing already-dead tool window?) created by chimerax-bug-report@…
[…]
11:44 AM Ticket #6478 (Crash in Qt event loop on Windows after changing to stick depiction) closed by Tom Goddard
can't reproduce
11:41 AM Ticket #6474 (Ribbon representation crash during simulation) closed by Tom Goddard
can't reproduce: Crashed when trying to compute the ribbons in this line getting the …
11:37 AM Ticket #6473 (Crash with suspiciously repetitive stack) closed by Tom Goddard
can't reproduce: Mac crash dump did not have any useful info on the crashing thread. …
11:28 AM Ticket #6468 (Crash in Qt event loop after saving sessions with maps) closed by Tom Goddard
can't reproduce: Crash was in _PyObject_Call apparently Qt calling a callback function …
11:22 AM Ticket #6477 (Blast error while web services down) closed by pett
duplicate
11:04 AM Ticket #6467 (Crash after opening sessions containing volumes) closed by Tom Goddard
can't reproduce: After several hundred commands the last command opened a session file. …
10:57 AM Ticket #6465 (Crash showing ribbons) closed by Tom Goddard
can't reproduce: Likely graphics driver crash, Intel Mac, no C traceback symbol names.
10:54 AM Ticket #6464 (Graphics driver crash, Linux, RTX 3080, in swap_buffers) closed by Tom Goddard
nonchimerax: Graphics driver crash. Modern graphics RTX 3080 laptop, driver from …
10:41 AM Ticket #6470 (Save dialog: 'SaveModelOptionWidget' object has no attribute '_name') closed by pett
duplicate: Hi Nitesh, Thanks for reporting this problem. It has been fixed for …
10:10 AM Ticket #6479 (Read EMAN HDF: could not broadcast input array from shape) created by chimerax-bug-report@…
[…]
9:30 AM Ticket #6478 (Crash in Qt event loop on Windows after changing to stick depiction) created by chimerax-bug-report@…
[…]
9:17 AM Ticket #6463 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
9:12 AM Ticket #6462 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
9:00 AM Ticket #6461 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
7:16 AM Ticket #6477 (Blast error while web services down) created by chimerax-bug-report@…
[…]
7:16 AM Ticket #6476 (Blast error while web services down) created by chimerax-bug-report@…
[…]
6:57 AM Ticket #6475 (Crash getting bundle list?) created by chimerax-bug-report@…
[…]
2:30 AM Ticket #6474 (Ribbon representation crash during simulation) created by davis797@…
[…]
2:24 AM Ticket #6473 (Crash with suspiciously repetitive stack) created by davis797@…
[…]

Mar 27, 2022:

8:09 PM Ticket #6472 (Show AlphaFold predicted aligned error (PAE) plots) created by Tom Goddard
Want to show residue-residue predicted aligned error (PAE) calculated …
7:56 PM Ticket #6471 (BLAST sequence search is hung) created by goddard@…
[…]
1:55 PM Ticket #6470 (Save dialog: 'SaveModelOptionWidget' object has no attribute '_name') created by nkkhandelwal@…
[…]
6:26 AM Ticket #6469 (AlphaFold vs. JAX) created by davis797@…
[…] model_1_error

Mar 25, 2022:

6:46 PM Ticket #6468 (Crash in Qt event loop after saving sessions with maps) created by chimerax-bug-report@…
[…]
12:23 PM Ticket #6467 (Crash after opening sessions containing volumes) created by chimerax-bug-report@…
[…]
11:13 AM Ticket #6466 (Failure opening entries 51 and 94 from PDBDev) created by Scooter Morris
[…]
9:03 AM Ticket #6465 (Crash showing ribbons) created by chimerax-bug-report@…
[…]
6:47 AM Ticket #6464 (Graphics driver crash, Linux, RTX 3080, in swap_buffers) created by chimerax-bug-report@…
[…]
6:20 AM Ticket #6463 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
5:43 AM Ticket #6462 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
5:37 AM Ticket #6461 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]

Mar 24, 2022:

6:28 PM Dev2022-3-24 edited by Tom Goddard
(diff)
4:53 PM Ticket #6460 (Bug reporter not in tool window list) closed by pett
duplicate
4:51 PM Ticket #6459 (Bug reporter not in tool window list) closed by pett
duplicate
4:50 PM Ticket #6458 (Bug reporter not in tool window list) closed by pett
can't reproduce: Bringing up Big Reporter on Linux and neither closing it by clicking …
4:33 PM Dev2022-3-24 edited by Tom Goddard
(diff)
4:17 PM Ticket #6453 (Segger: ModuleNotFoundError: No module named 'Surface') closed by Tom Goddard
fixed: Fixed. Segger error if group by connected used with visible only …
4:07 PM Ticket #6448 (Crash in lx4/session saving) closed by Greg Couch
limitation: There are several tracebacks in the log: * KeyError: "No known data …
3:40 PM Ticket #6457 (Problem saving settings file) closed by pett
duplicate
3:36 PM Ticket #6456 (Crash in event loop) closed by pett
can't reproduce
3:34 PM Ticket #6454 (Unknown crash) closed by pett
can't reproduce
3:28 PM Ticket #6452 (Crash saving session(?)) closed by pett
can't reproduce
2:28 PM Ticket #6446 (Crash using File→Open dialog on Windows and/or returning from function) closed by pett
can't reproduce: Hi Nebojsa, Thanks for reporting this problem. We are finding this …
1:06 PM Ticket #6444 (Keyboard interrupt (hang?)) closed by pett
can't reproduce
12:38 PM 2022-3-24 edited by Tom Goddard
(diff)
12:10 PM Ticket #6460 (Bug reporter not in tool window list) created by chimerax-bug-report@…
[…]
12:10 PM Ticket #6459 (Bug reporter not in tool window list) created by chimerax-bug-report@…
[…]
12:10 PM Ticket #6458 (Bug reporter not in tool window list) created by chimerax-bug-report@…
[…]
10:45 AM Ticket #6457 (Problem saving settings file) created by chimerax-bug-report@…
[…]
9:28 AM Ticket #6456 (Crash in event loop) created by chimerax-bug-report@…
[…]
9:19 AM Ticket #6455 (ISOLDE: crash in find_clashing_atoms) created by chimerax-bug-report@…
[…]
7:11 AM Ticket #6454 (Unknown crash) created by chimerax-bug-report@…
[…]
6:42 AM Ticket #6453 (Segger: ModuleNotFoundError: No module named 'Surface') created by chimerax-bug-report@…
[…]
6:14 AM Ticket #6452 (Crash saving session(?)) created by chimerax-bug-report@…
[…]
2:33 AM Ticket #6451 (ChimeraX 1.3 start up error) created by jonathan.lefebre@…
[…] ChimeraX1.3_log.txt
1:45 AM Ticket #6450 (Make open dialog modeless) created by Tom Goddard
The open file dialog is currently modal. Would be easier to use if …

Mar 23, 2022:

8:08 PM Ticket #6449 (Quick Start tutorial links give "Your Internet connection is blocked") created by Tom Goddard
On macOS 12.3 my development ChimeraX builds with Qt 6 and unsigned …
7:50 PM Ticket #6448 (Crash in lx4/session saving) created by nxb318@…
[…]
7:47 PM Ticket #6440 (Crash calculating mesh edges for square mesh volume display) closed by Tom Goddard
can't reproduce: Testing on a 480 by 480 by 480 map (EMDB 12873 at level 0.01) suggests …
7:20 PM Ticket #6447 (ChimeraX Mac build fails with Anaconda installed) closed by Tom Goddard
fixed: Fixed by taking /opt/anaconda3/bin out of the executable search path …
7:19 PM Ticket #6447 (ChimeraX Mac build fails with Anaconda installed) created by Tom Goddard
With Anaconda installed on my macOS 12.3 laptop with M1 CPU in …
2:01 PM Ticket #6446 (Crash using File→Open dialog on Windows and/or returning from function) created by nxb318@…
[…]
1:43 PM Ticket #6413 (Windows Qt6 editable combobox font problematic) closed by pett
fixed: Previous comment wasn't intended for this ticket. Anyway, have …
12:18 PM Ticket #6445 (ISOLDE/OpenMM: Error initializing context: clCreateContext) created by chimerax-bug-report@…
[…]
11:51 AM Ticket #6441 (Crash in self.graphics_window.mapFromGlobal(QCursor.pos())) closed by Tom Goddard
can't reproduce: Log has no commands, so appears to have crashed on startup. But …
11:46 AM Ticket #6444 (Keyboard interrupt (hang?)) created by chimerax-bug-report@…
[…]
11:31 AM Ticket #6438 (Crash switching from Rapid Access to main graphics Window) closed by Tom Goddard
can't reproduce: The user was running some plugin code that triggered when opening a …
11:16 AM Ticket #6443 (Make faulthandler handle multiple running ChimeraX instances) created by Tom Goddard
On Windows or Linux a user can easily start more than one instance of …
11:12 AM Ticket #6436 (Crash drawing status line) closed by Tom Goddard
can't reproduce: The fault handler output lists 3 "Windows fatal exception: access …
10:33 AM Ticket #6442 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
10:27 AM Ticket #6439 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
9:41 AM Ticket #6435 (Crash using non-native open file dialog on Windows) closed by pett
can't reproduce
9:38 AM Ticket #6442 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
5:25 AM Ticket #6441 (Crash in self.graphics_window.mapFromGlobal(QCursor.pos())) created by chimerax-bug-report@…
[…]
4:39 AM Ticket #6440 (Crash calculating mesh edges for square mesh volume display) created by chimerax-bug-report@…
[…]
2:25 AM Ticket #6439 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
1:39 AM Ticket #6438 (Crash switching from Rapid Access to main graphics Window) created by chimerax-bug-report@…
[…]

Mar 22, 2022:

8:09 PM Ticket #6437 (Windows fatal exception: code 0x800706ba. No crash) created by goddard@…
[…] crash_traceback.txt
6:56 PM Ticket #6426 (Crash in self.graphics_window.mapFromGlobal(QCursor.pos())) closed by Tom Goddard
can't reproduce: Looks like a crash at startup since the log had no commands. Log says …
5:54 PM phenix-done-3-24-22 edited by pett
(diff)
5:53 PM phenix-done-3-24-22 edited by pett
(diff)
5:46 PM phenix-done-3-24-22 edited by pett
(diff)
5:31 PM phenix-proposed-3-24-22 edited by pett
(diff)
5:31 PM phenix-proposed-3-24-22 edited by pett
(diff)
5:24 PM phenix-proposed-3-24-22 edited by pett
(diff)
5:11 PM phenix-what-3-24-22 edited by pett
(diff)
5:10 PM phenix-done-3-24-22 created by pett
4:56 PM phenix-proposed-3-24-22 edited by pett
(diff)
4:49 PM Ticket #6436 (Crash drawing status line) created by chimerax-bug-report@…
[…]
4:49 PM phenix-proposed-3-24-22 created by pett
4:23 PM phenix-what-3-24-22 edited by pett
(diff)
2:00 PM phenix-what-3-24-22 created by pett
1:59 PM phenix-3-24-22 created by pett
1:52 PM Features edited by pett
(diff)
1:38 PM Ticket #6435 (Crash using non-native open file dialog on Windows) created by chimerax-bug-report@…
[…]
1:24 PM Dev2022-3-24 created by Tom Goddard
1:23 PM 2022-3-24 created by Tom Goddard
1:20 PM DeveloperMeetings edited by Tom Goddard
(diff)
12:44 PM Ticket #6434 (Support pyproject.toml) created by Zach Pearson
We should not make this a high priority as many infrastructure …
10:31 AM Ticket #6433 (Crash using File→Open on Windows) closed by pett
can't reproduce
10:30 AM Ticket #6432 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
10:28 AM Ticket #6431 (Crash showing Rapid Access at startup) closed by pett
can't reproduce
10:27 AM Ticket #6430 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
10:25 AM Ticket #6427 ([ChimeraX] OpenGL.error.GLError: GLError with VirtualGL 3.0 and ...) closed by Greg Couch
nonchimerax: That appears to be a VirtualGL bug. Please file a bug at …
9:58 AM Ticket #6429 (Crash using File→Open on Windows and/or in return statement) closed by pett
duplicate: Hi Frank, This is a very intermittent (Windows only) problem and not …
9:53 AM Ticket #6428 (name 'critera' is not defined) closed by pett
duplicate: Hi Kelvin, Thanks for reporting this problem. This issue is fixed in …
7:09 AM Ticket #6433 (Crash using File→Open on Windows) created by chimerax-bug-report@…
[…]
6:21 AM Ticket #6432 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
6:01 AM Ticket #6431 (Crash showing Rapid Access at startup) created by chimerax-bug-report@…
[…]

Mar 21, 2022:

11:06 PM Ticket #6430 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
10:28 PM Ticket #6429 (Crash using File→Open on Windows and/or in return statement) created by f.sainsbury@…
[…]
9:35 PM Ticket #6428 (name 'critera' is not defined) created by wh-chung2@…
[…]
5:57 PM Ticket #6427 ([ChimeraX] OpenGL.error.GLError: GLError with VirtualGL 3.0 and ...) created by Chung-Han.Tsai@…
[…]
3:48 PM ChangeLog edited by Elaine Meng
(diff)
3:39 PM Ticket #6407 (Make combine command create shorter new chain ids) closed by pett
fixed: next_chain_id() was only incrementing single-character chains correctly
3:05 PM Ticket #6426 (Crash in self.graphics_window.mapFromGlobal(QCursor.pos())) created by chimerax-bug-report@…
[…]
2:43 PM Ticket #6425 (Qt6: Mac default button goes blank if dialog loses focus) created by Elaine Meng
On a Mac, bring up MatchMaker and then click into the model panel. …
1:47 PM Ticket #6424 (Problem restoring session: invalid load key) closed by pett
duplicate: Hi Sharmishtha, This problem occurs when trying to open a session …
1:40 PM Ticket #6424 (Problem restoring session: invalid load key) created by sharmishthamusalgaonkar@…
[…]
1:31 PM Ticket #6423 (Crash getting Ring information) closed by pett
duplicate
1:28 PM Ticket #6422 (Crash using File→Open on Windows) closed by pett
can't reproduce: Qt5
1:26 PM Ticket #6421 (ChimeraX does not work on windows server running RDS) closed by pett
duplicate: Asked/answered on the chimerax-users list.
1:25 PM Ticket #6420 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: Qt5
1:20 PM Ticket #6418 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: Qt6
1:18 PM Ticket #6417 (Crash using File→Open on Windows) closed by pett
can't reproduce: Qt5
12:15 PM Ticket #6410 (Crash in VerletIntegrator) closed by Tristan Croll
can't reproduce: Crashed simply doing: […] No idea what might have precipitated that.
11:54 AM Ticket #6412 (Crash while running AlphaFold prediction) closed by Tom Goddard
can't reproduce: Probably a Qt html widget crash in Qt 5.15. Hope that Qt 6 fixes it.
11:49 AM Ticket #6415 ('DefaultApi' object has no attribute 'newer_versions') closed by Zach Pearson
duplicate: Duplicate of #5984
10:17 AM Ticket #6411 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
10:13 AM Ticket #6409 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
5:59 AM Ticket #6423 (Crash getting Ring information) created by chimerax-bug-report@…
[…]
5:32 AM Ticket #6422 (Crash using File→Open on Windows) created by chimerax-bug-report@…
[…]
5:27 AM Ticket #6421 (ChimeraX does not work on windows server running RDS) created by fabian.glaser@…
[…]
4:50 AM Ticket #6420 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
2:08 AM Ticket #6419 (Crash using File→Open on Windows and/or in return statement) created by solli@…
[…]
1:58 AM Ticket #6418 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]

Mar 20, 2022:

11:35 PM Ticket #6417 (Crash using File→Open on Windows) created by chimerax-bug-report@…
[…]
8:44 PM Ticket #6416 (Out of space saving log text to file for loading as HTML) created by chimerax-bug-report@…
[…]
2:06 AM Ticket #6415 ('DefaultApi' object has no attribute 'newer_versions') created by chimerax-bug-report@…
[…]

Mar 19, 2022:

9:13 PM Ticket #6414 (Crash creating QWebEngineProfile) created by chimerax-bug-report@…
[…]
11:13 AM Ticket #6413 (Windows Qt6 editable combobox font problematic) created by Tony Schaefer
[…] cmd line descenders.zip
3:09 AM Ticket #6412 (Crash while running AlphaFold prediction) created by chimerax-bug-report@…
[…]
2:45 AM Ticket #6411 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
2:03 AM Ticket #6410 (Crash in VerletIntegrator) created by chimerax-bug-report@…
[…]

Mar 18, 2022:

11:58 PM Ticket #6409 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
6:01 PM Ticket #6408 (Saving GLTF: Structure' object has no attribute 'is_visible') closed by Tom Goddard
fixed: Fixed. Code was using is_visible attribute instead of visible …
5:58 PM Ticket #6408 (Saving GLTF: Structure' object has no attribute 'is_visible') created by goddard@…
[…]
5:55 PM Ticket #5031 (How to copy a Sequence Viewer subsequence to the clip board) closed by pett
fixed: Implemented same copy-sequence feature set that Chimera had. Dialog …
5:49 PM Ticket #6405 ("label height" not accepting non-integer) closed by Tom Goddard
duplicate: I see now. The error is from the label height GUI, menu entry Actions …
5:42 PM Ticket #6407 (Make combine command create shorter new chain ids) created by goddard@…
[…]
11:14 AM Ticket #6404 (Menu items not properly displayed in Segment Map pane) closed by Tom Goddard
fixed: If you mean the menu bar on the Segment Map (Segger) panel has …
9:17 AM Ticket #6406 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
4:21 AM Ticket #6406 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
2:02 AM Ticket #6405 ("label height" not accepting non-integer) created by j.r.lewandowski@…
[…]

Mar 17, 2022:

8:00 PM Ticket #6404 (Menu items not properly displayed in Segment Map pane) created by mcm35@…
[…]
4:19 PM Ticket #6370 (Breaking QCheckbox stateChanged signal change in Qt6) closed by Zach Pearson
wontfix: Closing for now since a workaround has been decided on. If at any …
3:34 PM Ticket #6392 (cannot import name 'QWebEngineDownloadRequest' from 'Qt.QtWebEngineCore') closed by Zach Pearson
fixed: Thank you for your bug report. I believe this problem was fixed some …
3:27 PM Ticket #6356 (PrefersNonDefaultGPU=true) closed by Greg Couch
nonchimerax: What is the output of "lspci | grep VGA"? I want to confirm that the …
2:19 PM Ticket #6362 (uic not in Qt shim) closed by Zach Pearson
not a bug: OK, closing for now but feel free to send me an email if you need me …
2:00 PM Ticket #6399 (Crash using File→Open dialog on Windows and/or returning from function) closed by pett
can't reproduce
1:56 PM Ticket #6398 (Crash in garbage collection during new object allocation) closed by pett
duplicate: Hi Kasey, Thanks for reporting this problem. We believe it was a …
1:50 PM Ticket #6403 (Add a centering option when saving GLTF) created by phil.cruz@…
Phil Cruz mentioned in today's NIAID / ChimeraX meeting that he needed …
1:49 PM Ticket #6397 (Crash using File→Open dialog on Windows and/or returning from function) closed by pett
can't reproduce
1:46 PM Ticket #6396 (Crash in event loop after matchmaker) closed by pett
can't reproduce
1:45 PM Ticket #6395 (Crash in event loop) closed by pett
can't reproduce
1:43 PM Ticket #6402 (QWebEnginePage has no view() method) created by pett
Reproduce by opening 5uhb and clicking on "rifampicin" in the …
1:40 PM NTTData edited by pett
(diff)
1:39 PM NTTData edited by pett
(diff)
1:36 PM NTTData edited by Elaine Meng
(diff)
1:23 PM NTTData edited by Elaine Meng
(diff)
1:00 PM Ticket #6394 (Crash using File→Open dialog on Windows and/or adding trigger handler) closed by pett
can't reproduce
12:53 PM Ticket #6393 (Crash in event loop) closed by pett
can't reproduce
12:20 PM 2022-3-17 edited by Tom Goddard
(diff)
12:20 PM 2022-3-17 edited by Tom Goddard
(diff)
11:04 AM Ticket #6401 (problem opening solid state NMR structures (7K3G)) created by J.Procter@…
[…]
10:56 AM Ticket #6400 (Toolshed offers Install button for ISOLDE when dependencies not met) created by goddard@…
[…]
10:54 AM Ticket #6391 (Phenix douse log link crashes ChimeraX) closed by pett
duplicate: It's because of the long atom spec issued by the link's "sel" command. …
7:42 AM Ticket #6399 (Crash using File→Open dialog on Windows and/or returning from function) created by chimerax-bug-report@…
[…]
7:15 AM Ticket #6398 (Crash in garbage collection during new object allocation) created by kaseyc327@…
[…]
7:06 AM Ticket #6397 (Crash using File→Open dialog on Windows and/or returning from function) created by chimerax-bug-report@…
[…]
3:06 AM Ticket #6396 (Crash in event loop after matchmaker) created by chimerax-bug-report@…
[…]
2:44 AM Ticket #6395 (Crash in event loop) created by chimerax-bug-report@…
[…]

Mar 16, 2022:

11:48 PM Ticket #6394 (Crash using File→Open dialog on Windows and/or adding trigger handler) created by chimerax-bug-report@…
[…]
11:26 PM Ticket #6393 (Crash in event loop) created by chimerax-bug-report@…
[…]
8:20 PM Ticket #6330 (KeyError handling Blast results) closed by Zach Pearson
fixed: I added some defensive code to the blastprotein bundle to handle the …
5:35 PM Ticket #6392 (cannot import name 'QWebEngineDownloadRequest' from 'Qt.QtWebEngineCore') created by murpholinox@…
[…]
2:00 PM Ticket #6391 (Phenix douse log link crashes ChimeraX) created by pett
[…]
10:51 AM Ticket #6388 (Crash using File→Open on Windows) closed by pett
can't reproduce
10:48 AM Ticket #6387 (Found H-bonds differ) closed by pett
not a bug: Hi, It looks like that when you used the tool you unchecked the …
10:33 AM Ticket #6385 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
10:30 AM Ticket #6390 (Crash using File→Open on Windows and/or in return statement) created by adrian.young@…
[…]
9:47 AM Ticket #6389 (Toolshed list of bundle developers gives error) created by Tom Goddard
Using the Toolshed web page "Bundle Developers" link gives a long …
9:03 AM Ticket #6388 (Crash using File→Open on Windows) created by chimerax-bug-report@…
[…]
5:31 AM Ticket #6387 (Found H-bonds differ) created by Qchao.sun@…
[…]
4:03 AM Ticket #6386 (Avoid opening a zillion alignments) created by chimerax-bug-report@…
[…]
3:17 AM Ticket #6385 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]

Mar 15, 2022:

5:13 PM Ticket #6384 (Host Trac using a cloud service) created by Tom Goddard
We should investigate hosting our Trac databases for Chimera and …
2:45 PM Ticket #6383 (MD Viewer: could not broadcast input array from shape (0) into shape (0,3)) created by parmar@…
[…] coords.pdb
1:54 PM Ticket #6380 (Qt6: SortOrder no longer castable to int) closed by pett
fixed: Hi Gulriz, This is fixed in tomorrow's daily build. --Eric Eric …
12:46 PM Ticket #6382 (Bad Qt6 import in help viewer causing Qt5 problems) closed by Zach Pearson
fixed: I believe this problem was fixed in …
12:29 PM Ticket #6382 (Bad Qt6 import in help viewer causing Qt5 problems) created by chimerax-bug-report@…
[…]
11:25 AM Ticket #4692 (Loading coordsets does not bring up slider + related problems) closed by pett
fixed: Was fixed in September of last year when the 'slider' option (default …
11:17 AM Ticket #6381 (Add a tug command) created by Tom Goddard
Would be nice to have a tug command that would allow tugging specified …
10:06 AM Ticket #6377 (Crash saving/encoding movie(?)) closed by Tom Goddard
can't reproduce: Top hits for this error code "Windows fatal exception: code …
9:57 AM 2022-3-17 created by Tom Goddard
9:56 AM DeveloperMeetings edited by Tom Goddard
(diff)
6:50 AM Ticket #6380 (Qt6: SortOrder no longer castable to int) created by gulriz.kurban@…
[…]
6:39 AM Ticket #6379 (Crash using File→Open on Windows and/or in return statement) created by martti.tolvanen@…
[…]
4:27 AM Ticket #6378 (Registration check: 'utf-8' codec can't decode byte) created by weberm@…
[…]

Mar 14, 2022:

9:38 PM Ticket #6377 (Crash saving/encoding movie(?)) created by chimerax-bug-report@…
[…]
5:48 PM Ticket #6376 (Segger menu bar text squished on Mac with Qt 6) closed by Tom Goddard
fixed: Fixed. Work around Qt bug with explicit width and height for File and …
5:42 PM Ticket #6376 (Segger menu bar text squished on Mac with Qt 6) created by goddard@…
[…]
5:17 PM Ticket #6375 (Segger make_surfaces recursion) closed by Tom Goddard
fixed: Fixed. The Segger menu entry Regions / Regions Overlapping Current …
3:58 PM Ticket #6371 (Graphics crash, macOS 10.14.6, Intel Iris Plus Graphics 650) closed by Tom Goddard
nonchimerax: Apple graphics driver crash.
1:27 PM Ticket #6348 (Parsing BlastProtein results failed: 'hits') closed by Zach Pearson
fixed: [https://github.com/RBVI/ChimeraX/commit/ffd748d1417c0346643bc57287d768
12:38 PM Ticket #6375 (Segger make_surfaces recursion) created by chimerax-bug-report@…
[…]
12:00 PM Ticket #6374 (Crash in removeDockWidget()) closed by pett
can't reproduce
11:59 AM ChangeLog edited by Tom Goddard
(diff)
11:57 AM Ticket #6372 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
11:53 AM Ticket #6369 (Qt6 shell tab-completion crash) closed by pett
duplicate: Duplicate of #6363; adding Tony to recipient list for that ticket
11:51 AM Ticket #6368 (H-bonds: acc_phi_psi() takes 8 positional arguments but 9 were given) closed by pett
can't reproduce: This *typically* happens for structures with bad connectivity, but I …

Mar 12, 2022:

10:48 PM Ticket #6374 (Crash in removeDockWidget()) created by chimerax-bug-report@…
[…]
10:58 AM Ticket #6373 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
7:42 AM Ticket #6372 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]

Mar 12, 2022:

11:06 PM Ticket #6371 (Graphics crash, macOS 10.14.6, Intel Iris Plus Graphics 650) created by chimerax-bug-report@…
[…]
10:41 PM Ticket #6370 (Breaking QCheckbox stateChanged signal change in Qt6) created by Tony Schaefer
[…]
10:18 PM Ticket #6369 (Qt6 shell tab-completion crash) created by Tony Schaefer
[…]
7:27 PM Ticket #6368 (H-bonds: acc_phi_psi() takes 8 positional arguments but 9 were given) created by chimerax-bug-report@…
[…]

Mar 11, 2022:

6:33 PM Ticket #6367 (Crash opening PDB file) created by heather.noriega@…
[…] Pert_2PEG_400_model_cordUNG.pdb
2:09 PM Ticket #6268 (Release PyQt6 to the daily builds) closed by Zach Pearson
fixed: It's out!
1:18 PM Ticket #6366 ("log metadata" info not preserved through sessions) created by Elaine Meng
[…]
12:19 PM Ticket #6365 (Loading pickled file in thread crashes) created by Tristan Croll
[…]
12:06 PM Ticket #6364 (Qt6 shell tab-completion crash) closed by pett
duplicate
11:44 AM Ticket #6360 (Graphics crash, macOS 12.2.1, Intel HD Graphics 615) closed by Tom Goddard
nonchimerax: Apple graphics driver crash.
11:44 AM Ticket #6364 (Qt6 shell tab-completion crash) created by pett
[…]
11:42 AM Ticket #6359 (Graphics crash, macOS 10.13.6, Intel Iris Plus Graphics 655) closed by Tom Goddard
nonchimerax: Apple graphics driver crash.
11:40 AM Ticket #6358 (Graphics crash, macOS 11.6.4, Intel Iris Plus Graphics 655, dual display) closed by Tom Goddard
nonchimerax: Apple graphics driver crash.
11:03 AM Ticket #6363 (Qt6 shell tab-completion crash) created by Tristan Croll
[…]
10:15 AM Ticket #6361 (ISOLDE Qt6 splash screen crash) closed by Tristan Croll
invalid: Wait, crap - my bad. Seems somehow I forgot to actually commit the fix …
9:54 AM Ticket #6362 (uic not in Qt shim) created by Tristan Croll
[…]
9:50 AM Ticket #6361 (ISOLDE Qt6 splash screen crash) created by Tristan Croll
[…]
9:43 AM Ticket #6357 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
8:45 AM Ticket #6360 (Graphics crash, macOS 12.2.1, Intel HD Graphics 615) created by chimerax-bug-report@…
[…]
6:44 AM Ticket #6359 (Graphics crash, macOS 10.13.6, Intel Iris Plus Graphics 655) created by chimerax-bug-report@…
[…]
3:24 AM Ticket #6358 (Graphics crash, macOS 11.6.4, Intel Iris Plus Graphics 655, dual display) created by chimerax-bug-report@…
[…]
12:52 AM Ticket #6357 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]

Mar 10, 2022:

6:32 PM Ticket #6356 (PrefersNonDefaultGPU=true) created by moimaian@…
[…] UCSF-ChimeraX-1.3.desktop
6:00 PM Ticket #6355 (Toolbar: AttributeError: 'QDropEvent' object has no attribute 'pos') created by Greg Couch
[…]
3:56 PM Dev2022-3-10 edited by Tom Goddard
(diff)
3:56 PM Ticket #6345 (BLAST search takes 60 seconds in daily build, 7 seconds in ChimeraX 1.3) closed by Zach Pearson
fixed
3:07 PM Ticket #6354 (Session restore: invalid load key) closed by pett
duplicate
3:05 PM Ticket #6353 (model loops: chain not in match maps) closed by pett
duplicate
3:04 PM Ticket #6352 (model loops: chain not in match maps) closed by pett
fixed
2:57 PM Ticket #6347 (Matchmaker: no reference chains) closed by pett
can't reproduce
2:55 PM Ticket #6351 (Crash in event loop) closed by pett
can't reproduce: Classic
2:47 PM Ticket #6350 (no region.destroy() method) closed by pett
fixed
2:46 PM 2022-3-10 edited by Tom Goddard
(diff)
12:05 PM Ticket #6349 (glClear: invalid framebuffer operation) closed by Tom Goddard
duplicate: OpenGL error trying to draw status line. Possibly related to …
10:39 AM Ticket #6354 (Session restore: invalid load key) created by chimerax-bug-report@…
[…]
9:49 AM Ticket #6353 (model loops: chain not in match maps) created by chimerax-bug-report@…
[…]
9:49 AM Ticket #6352 (model loops: chain not in match maps) created by chimerax-bug-report@…
[…]
9:45 AM Ticket #6344 (Various old errors) closed by pett
duplicate
6:52 AM Ticket #6351 (Crash in event loop) created by chimerax-bug-report@…
[…]
5:06 AM Ticket #6350 (no region.destroy() method) created by chimerax-bug-report@…
[…]
1:30 AM Ticket #6349 (glClear: invalid framebuffer operation) created by chimerax-bug-report@…
[…]

Mar 9, 2022:

7:25 PM Ticket #6336 (RealSense camera view clips VR gui elements) closed by Tom Goddard
fixed: Fixed. Code had TODO comment about exactly this problem saying VR …
5:21 PM ChangeLog edited by Tom Goddard
(diff)
5:14 PM ChangeLog edited by Tom Goddard
(diff)
4:27 PM Ticket #6348 (Parsing BlastProtein results failed: 'hits') created by goddard@…
[…]
3:37 PM Ticket #6303 (Help viewer context menu not working in Qt6) closed by Zach Pearson
fixed: [https://github.com/RBVI/ChimeraX/commit/8ec79323819f453f2bb6c3b12a6fdc
3:05 PM Ticket #6347 (Matchmaker: no reference chains) created by chimerax-bug-report@…
[…]
2:41 PM Ticket #6346 (Speed up AlphaFold database search possibly with mmseqs2) created by Tom Goddard
Currently the "alphafold match" command currently takes about 12 …
2:32 PM Ticket #6345 (BLAST search takes 60 seconds in daily build, 7 seconds in ChimeraX 1.3) created by goddard@…
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12:05 PM Ticket #6271 (in techpreview Help Viewer (browser), trying to copy text gives traceback) closed by Zach Pearson
fixed: As I said in comment:4:ticket:6270, QWebEnginePage moved to …
12:04 PM Ticket #6270 (in techpreview, trying to get context menu in ChimeraX help viewer ...) closed by Zach Pearson
fixed: As I said in comment:3:ticket:6303, QWebEnginePage moved to …
12:03 PM Ticket #6344 (Various old errors) created by chimerax-bug-report@…
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12:02 PM Ticket #6343 (Update search of AlphaFold database to January 2022 version) closed by Tom Goddard
fixed: Updated and tested. BLAST search of AlphaFold now takes 60 seconds.
12:02 PM Ticket #6343 (Update search of AlphaFold database to January 2022 version) created by Tom Goddard
EBI made their 3rd update to the AlphaFold database on January 27, …
11:51 AM Ticket #6335 (Toolshed install of bundles broken with Qt 6) closed by Zach Pearson
fixed: Should be fixed by …
10:03 AM Ticket #6341 (Graphics crash, macOS 11.6.3, Intel Iris Pro) closed by Tom Goddard
nonchimerax: Apple graphics driver crash on very old Mac laptop. Only Apple can …
9:59 AM Ticket #6339 (Failure creating downloads directory: No such file or directory) closed by Tom Goddard
wontfix: This user must have deleted their Downloads directory. This is so …
9:26 AM Ticket #6340 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
9:22 AM Ticket #6338 (Crash getting Structure._graphics_changeds attribute after selection ...) closed by pett
can't reproduce
8:48 AM Ticket #6342 (Crash registering webcam command during session save) created by chimerax-bug-report@…
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4:34 AM Ticket #6341 (Graphics crash, macOS 11.6.3, Intel Iris Pro) created by georgios.hatzopoulos@…
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4:10 AM Ticket #6340 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
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1:36 AM Ticket #6339 (Failure creating downloads directory: No such file or directory) created by chimerax-bug-report@…
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1:10 AM Ticket #6338 (Crash getting Structure._graphics_changeds attribute after selection ...) created by chimerax-bug-report@…
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Mar 8, 2022:

6:20 PM Ticket #6337 (Try newer RealSense depth cameras for mixed reality video capture) created by Tom Goddard
Begin forwarded message: From: Tom Goddard Subject: ChimeraX mixed …
5:34 PM Ticket #6336 (RealSense camera view clips VR gui elements) created by goddard@…
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4:39 PM Ticket #6335 (Toolshed install of bundles broken with Qt 6) created by goddard@…
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4:26 PM Ticket #6334 (Say Windows 11 supported on Download page) created by Tom Goddard
We should say that ChimeraX is supported on Windows 11 on the download …
2:09 PM Ticket #6333 (Show AlphaFold predicted aligned error (PAE) for selected residues) created by Tristan Croll
[…] P0C7U0_questionable_interface.cxs
1:17 PM Ticket #6332 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
1:15 PM Ticket #6331 (Unknown crash) closed by pett
can't reproduce
1:09 PM Ticket #6329 (Saving command history: No space left on device) closed by pett
nonchimerax
1:04 PM Ticket #6327 (Crash showing Rapid Access at startup) closed by pett
can't reproduce
1:00 PM Ticket #6326 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
10:24 AM 2022-3-10 created by Tom Goddard
10:23 AM DeveloperMeetings edited by Tom Goddard
(diff)
8:58 AM Ticket #6332 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
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7:22 AM Ticket #6331 (Unknown crash) created by chimerax-bug-report@…
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4:25 AM Ticket #6330 (KeyError handling Blast results) created by chimerax-bug-report@…
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3:41 AM Ticket #6329 (Saving command history: No space left on device) created by chimerax-bug-report@…
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2:00 AM Ticket #6328 (Crash using File→Open on Windows and/or in return statement) created by wh-chung2@…
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1:11 AM Ticket #6327 (Crash showing Rapid Access at startup) created by chimerax-bug-report@…
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Mar 7, 2022:

1:13 PM Ticket #6326 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
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11:54 AM Ticket #6085 (No QAbstractVideoSurface in Qt6) closed by Tom Goddard
fixed: Fixed. Made webcam command work with Qt6. Qt 6 greatly changed the …
11:45 AM Ticket #6323 (Crashed on quit using webcam command with Qt6) closed by Tom Goddard
fixed: Fixed. ChimeraX Python code was not holding references to the …
11:41 AM Ticket #6325 (Crash on exit after webcam off command deleting QMediaCaptureSession ...) closed by Tom Goddard
fixed: Fixed. Apparently if the QCamera is deleted by "webcam off" and later …
10:53 AM Ticket #6324 (Matchmaker: 'NoneType' object has no attribute 'setChecked') closed by pett
duplicate: Duplicate of #5207
10:46 AM Ticket #6325 (Crash on exit after webcam off command deleting QMediaCaptureSession ...) created by goddard@…
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10:44 AM Ticket #6324 (Matchmaker: 'NoneType' object has no attribute 'setChecked') created by chimerax-bug-report@…
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10:36 AM Ticket #6323 (Crashed on quit using webcam command with Qt6) created by goddard@…
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10:28 AM Ticket #6211 (Problem querying for new version: 'DefaultApi' object has no attribute ...) closed by Zach Pearson
duplicate: Should be fixed in any build from after 01/24
10:06 AM Ticket #6314 (Error while fetching from AlphaFold database) closed by Zach Pearson
fixed: Switched the default version on the backend from 2 to 1 and ran those …
9:55 AM Ticket #6319 (Crash saving .cmap file) closed by Tom Goddard
can't reproduce: PyTables crashes saving hdf5 file (*.cmap) on this user's Ubuntu 18.04 …
9:46 AM Ticket #6322 (Bad pseudobond / group attributes) closed by pett
can't reproduce: Would need the alternative_cox_position.cxs session file to have any …
9:23 AM Ticket #6321 (Crash saving .cmap file) closed by pett
duplicate
9:22 AM Ticket #6320 (Crash saving .cmap file) closed by pett
duplicate
4:51 AM Ticket #6322 (Bad pseudobond / group attributes) created by chimerax-bug-report@…
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3:41 AM Ticket #6321 (Crash saving .cmap file) created by chimerax-bug-report@…
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3:40 AM Ticket #6320 (Crash saving .cmap file) created by chimerax-bug-report@…
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3:38 AM Ticket #6319 (Crash saving .cmap file) created by chimerax-bug-report@…
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Mar 6, 2022:

9:12 AM Ticket #6318 (Crash creating QWebEngineProfile) created by chimerax-bug-report@…
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