![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Aug 5, 2022:
- 7:27 PM Ticket #7410 (Crash creating SEQCROW QMenuBar in ARM tech preview) created by
- […]
- 6:05 PM Ticket #7409 (Probable SEQCROW/Qt crash) closed by
- can't reproduce: SEQCROW makes extensive use of QMenuBar widgets whereas they are not …
- 5:53 PM Ticket #7409 (Probable SEQCROW/Qt crash) created by
- […]
- 5:26 PM Ticket #7406 (Make the "close session" command reset to default graphics settings) closed by
- fixed: Fixed. Using command "close session" instead of "close" will now …
- 5:02 PM Ticket #7066 (Douse tool enhancements) closed by
- fixed: Launcher implemented
- 3:17 PM Ticket #7408 (Graphics crash, macOS 12.5, AMD Radeon R9 M395) created by
- […]
- 2:09 PM Ticket #7401 (Maps not aligned) closed by
- not a bug: Ok. I hope to put in a fix soon (next week?) that will automatically …
- 1:58 PM Ticket #7407 (ArtiaX error after closing all models and opening new particle list) created by
- […]
- 1:34 PM Ticket #7404 (Rotate models: Require contiguous n x 3 x 4 array) closed by
- duplicate: Fixed a few days ago. Super annoying that numpy 1.23 changed the …
- 1:25 PM Ticket #7403 (Pseudobond drawing: Cylinder end point, radii or rotation array not ...) closed by
- duplicate
- 1:05 PM Ticket #3863 (Linking two chains merges them) closed by
- wontfix: Upon further review, I have decided to do nothing about this. I want …
- 12:18 PM Ticket #7406 (Make the "close session" command reset to default graphics settings) created by
- Moritz requests command to reset clipping / lighting / background / …
- 12:15 PM Ticket #7405 (Revert rotate independent mouse mode to normal rotation when models closed) created by
- […]
- 10:58 AM Ticket #7404 (Rotate models: Require contiguous n x 3 x 4 array) created by
- […]
- 10:31 AM Ticket #7403 (Pseudobond drawing: Cylinder end point, radii or rotation array not ...) created by
- […]
- 10:15 AM Ticket #7402 (Crash at startup showing Rapid Access) created by
- […]
- 9:32 AM Ticket #7401 (Maps not aligned) created by
- […] Screen Shot 2022-08-05 at 9.25.29 AM.png
- 9:00 AM Ticket #7399 (Pseudobond drawing: Cylinder end point, radii or rotation array not ...) closed by
- duplicate
- 4:43 AM Ticket #7400 (Crash at startup showing Rapid Access) created by
- […]
- 1:11 AM Ticket #7399 (Pseudobond drawing: Cylinder end point, radii or rotation array not ...) created by
- […]
Aug 4, 2022:
- 6:38 PM Ticket #7397 (vop: 'Place' object has no attribute 'position') closed by
- fixed: Fixed. The volume unroll command center option parsing was broken. A …
- 6:30 PM Ticket #166 (Side view display for orthographic camera) closed by
- fixed: Fixed. Side view scaling and bounding lines are now correct in …
- 5:38 PM Ticket #7398 (Crash showing Rapid Access at startup) closed by
- can't reproduce
- 5:26 PM Ticket #2739 (Poor visibility for side view clip planes) closed by
- fixed: Fixed. Made line colors match Chimera. Also eye and clip planes turn …
- 5:01 PM Ticket #7362 (Side view not going away) closed by
- fixed: Fixed. Seems this bug was introduced by Qt 6.3.1. The side view …
- 4:35 PM Ticket #7344 (MemoryError saving session) closed by
- nonchimerax: I'm surprised the ran out of memory lz4 compressing the ChimeraX …
- 4:20 PM Ticket #7396 (Make bug reporter distinguish Mac Intel and ARM ChimeraX versions) closed by
- worksforme: Not needed. The "Platform" line at the top of the bug report …
- 4:19 PM Ticket #7398 (Crash showing Rapid Access at startup) created by
- […]
- 3:02 PM 2022-8-4 edited by
- (diff)
- 2:22 PM Ticket #7397 (vop: 'Place' object has no attribute 'position') created by
- […]
- 2:19 PM Ticket #6191 (QT bug?) closed by
- can't reproduce: Insufficient information to reproduce.
- 2:08 PM Ticket #6669 (This copy of PyQt is unlicensed on macOS arm64) closed by
- nonchimerax: Fixed by Riverbank after prodding from Tom Goddard.
- 2:04 PM NIAID2022 edited by
- (diff)
- 2:02 PM NIAID2022 edited by
- (diff)
- 1:24 PM NIAID2022 edited by
- (diff)
- 12:26 PM Ticket #7396 (Make bug reporter distinguish Mac Intel and ARM ChimeraX versions) created by
- Currently bug reporter gives no indication if the Intel or ARM …
- 12:22 PM Ticket #7395 (Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with ...) created by
- Mac ARM ChimeraX is logging many warnings […] in ticket #7393.
- 10:30 AM Ticket #7389 (Freeze accessing Toolshed) closed by
- can't reproduce: Are you having network problems? "More Tools..." uses an internal web …
- 10:29 AM Ticket #7394 (Stop simulation: model is None) created by
- […]
- 10:26 AM Ticket #7393 (Pseudobond drawing: Cylinder end point, radii or rotation array not ...) closed by
- duplicate
- 10:13 AM Ticket #7392 (Crash in QApplication.quit()) closed by
- can't reproduce
- 9:41 AM Ticket #7393 (Pseudobond drawing: Cylinder end point, radii or rotation array not ...) created by
- […]
- 9:40 AM Ticket #7386 (Crash showing Rapid Access at startup) closed by
- can't reproduce
- 8:37 AM Ticket #7392 (Crash in QApplication.quit()) created by
- […]
- 8:33 AM Ticket #7391 (ArtiaX: ValueError: Unknown class name 'MarkerSetPlus') created by
- […]
- 6:16 AM Ticket #7390 (Crash in color button code) created by
- […]
- 5:56 AM Ticket #7389 (Freeze accessing Toolshed) created by
- […]
Aug 3, 2022:
- 8:16 PM Ticket #7388 (BLAST of NR database uses 180 Gbytes of resident memory on server) created by
- This ticket is about high server memory use by BLAST searches of NR …
- 6:57 PM Ticket #7384 (Pseudobond drawing: Cylinder end point, radii or rotation array not ...) closed by
- fixed: Fixed. Changed the arrays C++ code is_contiguous() method to accept 0 …
- 6:09 PM Ticket #7387 (BLAST of Uniref50, UniRef90, UniRef100 appears to be using old ...) created by
- Not sure if these are the uniref databases being used by blast …
- 6:07 PM Ticket #7386 (Crash showing Rapid Access at startup) created by
- […]
- 6:03 PM Ticket #7385 (Crash showing Rapid Access at startup) closed by
- can't reproduce
- 6:00 PM Ticket #7383 (UnicodeDecodeError reading PDB file) closed by
- can't reproduce: I am totally mystified by this stack trace. When reading a normal …
- 3:32 PM Ticket #7385 (Crash showing Rapid Access at startup) created by
- […]
- 12:33 PM Ticket #7384 (Pseudobond drawing: Cylinder end point, radii or rotation array not ...) created by
- […]
- 11:47 AM Ticket #7383 (UnicodeDecodeError reading PDB file) created by
- […]
- 10:34 AM Ticket #7382 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 10:33 AM Ticket #7377 (Crash reporter: ~/Library/Logs/DiagnosticReports permission denied) closed by
- duplicate: This error happens when ChimeraX checks to see if it crashed the last …
- 10:31 AM Ticket #7380 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 10:29 AM Ticket #7379 (Crash during partial structure deletion) closed by
- can't reproduce
- 10:26 AM Ticket #7378 (Crash deleting structure during session close) closed by
- can't reproduce: Not enough info to reproduce. Could well already be fixed.
- 10:21 AM Ticket #7376 (Crash in fork) closed by
- limitation: Was using 8.1GB at the time.
- 10:19 AM Ticket #7375 (Unknown crash after "volume level" command) closed by
- can't reproduce: Was using 8.6GB at the time
- 10:04 AM Ticket #7382 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 8:54 AM Ticket #7381 (ISOLDE GUI startup: __init__() got an unexpected keyword argument ...) created by
- […]
- 6:24 AM Ticket #7380 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 5:31 AM Ticket #7379 (Crash during partial structure deletion) created by
- […]
- 4:53 AM Ticket #7378 (Crash deleting structure during session close) created by
- […]
- 12:17 AM Ticket #7377 (Crash reporter: ~/Library/Logs/DiagnosticReports permission denied) created by
- […]
Aug 2, 2022:
- 11:11 PM Ticket #7322 (PAE data not opened) closed by
- fixed: Fixed. I finally figured this out. A change to ChimeraX on July 8 to …
- 10:02 PM Ticket #7376 (Crash in fork) created by
- […]
- 3:44 PM Ticket #7375 (Unknown crash after "volume level" command) created by
- […]
- 2:10 PM Ticket #7374 (Crash destroying tool during garbage collection) created by
- […]
- 11:56 AM Ticket #7369 ("close" fails to close models in certain situations) closed by
- fixed: Objects.invert() was failing to account for pseudobond groups. Fix: …
- 11:51 AM Ticket #7373 (Make segmentations overlap DICOM volumes properly) created by
- It took forever to figure out how to create a segmentation, and to my …
- 10:21 AM 2022-7-28 edited by
- (diff)
- 10:21 AM 2022-8-4 created by
- 10:19 AM DeveloperMeetings edited by
- (diff)
- 10:10 AM Ticket #7372 (Unknown crash) closed by
- can't reproduce: Was using 8.4GB at the time
- 10:06 AM Ticket #7370 (Problem reading IMOD file) closed by
- duplicate: Fixed 7 months ago. Ticket #5892.
- 8:14 AM Ticket #7368 (Crash handling symmetry) closed by
- duplicate: Back in the system. Thanks Scooter!
- 6:34 AM Ticket #7372 (Unknown crash) created by
- […]
- 3:43 AM Ticket #7371 (Toolshed installing wrong version) created by
- […]
Aug 1, 2022:
- 6:10 PM Ticket #7370 (Problem reading IMOD file) created by
- […]
- 5:58 PM Ticket #7369 ("close" fails to close models in certain situations) created by
- With 1nwd open (NMR ensemble with metal coordination groups), "close …
- 5:40 PM Ticket #7367 (Session save: function 'set_pbgroup_py_instance' not found) closed by
- duplicate: Hi Janice, Thanks for reporting this problem. It was fixed about a …
- 4:41 PM Ticket #7368 (Crash handling symmetry) created by
- […]
- 2:02 PM Ticket #7367 (Session save: function 'set_pbgroup_py_instance' not found) created by
- […]
- 1:06 PM Ticket #7366 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 11:25 AM Dev2022-8-1 edited by
- (diff)
- 11:23 AM Dev2022-8-1 edited by
- (diff)
- 11:18 AM Dev2022-8-1 edited by
- (diff)
- 11:09 AM Ticket #7366 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 10:56 AM Dev2022-7-25 edited by
- (diff)
- 10:56 AM Dev2022-7-26 edited by
- (diff)
- 10:55 AM Dev2022-8-1 edited by
- (diff)
- 10:55 AM Dev2022-8-1 created by
- 10:51 AM DeveloperMeetings edited by
- (diff)
- 10:51 AM DeveloperMeetings edited by
- (diff)
- 10:47 AM Ticket #7365 (Crash in garbage collection during new object allocation) closed by
- duplicate: Hi Soneya, Thanks for reporting this problem. Please upgrade to the …
- 10:41 AM Ticket #7364 (Draw status line: Attempt to retrieve context when no valid context) closed by
- can't reproduce: Status line redraw on expose event, no valid OpenGL context. Have …
- 10:33 AM Ticket #7363 (Crash in custom bundle initialization) closed by
- can't reproduce: Without access to this "Wiggle" bundle source, I don't know that …
- 10:26 AM Ticket #7361 (Crash using File→Open on Windows) closed by
- can't reproduce: 1.3
- 9:47 AM Ticket #7357 (glClear: invalid framebuffer operation) closed by
- can't reproduce: Same as #7356, same reporter.
- 9:46 AM Ticket #7356 (glClear: invalid framebuffer operation) closed by
- can't reproduce: OpenGL error on expose event of status line. I guess it is related to …
- 9:40 AM Ticket #7355 (Save dead dock widget shown state in session) closed by
- can't reproduce
- 9:36 AM Ticket #7351 (Restoring new session in old version) closed by
- not a bug
- 9:29 AM Ticket #7349 (Crash in event loop) closed by
- can't reproduce
- 9:27 AM Ticket #7348 (KeyError deleting 2D arrow) closed by
- duplicate: Hi Eduardo, Thanks for reporting this problem. It was fixed about …
- 9:17 AM Ticket #7347 (Crash using File→Open on Windows) closed by
- can't reproduce: 1.3
- 9:04 AM Ticket #7345 (Crash in event loop) closed by
- can't reproduce
- 8:04 AM Ticket #7365 (Crash in garbage collection during new object allocation) created by
- […]
- 6:33 AM Ticket #7364 (Draw status line: Attempt to retrieve context when no valid context) created by
- […]
Jul 31, 2022:
- 7:23 PM Ticket #7363 (Crash in custom bundle initialization) created by
- […]
- 9:32 AM Ticket #7362 (Side view not going away) created by
- […] Screen Shot 2022-07-31 at 9.30.51 AM.png
- 3:37 AM Ticket #7361 (Crash using File→Open on Windows) created by
- […]
Jul 30, 2022:
Jul 29, 2022:
- 5:12 PM Ticket #7359 (Implement Match→Align) created by
- […]
- 3:35 PM Ticket #7358 (Update AlphaFold database sequence searches for July 2022 release of ...) created by
- The EBI released an update to the AlphaFold database increasing from 1 …
- 2:12 PM Ticket #7357 (glClear: invalid framebuffer operation) created by
- […]
- 2:12 PM Ticket #7356 (glClear: invalid framebuffer operation) created by
- […]
- 2:02 PM Ticket #7355 (Save dead dock widget shown state in session) created by
- […]
- 1:48 PM Ticket #7353 (AlphaFold Error Plot gui may fetch PAE with the wrong database version) closed by
- fixed: Fixed. I made the AlphaFold Error Plot tool look at the structure …
- 12:21 PM Ticket #7354 (AlphaFold database "version" number differs from "release" number ...) created by
- AlphaFold database has had 4 releases numbered 1,2,3,4 on their FAQ …
- 11:55 AM Ticket #7353 (AlphaFold Error Plot gui may fetch PAE with the wrong database version) created by
- […]
- 11:45 AM Ticket #7352 (alphafold fetch command ignores version option when fetching PAE data) closed by
- fixed: Fixed. I also added a "version" option to the "alphafold pae" command …
- 11:39 AM Ticket #7336 (AlphaFold reporting old files) closed by
- fixed: Fixed. Does not require new ChimeraX since fix was in script fetched …
- 11:30 AM Ticket #7352 (alphafold fetch command ignores version option when fetching PAE data) created by
- […]
- 11:26 AM Ticket #7351 (Restoring new session in old version) created by
- […]
- 11:10 AM Ticket #7350 (AlphaFold PAE domains divide by zero with AlphaFold database version 3) closed by
- fixed: Fixed. Made minimum PAE value 0.2 when computing domains.
- 10:49 AM Ticket #7350 (AlphaFold PAE domains divide by zero with AlphaFold database version 3) created by
- […]
- 7:19 AM Ticket #7349 (Crash in event loop) created by
- […]
- 7:18 AM Ticket #7348 (KeyError deleting 2D arrow) created by
- […]
- 4:19 AM Ticket #7347 (Crash using File→Open on Windows) created by
- […]
- 2:23 AM Ticket #7346 (Make alphafold fetch and pae commands work with version 3 of the ...) created by
- […] alphafold.diff
Jul 28, 2022:
- 11:12 PM Ticket #7345 (Crash in event loop) created by
- […]
- 6:16 PM Ticket #7344 (MemoryError saving session) created by
- […]
- 6:05 PM 2022-7-28 edited by
- (diff)
- 5:15 PM Ticket #7343 (Avoid pages of intimidating orange warning text on Toolshed install) created by
- […]
- 5:01 PM Ticket #7337 (Selection demotion: Values array length does not match objects array length) closed by
- fixed: Fixed. If the number of atoms has changed the select up/down will …
- 4:43 PM Ticket #7341 (Crash importing numpy) closed by
- can't reproduce: No clues. Unlikely that numpy was the actual cause of the crash. …
- 3:43 PM Ticket #4749 (Specify first, last, skip when reading MD frames) closed by
- fixed: Available as start/end/skip keywords
- 3:41 PM Ticket #5874 (Renumber residues) closed by
- fixed: Command and tool available in current daily builds.
- 3:39 PM Ticket #3197 (command to change chain IDs) closed by
- fixed: Command and tool available in current daily builds.
- 2:00 PM Ticket #7338 (Volume histogram: cannot convert float NaN to integer) closed by
- nonchimerax: It looks like the hdf data file opened contained NaN values. …
- 1:46 PM Ticket #7340 (initial 'visibility false' not honored for 2D arrow) closed by
- fixed
- 1:14 PM Ticket #7342 (Axes/Planes/Centroids tool) created by
- ticket created for purposed of milestoning
- 12:32 PM 2022-7-28 edited by
- (diff)
- 10:57 AM Ticket #7341 (Crash importing numpy) created by
- […]
- 9:33 AM Ticket #7340 (initial 'visibility false' not honored for 2D arrow) created by
- As per summary
- 9:09 AM Ticket #7339 (Crash in event loop) closed by
- can't reproduce: Had just opened a session; was using 15GB at the time.
- 6:04 AM Ticket #7339 (Crash in event loop) created by
- […]
- 12:28 AM Ticket #7338 (Volume histogram: cannot convert float NaN to integer) created by
- […]
Jul 27, 2022:
- 9:54 PM Ticket #7337 (Selection demotion: Values array length does not match objects array length) created by
- […]
- 2:28 PM Ticket #7335 (Crash showing Rapid Access at startup) closed by
- can't reproduce
- 2:24 PM Ticket #7336 (AlphaFold reporting old files) created by
- […]
- 12:07 PM Ticket #7335 (Crash showing Rapid Access at startup) created by
- […]
- 11:56 AM Ticket #7334 (Add command option to fitmap to write fit positions and metrics to a ...) closed by
- fixed: Done. I added a logFits option to the fitmap command that takes a …
- 11:49 AM Ticket #7334 (Add command option to fitmap to write fit positions and metrics to a ...) created by
- Begin forwarded message: From: Christian Tüting via ChimeraX-users …
- 1:50 AM Ticket #7333 (Problem confirming SSL certificate for PyPi) created by
- […]
Jul 26, 2022:
- 7:30 PM Ticket #7332 (Gaussian molecular surface selection outline not shown) closed by
- fixed: Fixed. Surface code did not correctly display highlight if surface …
- 4:33 PM Ticket #7328 (Mouse select of low res molecular surface does not select it) closed by
- fixed: I made a separate ticket #7332 for Gaussian surfaces not showing a …
- 4:32 PM Ticket #7332 (Gaussian molecular surface selection outline not shown) created by
- […]
- 10:14 AM 2022-7-21 edited by
- (diff)
- 10:13 AM 2022-7-28 created by
- 10:12 AM DeveloperMeetings edited by
- (diff)
- 9:53 AM Dev2022-7-26 created by
- 9:45 AM DeveloperMeetings edited by
- (diff)
- 9:28 AM Ticket #7330 (Crash during fork) closed by
- can't reproduce: Hi Margot, Thank for reporting this problem. ChimeraX 1.3 and 1.4 …
- 9:17 AM Ticket #7329 (Volume Viewer after session restore: wrapped C/C++ object of type ...) closed by
- duplicate: Duplicate of #7103
- 9:04 AM Ticket #7331 (Opening ORCA output file: could not broadcast input array) created by
- […] 16101896_MnCO3_tBuNHC_Ph_THF_optfreq.out
- 4:35 AM Ticket #7330 (Crash during fork) created by
- […]
Jul 25, 2022:
- 6:36 PM Ticket #7329 (Volume Viewer after session restore: wrapped C/C++ object of type ...) created by
- […]
- 4:22 PM Ticket #7314 (Crash in mapFromGlobal(QCursor.pos())) closed by
- can't reproduce: Seems like a Qt 6 bug.
- 4:20 PM Ticket #7313 (Graphics crash, macOS 12.3.1, Intel Iris Graphics 6100) closed by
- nonchimerax: Apple graphics driver crash.
- 3:48 PM Ticket #7328 (Mouse select of low res molecular surface does not select it) created by
- […]
- 3:44 PM Ticket #7325 (Update surface selection: index is out of bounds for axis) closed by
- fixed: Fixed. Use no vertex to atom map if surface geometry was replaced by …
- 3:07 PM Dev2022-7-25 edited by
- (diff)
- 3:00 PM Dev2022-7-25 created by
- 2:52 PM DeveloperMeetings edited by
- (diff)
- 10:51 AM Ticket #7320 (Crash creating QWebEngineProfile at startup) closed by
- can't reproduce: This ChimeraX crash seems to be a bug in the Qt window toolkit. We …
- 10:48 AM Ticket #7323 (Graphics crash, macOS 11.6.7, Intel Iris Plus Graphics 650) closed by
- nonchimerax: Apple graphics driver crash.
- 9:59 AM Ticket #7327 (Index error opening regular PDB in MD Viewer) closed by
- limitation
- 9:57 AM Ticket #7326 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: Hi Julia, Thanks for reporting this problem. We believe it is fixed …
- 9:45 AM Ticket #7324 (QWebEngine crash: Calling windowShouldClose: on the delegate for the ...) closed by
- can't reproduce: Hi Carina, I'm not certain this will help but you shouldn't run …
- 9:34 AM Ticket #7321 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 8:11 AM Ticket #7327 (Index error opening regular PDB in MD Viewer) created by
- […]
- 2:12 AM Ticket #7326 (Crash using File→Open on Windows and/or in return statement) created by
- […]
Jul 24, 2022:
Jul 23, 2022:
Jul 22, 2022:
- 9:34 PM Dev2022-7-18 edited by
- (diff)
- 9:33 PM Dev2022-7-18 edited by
- (diff)
- 7:48 AM Ticket #7323 (Graphics crash, macOS 11.6.7, Intel Iris Plus Graphics 650) created by
- […]
- 6:14 AM Ticket #7322 (PAE data not opened) created by
- […]
Jul 21, 2022:
- 11:21 PM Ticket #7321 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 4:27 PM Ticket #7320 (Crash creating QWebEngineProfile at startup) created by
- […]
- 1:17 PM Ticket #7315 (PDBio.cpp buffer overflow) closed by
- fixed: Oooh, that _is_ nice. I didn't allocate space for the '\0' terminator …
- 1:12 PM Ticket #7318 (Build Structure: 'possible_name' referenced before assignment) closed by
- fixed: Fix: …
- 12:20 PM NIAID2022 edited by
- (diff)
- 11:53 AM Ticket #7077 (Remove distutils) closed by
- fixed: A [https://github.com/RBVI/ChimeraX/search?q=distutils&type=commits …
- 10:11 AM Ticket #7316 (app vs. installer) closed by
- not a bug: Hi Runrun, When you download ChimeraX for a Mac you get a .dmg file. …
- 5:39 AM Ticket #7319 (Crash showing Rapid Access at startup) created by
- […]
- 2:25 AM Ticket #7318 (Build Structure: 'possible_name' referenced before assignment) created by
- […]
Jul 20, 2022:
- 5:43 PM Ticket #7317 (On Mac at exit "Persistent UI failed to open file window_1.data") closed by
- can't reproduce: Did not reproduce on second try running same ChimeraX on same machine …
- 5:26 PM Ticket #7317 (On Mac at exit "Persistent UI failed to open file window_1.data") created by
- […]
- 5:10 PM Ticket #7316 (app vs. installer) created by
- […]
- 5:07 PM Ticket #7315 (PDBio.cpp buffer overflow) created by
- Noticed this nice warning on the Mac M1 build output. …
- 4:57 PM Ticket #7314 (Crash in mapFromGlobal(QCursor.pos())) created by
- […]
- 2:51 PM Ticket #7313 (Graphics crash, macOS 12.3.1, Intel Iris Graphics 6100) created by
- […]
- 11:13 AM Ticket #7312 (Crash using File→Open on Windows) closed by
- can't reproduce: 1.3
- 10:27 AM Ticket #7311 (Many startup errors) closed by
- fixed: Reverted the change but noted that MouseModes has a silent dependency …
- 9:52 AM Ticket #7306 (Inadequate OpenGL despite latest graphics driver) closed by
- nonchimerax: Unfortunately the latest graphics driver sometimes has bugs in it. …
- 9:48 AM Ticket #7312 (Crash using File→Open on Windows) created by
- […]
- 9:26 AM Ticket #7310 (~tile / tile off not in 1.3?) closed by
- not a bug: As you suspected, version 1.3 does not have "tile off" -- if you look …
- 8:57 AM Ticket #7305 (Basic Actions session save: 'QEventLoop' object has no attribute 'exec_') closed by
- duplicate: Hi Tent, Thanks for reporting this problem. It has been fixed and …
- 8:13 AM Ticket #7311 (Many startup errors) created by
- […]
- 8:12 AM Ticket #7310 (~tile / tile off not in 1.3?) created by
- […]
- 7:59 AM Ticket #7309 (volume sel step 1: index out of range for ImageJ TIFF stack) created by
- […]
- 2:17 AM Ticket #7308 (ISOLDE residue validation: No dihedral with that name is registered ...) created by
- […]
- 12:12 AM Ticket #7307 (Ubuntu 20.04 installation and keyboard problems) created by
- […]
Jul 19, 2022:
- 10:54 PM Ticket #7306 (Inadequate OpenGL despite latest graphics driver) created by
- […] picture1.jpg picture2.jpg …
- 3:30 PM Ticket #7287 (KeyError deleting 2D arrow) closed by
- fixed: Fix: …
- 2:12 PM Ticket #7305 (Basic Actions session save: 'QEventLoop' object has no attribute 'exec_') created by
- […]
- 1:54 PM Ticket #7302 (Model panel problem during movie script) closed by
- fixed: Thanks for reporting this problem. I have just committed a fix, and …
- 1:31 PM Ticket #7288 (Bad sequence pointer) closed by
- fixed: Fix: …
- 11:45 AM Ticket #7304 (OpenGL error on WSL) closed by
- limitation: That is a Microsoft bug. For now, you need to run the Windows version …
- 11:25 AM Ticket #7304 (OpenGL error on WSL) created by
- […]
- 11:10 AM Ticket #7300 (Problem with MD Viewer after model split) closed by
- can't reproduce: Maybe if reported with a current version of ChimeraX that doesn't …
- 11:09 AM 2022-7-21 created by
- 11:06 AM DeveloperMeetings edited by
- (diff)
- 10:52 AM Ticket #7299 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 10:50 AM Ticket #7298 ("help renumber" not working) closed by
- fixed: Caused by installing Renumber Residues and Change Change IDs into the …
- 10:16 AM Ticket #7303 (Black screen on Ubuntu 22.04) created by
- I am using Ubuntu 22.04 LTS and I have installed ChimeraX from …
- 8:11 AM Ticket #7302 (Model panel problem during movie script) created by
- […]
- 7:54 AM Ticket #7301 (Freeze on Ubuntu 22.04 + registration date/time error) created by
- […]
- 7:05 AM Ticket #7300 (Problem with MD Viewer after model split) created by
- […]
- 6:28 AM Ticket #7299 (Crash using File→Open on Windows and/or in return statement) created by
- […]
Jul 18, 2022:
- 5:55 PM Ticket #7297 (glClear: invalid framebuffer operation) closed by
- can't reproduce: OpenGL error drawing status line. Reporter says they are using …
- 5:20 PM Ticket #7298 ("help renumber" not working) created by
- […]
- 4:06 PM ChangeLog edited by
- (diff)
- 4:05 PM ChangeLog edited by
- (diff)
- 3:46 PM ChangeLog edited by
- (diff)
- 3:38 PM Dev2022-7-18 edited by
- (diff)
- 3:00 PM Ticket #7297 (glClear: invalid framebuffer operation) created by
- […]
- 1:34 PM Ticket #7294 (Pseudobond reader not bulletproof to loop pseudobonds) reopened by
- 1:33 PM Ticket #7294 (Pseudobond reader not bulletproof to loop pseudobonds) closed by
- can't reproduce: I can't reproduce this just by trying to form a loop pseudobond. Nor …
- 12:22 PM Ticket #7293 (Graphics crash, macOS 12.3.1, Intel Iris Plus Graphics) closed by
- nonchimerax: Intel Mac graphics driver crash.
- 11:44 AM Ticket #7296 (Crash loading dylib) created by
- […]
- 11:14 AM Ticket #7295 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 11:07 AM Ticket #7292 (No space left on device) closed by
- nonchimerax
- 11:06 AM Ticket #7291 (No space left on device) closed by
- nonchimerax
- 11:02 AM Ticket #7289 (Crash in event loop) closed by
- can't reproduce
- 10:25 AM Ticket #7236 (AlphaFold RFE: don't minimize by default) closed by
- fixed: Done. I changed the AlphaFold prediction energy minimization option …
- 10:22 AM Ticket #7260 (Change AlphaFold prediction to use ColabFold for 5x faster runs) closed by
- fixed
- 8:26 AM Ticket #7295 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 8:23 AM Ticket #7294 (Pseudobond reader not bulletproof to loop pseudobonds) created by
- […]
Jul 17, 2022:
Jul 16, 2022:
- 12:42 PM Ticket #7292 (No space left on device) created by
- […]
- 12:41 PM Ticket #7291 (No space left on device) created by
- […]
- 10:35 AM Ticket #7290 (Crash loading dylib) created by
- […]
- 8:54 AM Ticket #7289 (Crash in event loop) created by
- […]
- 5:27 AM Ticket #7288 (Bad sequence pointer) created by
- […]
Jul 15, 2022:
- 9:33 PM DeveloperMeetings edited by
- (diff)
- 9:32 PM Dev2022-7-18 edited by
- (diff)
- 9:32 PM Dev2022-7-18 edited by
- (diff)
- 9:32 PM Dev2022-7-18 created by
- 7:31 PM Ticket #7199 (Can't import libGLU.so.1) closed by
- nonchimerax: Missing libGLU. Needs to be installed on the system. Presumably this …
- 11:40 AM Ticket #7287 (KeyError deleting 2D arrow) created by
- […]
- 11:24 AM Ticket #7281 (ViewDockX saving session: 'QEventLoop' object has no attribute 'exec_') closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/446ac4d81258d1d5e651f40867d2b4 …
- 11:24 AM Ticket #7201 (ViewDockX saving session: 'QEventLoop' object has no attribute 'exec_') closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/446ac4d81258d1d5e651f40867d2b4 …
- 11:06 AM Ticket #7284 (Crash in event loop after volume command) closed by
- can't reproduce: Bug report has no clues about what caused this crash. Was in the Qt …
- 10:16 AM Ticket #7285 (Unknown crash) closed by
- can't reproduce
- 10:06 AM Ticket #7283 (Disconnected ribbon) closed by
- not a bug: Hi Qinglong, The 8OG residue seems to have a spurious OP3 atom that …
- 4:30 AM Ticket #7286 (Unknown crash) created by
- […]
- 3:33 AM Ticket #7285 (Unknown crash) created by
- […]
- 3:15 AM Ticket #7284 (Crash in event loop after volume command) created by
- […]
Jul 14, 2022:
- 3:44 PM 2022-7-14 edited by
- (diff)
- 3:43 PM 2022-7-14 edited by
- (diff)
- 2:51 PM Ticket #7283 (Disconnected ribbon) created by
- […] …
- 1:01 PM Ticket #7282 (Crash in event loop) created by
- […]
- 1:01 PM Ticket #7280 (Crash creating QWebEngineProfile at startup and/or running AlphaFold ...) closed by
- can't reproduce
- 12:58 PM Ticket #7279 (Attempt to draw dead arrow) closed by
- duplicate: Hi Abhilash, Thanks for reporting this problem. It was fixed about 4 …
- 12:42 PM Ticket #7281 (ViewDockX saving session: 'QEventLoop' object has no attribute 'exec_') created by
- […]
- 12:38 PM Ticket #7280 (Crash creating QWebEngineProfile at startup and/or running AlphaFold ...) created by
- […]
- 11:12 AM Ticket #7279 (Attempt to draw dead arrow) created by
- […]
- 10:21 AM Ticket #5088 (Github Actions: Ubuntu 20.04 build fails on first curl) closed by
- worksforme: Over the last few days I've tried many cloud builds, each one either …
- 9:48 AM Ticket #7278 (ImageJ hyperstack shape and axes do not match) closed by
- duplicate: Fixed about 6 months ago.
- 9:13 AM Ticket #7277 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 9:08 AM Ticket #7275 (Crash in fork) closed by
- limitation: Was using 8.7GB at the time and was forking off a local Modeller process.
- 7:35 AM Ticket #7278 (ImageJ hyperstack shape and axes do not match) created by
- […]
Jul 13, 2022:
- 8:29 PM Ticket #7277 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 6:20 PM Ticket #7276 (MemoryError saving session) created by
- […]
- 3:54 PM Ticket #7275 (Crash in fork) created by
- […]
- 2:19 PM Ticket #7274 (Make Mac distribution dmg file smaller using LZMA compression) created by
- Zach observed that the Mac distribution dmg file (.dmg) can be made …
- 1:43 PM Ticket #7273 (Crash in fork) closed by
- limitation: Was using 8.7GB at the time. No crash log or Python traceback.
- 12:27 PM Ticket #7273 (Crash in fork) created by
- […]
- 10:35 AM Ticket #7271 (Opening new session in old ChimeraX) closed by
- not a bug: Current code throws RestoreError instead of TypeError
- 7:45 AM Ticket #7272 (Shader does not have uniform variable "num_clip_planes") created by
- […]
- 4:59 AM Ticket #7271 (Opening new session in old ChimeraX) created by
- […]
Jul 12, 2022:
- 9:22 PM Ticket #7270 (ISOLDE: sim_manager is None) created by
- […]
- 5:43 PM Ticket #7256 (Crash in swapaa) closed by
- fixed: Hi Amanda, I have committed a fix for this and the fix will be in the …
- 1:30 PM Ticket #7269 (downloading and saving maps from EMDB) closed by
- not a bug: Redirected to chimerax-users list, since it is really a usage question.
- 1:24 PM Ticket #7267 (Crash showing Rapid Access at startup) closed by
- can't reproduce
- 1:17 PM Ticket #7263 (Long atom spec crashes ChimeraX) closed by
- duplicate: Hi Kavita, I think the rule of thumb to try to sidestep this …
- 11:06 AM Ticket #7265 (QMainWindowLayout::tabPosition called with out-of-bounds value '0') closed by
- can't reproduce
- 11:05 AM Ticket #7264 (Crash showing Rapid Access at startup) closed by
- can't reproduce
- 10:48 AM Ticket #7007 (Long atom spec crashes ChimeraX) closed by
- duplicate: Adding reporter to cc list for main version of this ticket
- 10:43 AM Ticket #7262 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 10:40 AM Ticket #7261 (Crash in fork) closed by
- can't reproduce: Was using 9.2GB at the time somehow -- after opening just one …
- 10:28 AM Ticket #7257 (Callback to dead color button) closed by
- fixed
- 10:03 AM Ticket #7269 (downloading and saving maps from EMDB) created by
- […]
- 10:02 AM Ticket #7268 (Problem with session file) created by
- […] Capsid.cxs
- 9:50 AM Ticket #7267 (Crash showing Rapid Access at startup) created by
- […]
- 9:35 AM 2022-7-14 created by
- 9:33 AM DeveloperMeetings edited by
- (diff)
- 9:31 AM Ticket #7266 (Renew Windows code signing certificate, expires July 29, 2022) created by
- The daily build email says the Windows code signing certificate …
- 8:08 AM Ticket #7265 (QMainWindowLayout::tabPosition called with out-of-bounds value '0') created by
- […]
- 8:00 AM Ticket #7264 (Crash showing Rapid Access at startup) created by
- […]
- 7:56 AM Ticket #7263 (Long atom spec crashes ChimeraX) created by
- […]
Jul 11, 2022:
- 9:20 PM Ticket #7262 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 6:45 PM Dev2022-7-11 edited by
- (diff)
- 6:37 PM Ticket #7261 (Crash in fork) created by
- […]
- 5:55 PM Ticket #7260 (Change AlphaFold prediction to use ColabFold for 5x faster runs) created by
- The ColabFold google colab page for running AlphaFold jobs uses a …
- 5:44 PM Ticket #7259 (Opening PDB mmcif as coordset gives disconnected residues) closed by
- duplicate
- 5:34 PM Ticket #7258 (Make AlphaFold prediction handle energy minimization failure) closed by
- fixed: Done. Return unrelaxed structure prediction and warn when …
- 5:14 PM Ticket #7259 (Opening PDB mmcif as coordset gives disconnected residues) created by
- […]
- 4:52 PM Ticket #7258 (Make AlphaFold prediction handle energy minimization failure) created by
- AlphaFold prediction fails about 5% of the time with an OpenMM energy …
- 4:30 PM Ticket #7257 (Callback to dead color button) created by
- […]
- 1:24 PM Ticket #7256 (Crash in swapaa) created by
- […]
- 1:16 PM ChangeLog edited by
- (diff)
- 1:11 PM Dev2022-7-11 edited by
- (diff)
- 1:11 PM DeveloperMeetings edited by
- (diff)
- 1:10 PM Dev2022-7-11 edited by
- (diff)
- 1:09 PM Dev2022-7-11 created by
- 11:17 AM Ticket #7255 (Crash in event loop) closed by
- can't reproduce
- 11:05 AM Ticket #7251 (Windows fatal exception in mouse_pause_tracking) closed by
- can't reproduce: It appears ChimeraX crashed while it was trying to figure out what …
- 10:39 AM Ticket #7253 (Crash using File→Open on Windows) closed by
- can't reproduce: 1.4, pre-3.9.11
- 10:37 AM Ticket #7252 (Crash creating QWebEngineProfile at startup) closed by
- duplicate
- 10:11 AM Ticket #7255 (Crash in event loop) created by
- […]
Jul 10, 2022:
- 1:34 PM Ticket #7254 (Use arbitrary folder with cxcmd link) created by
- […]
- 9:53 AM Ticket #7253 (Crash using File→Open on Windows) created by
- […]
- 6:36 AM Ticket #7252 (Crash creating QWebEngineProfile at startup) created by
- […]
- 2:33 AM Ticket #7251 (Windows fatal exception in mouse_pause_tracking) created by
- […]
Jul 9, 2022:
- 10:51 AM Ticket #7250 (Cloud builds) created by
- We want the ability to build ChimeraX in the cloud, download the …
- 7:32 AM Ticket #7249 (Unable to restore "SchemesManager" object) created by
- […]
Jul 8, 2022:
- 7:26 PM Ticket #6619 (In AlphaFold PAE plot show multimer chain boundaries) closed by
- fixed: This was added a few months ago.
- 6:15 PM Ticket #7211 (Bad curly-brackets label fouls up subsequent label attempts) closed by
- fixed: The badly labeled residues will continue to show no labels and throw …
- 6:00 PM ChangeLog edited by
- (diff)
- 2:48 PM Ticket #7248 (Crash saving atomic session state) closed by
- duplicate: Basically the same as #7247, though this time using 26.4 GB.
- 2:44 PM Ticket #7247 (Crash saving atomic session state) closed by
- can't reproduce: Seems to somehow be a lack of memory issue. Was using 13.6 GB at the …
- 12:27 PM Ticket #7248 (Crash saving atomic session state) created by
- […]
- 12:10 PM Ticket #7247 (Crash saving atomic session state) created by
- […]
- 11:36 AM Ticket #7246 (Make PAE plots work on trimmed AlphaFold structures) closed by
- fixed: Done. If the AlphaFold model has multiple chains and whole chains are …
- 11:31 AM Ticket #7246 (Make PAE plots work on trimmed AlphaFold structures) created by
- Currently predicted aligned error plots can only be shown with the …
- 10:08 AM Ticket #7245 ("spacings" is empty) created by
- […]
- 9:13 AM Ticket #7244 (Crash in event loop) closed by
- can't reproduce
- 9:10 AM Ticket #7243 (MD Viewer: Values array length does not match objects array length) closed by
- duplicate
- 9:08 AM Ticket #7242 (MD Viewer: Values array length does not match objects array length) closed by
- duplicate
- 9:04 AM Ticket #7241 (open/save commands not logged) closed by
- fixed: Hi Utz, No, that is a bug. The open/save commands use a more …
- 8:37 AM Ticket #7211 (Bad curly-brackets label fouls up subsequent label attempts) reopened by
- Upon further reflection, it would be better to treat objects lacking …
- 6:05 AM Ticket #7244 (Crash in event loop) created by
- […]
- 2:50 AM Ticket #7243 (MD Viewer: Values array length does not match objects array length) created by
- […]
- 2:50 AM Ticket #7242 (MD Viewer: Values array length does not match objects array length) created by
- […]
- 2:08 AM Ticket #7241 (open/save commands not logged) created by
- […]
Jul 7, 2022:
- 5:32 PM Ticket #7238 (Added trim option to AlphaFold panel) closed by
- fixed: Done. I added an option to the AlphaFold user interface "Trim fetched …
- 5:31 PM Ticket #7240 (Allow BLAST to use a trim option when opening AlphaFold results) created by
- I'd like to be able to pass the BLAST tool a database-specific option …
- 3:56 PM Ticket #7237 (colormapOnGpu shader error) closed by
- fixed: Fixed in tonight's daily builds (dated July 8). The error was from …
- 3:05 PM Ticket #7239 (Log link to associated EMDB entry when PDB model opened) created by
- Would be useful when opening a PDB model that was solved from a map in …
- 2:55 PM Ticket #7238 (Added trim option to AlphaFold panel) created by
- Phil would like to be able to turn off trimming when fetching …
- 2:51 PM 2022-7-7 edited by
- (diff)
- 2:26 PM Ticket #7233 (Segger infinite loop making surfaces) closed by
- duplicate: This was fixed 4 months ago and the fix is in ChimeraX 1.4. You are …
- 2:08 PM NIAID2022 edited by
- (diff)
- 2:03 PM NIAID2022 edited by
- (diff)
- 2:01 PM NIAID2022 edited by
- (diff)
- 1:46 PM NIAID2022 edited by
- (diff)
- 1:23 PM NIAID2022 edited by
- (diff)
- 11:00 AM ChangeLog edited by
- (diff)
- 10:56 AM ChangeLog edited by
- (diff)
- 6:17 AM Ticket #7237 (colormapOnGpu shader error) created by
- […]
- 3:17 AM Ticket #7236 (AlphaFold RFE: don't minimize by default) created by
- […]
Jul 6, 2022:
- 10:18 PM Ticket #7235 (Crash using color panel) created by
- […]
- 6:45 PM FAI edited by
- (diff)
- 6:43 PM Ticket #7234 (Apple notarization altool command will be discontinued Fall 2023) created by
- A command that the ChimeraX Mac notarization script uses to notarize …
- 2:24 PM Ticket #7233 (Segger infinite loop making surfaces) created by
- […]
- 12:18 PM Ticket #7232 (RFE: CASTp pocket browser) created by
- The Chimera GUI that lists the pockets and can be sorted by volume, …
- 12:00 PM Ticket #7231 (update MUSCLE seq align webservice from version 3 to 5) created by
- According to the MUSCLE website <https://drive5.com/muscle/>, version …
- 11:52 AM Ticket #7229 (Crash in Qt on exit) closed by
- duplicate
- 11:46 AM Ticket #7230 ("toolshed reload" screws up commands) created by
- […]
- 11:37 AM Ticket #7229 (Crash in Qt on exit) created by
- […]
- 9:32 AM Ticket #7228 (Graphics crash, macOS 10.15.7, Intel Iris Plus Graphics) closed by
- nonchimerax: Apple graphics driver crash.
- 8:47 AM Ticket #7227 (Crash in Qt handling mouse event) closed by
- can't reproduce: No Python stack trace.
- 8:44 AM Ticket #7226 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: Hi Francesco, Thanks for reporting this problem. We believe it is …
- 8:41 AM Ticket #7225 (Crash creating QWebEngineProfile at startup) closed by
- duplicate
- 8:40 AM Ticket #7223 (Crash in fork) closed by
- can't reproduce: Was using 10.3GB. Last command was "movie encode", so was probably …
- 8:32 AM Ticket #7228 (Graphics crash, macOS 10.15.7, Intel Iris Plus Graphics) created by
- […]
- 7:55 AM Ticket #7227 (Crash in Qt handling mouse event) created by
- […]
- 5:42 AM Ticket #7226 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 2:21 AM Ticket #7225 (Crash creating QWebEngineProfile at startup) created by
- […]
- 12:01 AM Ticket #7224 (REST server key file contains private key on Mac ARM64) created by
- The rest_server bundles generates a server.pem self-signed certificate …
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