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Sep 3, 2023:

4:19 AM Ticket #9704 (MemoryError opening mmCIF files) created by chimerax-bug-report@…: […]
4:19 AM Ticket #9703 (MemoryError opening mmCIF files) created by chimerax-bug-report@…: […]
12:29 AM Ticket #9702 (Crash handling text input) created by chimerax-bug-report@…: […]

Sep 1, 2023:

8:16 PM Ticket #9701 (MemoryError open mmCIF) created by chimerax-bug-report@…: […]
3:25 PM Ticket #2015 ("mc" accelerator equivalent) closed by Tom Goddard: fixed: The marker command "position cofr" option does this.
12:33 PM Ticket #9700 (Add info commands to report atom and residue colors in hex notation) closed by Tom Goddard: fixed: Done. I added "info atomcolor" and "info rescolor" commands to report …
12:30 PM Ticket #9700 (Add info commands to report atom and residue colors in hex notation) created by matzov.donna@…: From: Matzov Donna via ChimeraX-users <chimerax-users@…> …
12:24 PM Ticket #9699 (Residue.ribbon_color[:3] -> error, slicing on tinyarray not supported) closed by Tom Goddard: fixed: Fixed. I changed Residue ribbon_color and ring_color to return tuples …
12:20 PM Ticket #9699 (Residue.ribbon_color[:3] -> error, slicing on tinyarray not supported) created by goddard@…: […]
11:26 AM Ticket #9696 (restore_snapshot for "Volume" returned None) closed by Tom Goddard: fixed: Fixed. User restored a session and a volume file was missing and they …
10:35 AM Ticket #9698 (scipy import failure on Windows) created by chimerax-bug-report@…: […]
10:00 AM Ticket #9695 (MemoryError open mmCIF) closed by pett: duplicate
9:59 AM Ticket #9694 (Crash showing Rapid Access at startup) closed by pett: can't reproduce
9:58 AM Ticket #9693 (MemoryError open mmCIF) closed by pett: duplicate: Attached file worked on my Mac
9:49 AM Ticket #9692 (MemoryError open mmCIF) closed by pett: duplicate
9:47 AM Ticket #9691 (MemoryError open mmCIF) closed by pett: duplicate
9:18 AM Ticket #9697 (SEQCROW: 'dict' object has no attribute 'other') created by joegair@…: […]
7:29 AM Ticket #9696 (restore_snapshot for "Volume" returned None) created by chimerax-bug-report@…: […]
2:09 AM Ticket #9695 (MemoryError open mmCIF) created by chimerax-bug-report@…: […]
1:45 AM Ticket #9694 (Crash showing Rapid Access at startup) created by chimerax-bug-report@…: […]
1:08 AM Ticket #9693 (MemoryError open mmCIF) created by chimerax-bug-report@…: […] 1bvn.cif
12:55 AM Ticket #9692 (MemoryError open mmCIF) created by chimerax-bug-report@…: […]

Aug 31, 2023:

11:00 PM Ticket #9691 (MemoryError open mmCIF) created by chimerax-bug-report@…: […]
5:55 PM Ticket #9680 (Crash in structure_chain_trace_atoms) closed by Tom Goddard: can't reproduce: Crashed in structure_chain_trace_atoms(void *mol) C++ code in molc.cpp …
5:48 PM Ticket #9681 (Crash generating dump traceback?) closed by Tom Goddard: duplicate: Similar to #9682.
5:48 PM Ticket #9682 (Crash in dump_traceback) closed by Tom Goddard: can't reproduce: Same crash from same reporter as #9681, with same Qt error printed to …
3:28 PM Ticket #9686 (Crash opening PDB file) closed by pett: nonchimerax
3:28 PM Ticket #9687 (Crash opening PDB file) closed by pett: nonchimerax
3:28 PM Ticket #9688 (Crash opening PDB file) closed by pett: nonchimerax
3:24 PM Ticket #9690 (wrapped C/C++ object of type QScreen has been deleted) closed by pett: duplicate
2:57 PM Ticket #9689 (Sorting error for chains in same structure with same ID) closed by pett: fixed: Hi Sebastian, Thanks for reporting this problem. I have committed a …
2:48 PM Ticket #9690 (wrapped C/C++ object of type QScreen has been deleted) created by chimerax-bug-report@…: […]
1:58 PM 2023-8-31 edited by Scooter Morris: (diff)
1:58 PM 2023-8-31 edited by Scooter Morris: (diff)
1:49 PM 2023-8-31 edited by Tom Goddard: (diff)
1:48 PM Dev2023-9-4 edited by Zach Pearson: (diff)
1:38 PM Ticket #9689 (Sorting error for chains in same structure with same ID) created by sebastian.guettler@…: […]
12:52 PM NIAID2023 edited by Elaine Meng: (diff)
12:24 PM Ticket #9685 (Crash setting pseudobond group color) closed by pett: can't reproduce
12:17 PM Ticket #9684 (Cycle detected saving session with GLTF model) closed by Tom Goddard: duplicate: This was fixed about a week ago. No gltf model could be saved due to …
10:56 AM Ticket #9683 (Crash in event loop) closed by pett: can't reproduce
10:44 AM Ticket #9688 (Crash opening PDB file) created by todd.minehardt@…: […]
10:40 AM Ticket #9687 (Crash opening PDB file) created by todd.minehardt@…: […]
9:38 AM Ticket #9679 (Crash handling text input) closed by pett: can't reproduce
9:29 AM Ticket #9686 (Crash opening PDB file) created by todd.minehardt@…: […]
9:24 AM Ticket #9685 (Crash setting pseudobond group color) created by chimerax-bug-report@…: […]
8:23 AM Ticket #9684 (Cycle detected saving session with GLTF model) created by chimerax-bug-report@…: […]
7:58 AM Ticket #9683 (Crash in event loop) created by chimerax-bug-report@…: […]
7:00 AM Ticket #9682 (Crash in dump_traceback) created by chimerax-bug-report@…: […]
6:58 AM Ticket #9681 (Crash generating dump traceback?) created by chimerax-bug-report@…: […]
6:22 AM Ticket #9680 (Crash in structure_chain_trace_atoms) created by chimerax-bug-report@…: […]
5:35 AM Ticket #9679 (Crash handling text input) created by chimerax-bug-report@…: […]

Aug 30, 2023:

7:38 PM Ticket #9678 (Oculus Quest fails to connect by AirLink) created by Tom Goddard: The Quest Pro and Quest 2 headsets sometimes cannot be connected to a …
4:18 PM Ticket #9677 (Segmentation systems should use instanced drawing where they can) created by Zach Pearson: Currently the previews of a segmentation in 2D use copies of the …
3:55 PM Ticket #9671 (Fetch failure forming HTML user agent) closed by Greg Couch: can't reproduce: Looks like it seg faulted in the standard library.
2:19 PM Ticket #9675 (ChimeraX won't start - dell precision M6500) closed by Greg Couch: limitation: So what do you mean by "won't start"? Do you see any dialog at all? …
2:03 PM Ticket #9676 (javaScriptConsoleMessage KeyError) closed by pett: duplicate: Hi Alessandro, Thanks for reporting this problem. We believe it is …
1:46 PM Ticket #9674 (QOpenGLContext::makeCurrent() called with non-opengl surface, Windows, ...) closed by Tom Goddard: can't reproduce: User opened a session after startup and graphics context could not be …
1:25 PM Ticket #9672 (Graphics crash, macOS 11.4, Radeon Pro 580) closed by Tom Goddard: nonchimerax: Apple Radeon graphics driver crash.
12:01 PM Ticket #9673 (Sequence viewer: bad nextCheckState() return value) closed by pett: fixed
11:55 AM Ticket #9663 (Graphics crash, macOS 13.5, Apple M1 Pro) closed by Tom Goddard: limitation: The crash report shows it crashed in Apple's OpenGL graphics driver. …
11:36 AM Ticket #9669 (hbonds: wrong number of acc_phi_psi() positional arguments) closed by pett: not a bug: Hi Sajid, Your PDB has bad CONECT records, which result in bad / …
10:56 AM Ticket #9668 (MemoryError open mmCIF) closed by pett: duplicate
10:23 AM Ticket #9666 (MemoryError open mmCIF) closed by pett: duplicate
10:03 AM Ticket #9676 (javaScriptConsoleMessage KeyError) created by ale_nicoli@…: […]
10:00 AM Ticket #9664 (Crash reading PDB file) closed by pett: can't reproduce
7:01 AM Ticket #9675 (ChimeraX won't start - dell precision M6500) created by l.sorci@…: […]
6:50 AM Ticket #9674 (QOpenGLContext::makeCurrent() called with non-opengl surface, Windows, ...) created by chimerax-bug-report@…: […]
6:41 AM Ticket #9673 (Sequence viewer: bad nextCheckState() return value) created by chimerax-bug-report@…: […]
4:57 AM Ticket #9672 (Graphics crash, macOS 11.4, Radeon Pro 580) created by chimerax-bug-report@…: […]
4:55 AM Ticket #9671 (Fetch failure forming HTML user agent) created by chimerax-bug-report@…: […]
1:08 AM Ticket #9670 (MemoryError open mmCIF) created by han.tran.220143@…: […]

Aug 29, 2023:

10:29 PM Ticket #9669 (hbonds: wrong number of acc_phi_psi() positional arguments) created by sajidulghafoor@…: […] saved modified mutated 10 and 10 and 5 and 5.pdb
8:08 PM Ticket #9668 (MemoryError open mmCIF) created by chimerax-bug-report@…: […]
8:07 PM Ticket #9667 (MemoryError open mmCIF) created by rg8df@…: […]
8:05 PM Ticket #9666 (MemoryError open mmCIF) created by chimerax-bug-report@…: […]
6:02 PM Ticket #9665 (volume defaultvalues command: KeyError: 'tilted_slab') closed by Tom Goddard: fixed: Fixed. Forgot to remove tilted_slab option from volume defaultvalues …
5:59 PM Ticket #9665 (volume defaultvalues command: KeyError: 'tilted_slab') created by goddard@…: […]
5:54 PM Ticket #9652 (Volume rendering modes not honored) closed by Tom Goddard: fixed: Fixed. A change in the volume command code a few days ago made when …
3:25 PM Ticket #9664 (Crash reading PDB file) created by chimerax-bug-report@…: […]
2:39 PM Ticket #9663 (Graphics crash, macOS 13.5, Apple M1 Pro) created by Prashant.k.singh@…: […]
11:16 AM Ticket #9661 (glClear: invalid framebuffer operation) closed by Tom Goddard: can't reproduce: glClear() invalid framebuffer operation in status line on expose …
10:13 AM Ticket #9662 (build start smiles) created by bshepard1@…: […]
10:10 AM 2023-8-31 created by Tom Goddard
10:10 AM 2023-8-24 edited by Tom Goddard: (diff)
10:09 AM Dev2023-9-4 created by Tom Goddard
10:07 AM DeveloperMeetings edited by Tom Goddard: (diff)
9:47 AM Ticket #9659 (ArtiaX: wrapped C/C++ object of type QComboBox has been deleted) closed by pett: duplicate
9:24 AM Ticket #9656 (Crash using open/save dialog) closed by pett: can't reproduce
9:23 AM Ticket #9655 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by pett: duplicate
5:49 AM Ticket #9661 (glClear: invalid framebuffer operation) created by chimerax-bug-report@…: […]
1:35 AM Ticket #9660 (Color key vertical proportional spacing wrong) created by lizq@…: […] Snipaste_2023-08-29_16-34-46.png
1:17 AM Ticket #9659 (ArtiaX: wrapped C/C++ object of type QComboBox has been deleted) created by chimerax-bug-report@…: […]
1:17 AM Ticket #9658 (ArtiaX: wrapped C/C++ object of type QComboBox has been deleted) created by chimerax-bug-report@…: […]

Aug 28, 2023:

11:49 PM Ticket #9657 (Crash using open/save dialog) created by clemens.grimm@…: […]
11:47 PM Ticket #9656 (Crash using open/save dialog) created by chimerax-bug-report@…: […]
11:21 PM Ticket #9645 (Toolshed compatibility reporting wrong) closed by Greg Couch: limitation: Not compatible is correct. I'll look into giving the reason why in …
10:56 PM Ticket #9644 (Toolshed search broken) closed by Greg Couch: fixed: Fixed. Was typo in conversion to Django 4.
7:02 PM Ticket #9651 (OpenXR: IndexError into frame buffers) closed by Tom Goddard: fixed: Fixed. Surprisingly my tests on Vive Pro with OpenXR never give this …
6:19 PM Ticket #9655 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…: […]
6:15 PM Ticket #9638 (glDrawBuffer: invalid operation while setting volume level) closed by Tom Goddard: can't reproduce: OpenGL graphics error, apparently no GL_BACK buffer when expose event …
5:29 PM ChangeLog edited by Elaine Meng: (diff)
5:27 PM ChangeLog edited by Elaine Meng: (diff)
5:13 PM Ticket #9604 (Mol2 type not updated) closed by pett: fixed: ChimeraX will now not output the mol2 types from the input if it seems …
5:03 PM Ticket #9635 (Read HDF5 during session restore: file signature not found) closed by Tom Goddard: nonchimerax: When you try to open a ChimeraX session open …
4:39 PM Ticket #9654 (Allow saving movie frames with transparent background) closed by Tom Goddard: fixed: Added movie record transparentBackground option. This feature is …
4:34 PM Ticket #9654 (Allow saving movie frames with transparent background) created by christian.schafmeister@…: Begin forwarded message: From: Christian Schafmeister <> Subject: Re: …
4:22 PM Dev2023-8-28 edited by Tom Goddard: (diff)
2:44 PM Ticket #9653 (MouseModes: uses_wheel is unused) created by Zach Pearson: The MouseMode base class has a uses_wheel property that looks like …
2:28 PM Ticket #9652 (Volume rendering modes not honored) created by goddard@…: […]
11:32 AM Ticket #9650 (ArtiaX: problem loading Star file) closed by pett: duplicate
11:30 AM Ticket #9648 (Web service failure) closed by pett: not a bug: Hi Debbie, The way that Chimera and ChimeraX communicate with their …
11:22 AM Ticket #9646 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by pett: duplicate: Hi Luca, Thanks for reporting this problem. We believe it is caused …
11:15 AM Ticket #9643 (Crash using File→Open dialog on Windows and/or returning from function) closed by pett: can't reproduce: 1.3
11:14 AM Ticket #9642 (Crash handling text input) closed by pett: can't reproduce
11:09 AM Ticket #9639 (Crash in modal dialog during screen change) closed by pett: can't reproduce
11:05 AM Ticket #9637 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by pett: duplicate
10:13 AM Ticket #9651 (OpenXR: IndexError into frame buffers) created by victor.starrkramer@…: […] 8a40.pdb

Aug 27, 2023:

8:21 PM Ticket #9650 (ArtiaX: problem loading Star file) created by chimerax-bug-report@…: […]
7:20 PM Ticket #9649 (ArtiaX: problem loading Star file) created by chimerax-bug-report@…: […]
4:51 AM Ticket #9648 (Web service failure) created by debbie.shalev@…: […]

Aug 26, 2023:

4:43 PM Ticket #9647 (ISOLDE: UNL template has no bonds) created by Tristan Croll: […]
11:47 AM Ticket #9646 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by lgebert@…: […]

Aug 25, 2023:

10:30 PM Ticket #9645 (Toolshed compatibility reporting wrong) created by Tristan Croll: […]
10:28 PM Ticket #9644 (Toolshed search broken) created by Tristan Croll: […]
8:08 PM Ticket #9643 (Crash using File→Open dialog on Windows and/or returning from function) created by chimerax-bug-report@…: […]
7:50 PM Ticket #9642 (Crash handling text input) created by chimerax-bug-report@…: […]
6:25 PM Ticket #9641 (VR glitches on Nvidia 4070 Ti graphics) created by phil.cruz@…: Phil Cruz reports that the BCBB BioViz lab has several new computers …
6:08 PM Ticket #9640 (Use OpenXR instead of SteamVR for virtual reality rendering) created by Tom Goddard: The OpenXR API for virtual reality has gained wide-spread acceptance. …
12:15 PM Dev2023-8-28 edited by Zach Pearson: (diff)
12:15 PM Dev2023-8-28 edited by Zach Pearson: (diff)
12:14 PM Ticket #9634 (Blast from AlphaFold: self.job.model_name is None) closed by Zach Pearson: fixed: Should already be fixed in the daily builds.
6:56 AM Ticket #9639 (Crash in modal dialog during screen change) created by chimerax-bug-report@…: […]

Aug 24, 2023:

10:57 PM Ticket #9638 (glDrawBuffer: invalid operation while setting volume level) created by chimerax-bug-report@…: […]
8:14 PM Ticket #9637 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…: […]
6:53 PM Ticket #9636 (Cannot open *.glb.gz or *.dae.gz files) created by phil.cruz@…: Phil reported in today's NIAID ChimeraX meeting that David Chen was …
4:41 PM NIAID2023 edited by pett: (diff)
4:40 PM NIAID2023 edited by pett: (diff)
4:39 PM NIAID2023 edited by pett: (diff)
3:40 PM 2023-8-24 edited by Tom Goddard: (diff)
12:06 PM Ticket #9635 (Read HDF5 during session restore: file signature not found) created by dparrell@…: […] TS14_cm.cxs
10:48 AM Ticket #9632 (Graphics crash, macOS 11.4, Radeon Pro 580) closed by Tom Goddard: nonchimerax: Apple Radeon graphics driver crash.
10:38 AM Ticket #9634 (Blast from AlphaFold: self.job.model_name is None) created by chimerax-bug-report@…: […]
10:38 AM Ticket #9633 (MemoryError opening mmCIF) closed by pett: duplicate
10:36 AM Ticket #9631 (Crash in event loop, was running RestServer) closed by pett: can't reproduce
7:23 AM Ticket #9633 (MemoryError opening mmCIF) created by chimerax-bug-report@…: […]

Aug 23, 2023:

11:55 PM Ticket #9632 (Graphics crash, macOS 11.4, Radeon Pro 580) created by chimerax-bug-report@…: […]
6:58 PM Ticket #9631 (Crash in event loop, was running RestServer) created by chimerax-bug-report@…: […]
6:04 PM Ticket #9630 (Add a command to set volume defaults) closed by Tom Goddard: fixed: Fixed. I added a new command "volume defaultvalues" that lets you set …
5:52 PM Ticket #9630 (Add a command to set volume defaults) created by olibclarke@…: […]
5:42 PM Ticket #9629 (Custom toolbar icons) created by olibclarke@…: I love the ability to customize the home tab of the toolbar, but there …
2:20 PM Ticket #9484 (Unable to save session because ModellerWebJob class not found) closed by pett: fixed: Saving a session now works with a running Modeller job without …
2:17 PM ChangeLog edited by Elaine Meng: (diff)
1:28 PM Ticket #9628 (Mouse wheel translate does not move clip planes) closed by Tom Goddard: fixed: Fixed. Mouse wheel translate should do a z-translation which should …
1:24 PM Ticket #9628 (Mouse wheel translate does not move clip planes) created by goddard@…: […]
10:52 AM Ticket #9625 (Graphics crash, macOS 12.6.7, AMD Radeon R9 M390) closed by Tom Goddard: nonchimerax: Apple Radeon graphics driver crash.
10:14 AM Ticket #9619 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by pett: duplicate
9:57 AM Ticket #9618 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by pett: duplicate
9:31 AM Ticket #9627 (Alias menu) created by olibclarke@…: Implement an alias menu, like in Chimera
7:49 AM Ticket #9626 (Crash opening mmCIF file) created by chimerax-bug-report@…: […]
4:36 AM Ticket #9625 (Graphics crash, macOS 12.6.7, AMD Radeon R9 M390) created by chimerax-bug-report@…: […]

Aug 22, 2023:

8:03 PM Ticket #9624 (Crash opening mmCIF file) created by tnguy028@…: […]
5:31 PM Ticket #9623 (Trackpad pinch zoom rotates too much) closed by Tom Goddard: fixed: Fixed. I reduced the default ChimeraX Trackpad twist speed from 6 to …
5:19 PM Ticket #9623 (Trackpad pinch zoom rotates too much) created by olibclarke@…: From: Oliver Clarke via ChimeraX-users <chimerax-users@…> …
5:08 PM Ticket #9622 (Crash opening mmCIF file) created by tnguy028@…: […]
4:43 PM Ticket #9612 (Graphics crash, macOS 11.4, Radeon Pro 580) closed by Tom Goddard: nonchimerax: Apple Radeon graphics crash.
4:20 PM Ticket #9599 (read_full_array: Device not configured) closed by Tom Goddard: nonchimerax: The user tried to show a volume file at step 1 but the external disk …
3:58 PM Ticket #9594 (VR transmitting session: cycle detected) closed by Tom Goddard: fixed: Fixed. Session saving with a GLTF model open always failed with this …
12:47 PM Ticket #9595 (Graphics crash, macOS 12.5.1, Intel Iris Plus Graphics 655) closed by Tom Goddard: nonchimerax: Apple Intel graphics driver crash.
12:32 PM Ticket #9621 (Crash opening mmCIF file) created by tnguy028@…: […]
12:14 PM Ticket #9620 (Crash writing mmCIF) created by chimerax-bug-report@…: […]
12:08 PM Ticket #9589 (Graphics crash, macOS 11.4, Radeon Pro 580) closed by Tom Goddard: nonchimerax: Mac Radeon graphics driver crash.
12:05 PM Ticket #9580 (HTTP Error 500 fetching palette info) closed by Tom Goddard: fixed: Fixed. A coloring command with palette named red-orange-blue tried to …
11:53 AM Ticket #9564 (GUI blank after upgrade 1.1 → 1.6) closed by Tom Goddard: nonchimerax: This is a bug in your Intel graphics driver. The Qt window toolkit …
11:42 AM DeveloperMeetings edited by Tom Goddard: (diff)
11:41 AM Dev2023-8-28 created by Tom Goddard
11:40 AM 2023-8-24 created by Tom Goddard
11:39 AM DeveloperMeetings edited by Tom Goddard: (diff)
11:39 AM Dev2023-8-21 created by Tom Goddard
11:36 AM Dev2023-8-14 edited by Tom Goddard: (diff)
11:35 AM DeveloperMeetings edited by Tom Goddard: (diff)
10:58 AM Ticket #9619 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…: […]
10:54 AM Ticket #9586 (KeyError matching selected regions) closed by pett: fixed: Fix will be in tomorrow's daily build
10:44 AM Ticket #9618 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…: […]
10:40 AM Ticket #9614 (MatchMaker: KeyError with domain matching) closed by pett: duplicate: duplicate of #9586
9:17 AM Ticket #9616 (Crash in QFormLayout.removeRow()) closed by pett: can't reproduce: The only call to QFormLayout.removeRow() is in the Modeller tool, but …
9:02 AM Ticket #9617 ("pip install" failure) created by goddard@…: […]
8:50 AM Ticket #9616 (Crash in QFormLayout.removeRow()) created by chimerax-bug-report@…: […]
8:39 AM Ticket #9613 (Crash handling text input) closed by pett: can't reproduce
8:36 AM Ticket #9611 (Crash in garbage collection) closed by pett: can't reproduce
7:34 AM Ticket #9615 (ISOLDE: sim_manager is None) created by cnp@…: […]
5:40 AM Ticket #9614 (MatchMaker: KeyError with domain matching) created by chimerax-bug-report@…: […]
5:09 AM Ticket #9613 (Crash handling text input) created by chimerax-bug-report@…: […]

Aug 21, 2023:

11:08 PM Ticket #9612 (Graphics crash, macOS 11.4, Radeon Pro 580) created by chimerax-bug-report@…: […]
8:18 PM Ticket #9611 (Crash in garbage collection) created by chimerax-bug-report@…: […]
2:46 PM Ticket #9610 (Phi-setting error interferes with Selection Inspector) created by pett: […]
2:30 PM Ticket #9532 (Zero-height help window) closed by pett: fixed: Seems that the problem is that when the Help Viewer is initially …
1:20 PM Ticket #9609 (ISOLDE: problem loading residue templates) created by chimerax-bug-report@…: […]
12:47 PM Ticket #9608 (Registration mailing-list subscription: HTTP 404 failure) created by pett: […]
11:55 AM Ticket #9607 (remotecontrol: Broken pipe) closed by pett: not a bug: Presumably the client crashed while getting output
11:49 AM Ticket #9606 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by pett: duplicate
11:38 AM Ticket #9603 (Session restore: invalid load key) closed by pett: duplicate
11:28 AM Ticket #9602 (Long atom spec crashes ChimeraX) closed by pett: duplicate: dup of #4842
11:24 AM Ticket #9601 (MatchMaker: 'NoneType' object has no attribute 'setChecked') closed by pett: duplicate
11:07 AM Ticket #9600 (Color by attribute failure) closed by pett: duplicate: Hi Suhani, Thanks for reporting this problem. It has been fixed in …
9:49 AM Ticket #9607 (remotecontrol: Broken pipe) created by chimerax-bug-report@…: […]
9:23 AM Ticket #9606 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…: […]
4:10 AM Ticket #9605 (Join models with peptide bond: insert-before residue not found in _residues) created by chimerax-bug-report@…: […]
2:25 AM Ticket #9604 (Mol2 type not updated) created by ute.roehrig@…: […] fluorobenzene.mol2
1:18 AM Ticket #9603 (Session restore: invalid load key) created by hrb@…: […]

Aug 20, 2023:

4:16 PM Ticket #9602 (Long atom spec crashes ChimeraX) created by chimerax-bug-report@…: […]
12:03 AM Ticket #9601 (MatchMaker: 'NoneType' object has no attribute 'setChecked') created by chimerax-bug-report@…: […]

Aug 19, 2023:

11:33 PM Ticket #9600 (Color by attribute failure) created by suhu.bh1421@…: […]

Aug 18, 2023:

2:40 PM Ticket #9599 (read_full_array: Device not configured) created by chimerax-bug-report@…: […]

Aug 17, 2023:

6:06 PM Ticket #9585 (chain identity attribute non-functional) closed by pett: fixed: Apparently broken on 8/25/21. Fix: …
1:08 PM Ticket #9598 (Crash using File→Open dialog on Windows and/or returning from function) closed by pett: can't reproduce: 1.3
12:04 PM Ticket #9598 (Crash using File→Open dialog on Windows and/or returning from function) created by chimerax-bug-report@…: […]
9:51 AM Ticket #9596 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by pett: duplicate: Hi Duc, Thanks for reporting this problem. In our experience it …
8:00 AM NIAID2023 edited by Elaine Meng: (diff)
4:11 AM Ticket #9597 (Antechamber doesn't like blank residue name) created by Tristan Croll: […] PGN_R.pdb
1:46 AM Ticket #9596 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by minhducdkh@…: […]

Aug 16, 2023:

4:51 PM ChangeLog edited by pett: (diff)
3:51 PM ChangeLog edited by pett: (diff)
3:51 PM ChangeLog edited by pett: (diff)
2:56 PM Ticket #9595 (Graphics crash, macOS 12.5.1, Intel Iris Plus Graphics 655) created by chimerax-bug-report@…: […]
11:21 AM Ticket #9594 (VR transmitting session: cycle detected) created by meghan.mccarthy@…: […]
9:35 AM Ticket #9593 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by pett: duplicate
9:27 AM Ticket #9592 (Crash using open/save dialog) closed by pett: can't reproduce
9:25 AM Ticket #9591 (Crash in event loop during remote control) closed by pett: can't reproduce
9:23 AM Ticket #9590 (Crash in event loop during remote control) closed by pett: can't reproduce: Not a lot to go on
9:18 AM Ticket #9588 (Crash in event loop) closed by pett: can't reproduce
5:34 AM Ticket #9593 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…: […]

Aug 15, 2023:

11:37 PM Ticket #9592 (Crash using open/save dialog) created by chimerax-bug-report@…: […]
11:30 PM Ticket #9591 (Crash in event loop during remote control) created by chimerax-bug-report@…: […]
11:29 PM Ticket #9590 (Crash in event loop during remote control) created by chimerax-bug-report@…: […]
10:21 PM Ticket #9429 (BlastProtein failed: 'bytes' object has no attribute 'items') closed by pett: fixed
10:16 PM Ticket #9589 (Graphics crash, macOS 11.4, Radeon Pro 580) created by chimerax-bug-report@…: […]
5:59 PM Ticket #9588 (Crash in event loop) created by chimerax-bug-report@…: […]
2:05 PM Ticket #9587 (Histogram widget: operands could not be broadcast together with shapes) closed by pett: duplicate: Hi Kamalendu, Thanks for reporting this problem. It has been fixed, …
1:47 PM Ticket #9587 (Histogram widget: operands could not be broadcast together with shapes) created by kamalendu-pal@…: […]
12:59 PM Ticket #9584 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by pett: duplicate
11:52 AM Ticket #9586 (KeyError matching selected regions) created by kamalendu-pal@…: […]
11:46 AM Ticket #9585 (chain identity attribute non-functional) created by Elaine Meng: This chain identity (pseudo?)attribute that we added and that I am …
10:50 AM Ticket #9584 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…: […]
8:07 AM Ticket #9583 (SEQCROW: 'ArtistList' object has no attribute 'remove') created by chimerax-bug-report@…: […]

Aug 14, 2023:

5:09 PM Ticket #9582 (Cannot find Python) created by davis797@…: […]
4:00 PM Ticket #9581 (Rotamer library needs access to ui_name) created by pett: […]
3:48 PM Ticket #9577 (Crash using File→Open dialog on Windows and/or returning from function) closed by pett: can't reproduce: 1.3
3:47 PM Ticket #9576 (QPainter::begin: Paint device returned engine == 0) closed by pett: duplicate
3:46 PM Ticket #9575 (Histogram widget: operands could not be broadcast together with shapes) closed by pett: duplicate
3:42 PM Ticket #9574 (Restoring new session in old ChimeraX) closed by pett: limitation: Hi Anushka, ChimeraX session files are typically not backwards …
3:00 PM Ticket #9573 (Opal web service failure) closed by pett: not a bug: Hi Stefan, We have gone to a different web service infrastructure …
2:31 PM Ticket #9580 (HTTP Error 500 fetching palette info) created by rkrishnan@…: […]
2:23 PM Ticket #9572 (Crash opening mmCIF) closed by Greg Couch: can't reproduce: Need test file.
1:52 PM Ticket #9571 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by pett: duplicate: Hi Tarhan, Thanks for reporting this problem. In our experience it …
1:47 PM Ticket #9570 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by pett: duplicate
1:39 PM Ticket #9569 (MemoryError opening mmCIF) closed by pett: duplicate
1:33 PM Ticket #9579 (Mol2 'skip' atoms not accounted for in summaries) created by pett: The number of atoms/bonds/residues output in the MOLECULE section does …
12:31 PM Ticket #9578 (ISOLDE: wrapped C/C++ object of type QToolButton has been deleted) created by jheld@…: […]
11:57 AM Ticket #9568 (Restore new session in old ChimeraX) closed by pett: duplicate
11:57 AM Ticket #8989 (TCIA 1.3.6.1.4.1.9328.50.17.177679383028944381508162168149189677080 ...) closed by Zach Pearson: fixed: [https://github.com/RBVI/ChimeraX/commit/6c4caa2a6758e70ab0bccd2e7f67a1 …
11:50 AM Ticket #9567 (Restore new session in old ChimeraX) closed by pett: duplicate
11:48 AM Ticket #9566 (Antechamber failure) closed by pett: limitation: Hi Boaz, The calculation always works on my Mac (though it does have …
11:17 AM Ticket #9419 (SEG models opened from files should appear in Segmentation menu) closed by Zach Pearson: fixed: [https://github.com/RBVI/ChimeraX/commit/864fbd826898a4ca0f39b1ec081565 …
11:07 AM Ticket #9563 ('SaveOptionsWidget' object has no attribute 'compute_sheets') closed by pett: duplicate
10:50 AM Ticket #9562 (numpy.bool defunct) closed by pett: duplicate: Hi, Thanks for reporting this problem. It was actually fixed in the …
8:57 AM Ticket #9577 (Crash using File→Open dialog on Windows and/or returning from function) created by chimerax-bug-report@…: […]
8:53 AM Ticket #9576 (QPainter::begin: Paint device returned engine == 0) created by chimerax-bug-report@…: […]
6:54 AM Ticket #9575 (Histogram widget: operands could not be broadcast together with shapes) created by chimerax-bug-report@…: […]
5:05 AM Ticket #9574 (Restoring new session in old ChimeraX) created by anushka.ghosh@…: […]
4:51 AM Ticket #9573 (Opal web service failure) created by stefan.knight@…: […]
4:11 AM Ticket #9572 (Crash opening mmCIF) created by chimerax-bug-report@…: […]
12:42 AM Ticket #9571 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by tei19@…: […]

Aug 13, 2023:

2:45 PM Ticket #9570 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…: […]
1:41 PM Ticket #9569 (MemoryError opening mmCIF) created by chimerax-bug-report@…: […]
9:21 AM Ticket #9568 (Restore new session in old ChimeraX) created by chimerax-bug-report@…: […]
4:08 AM Ticket #9567 (Restore new session in old ChimeraX) created by chimerax-bug-report@…: […]

Aug 12, 2023:

9:53 AM Ticket #9566 (Antechamber failure) created by bshaanan@…: […] 1qs0_couloumbic.log
5:12 AM Ticket #9565 (Session restore: invalid start byte) created by tim.passchier@…: […]

Aug 11, 2023:

4:09 PM Ticket #9274 (Seg brush modes) closed by Zach Pearson: fixed: [https://github.com/RBVI/ChimeraX/commit/dbec000c9d517d69b081d667207650 …
1:33 PM Ticket #9564 (GUI blank after upgrade 1.1 → 1.6) created by sudeshi.seneviratne@…: […] chimera GUI bug.PNG
12:48 PM Ticket #9550 (Side view expose event: glDrawBuffer: invalid operation) closed by Tom Goddard: can't reproduce: Actually I don't think it lost the OpenGL context entirely, because …
12:32 PM Ticket #9563 ('SaveOptionsWidget' object has no attribute 'compute_sheets') created by chimerax-bug-report@…: […]

Aug 10, 2023:

11:13 PM Ticket #9562 (numpy.bool defunct) created by harinivachu@…: […]
5:47 PM Ticket #9556 (KeyError writing Mol2 file) closed by pett: fixed: Hi Eliza, Thanks for reporting yet another error with the Mol2 …
4:07 PM Ticket #9561 (Crash showing Rapid Access at startup) closed by pett: nonchimerax
4:03 PM Ticket #9560 (Possibly of interest: new Chemical Components Dictionary tool from PDBe) closed by pett: not a bug: I forwarded these by hand to chimerax-programmers@…
2:54 PM Ticket #9561 (Crash showing Rapid Access at startup) created by ria2@…: […]
2:50 PM Ticket #9558 (Crash in event loop) closed by pett: can't reproduce
2:45 PM Ticket #9555 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by pett: can't reproduce: Symptoms described match what we expect. User was running AlphaFold …
2:34 PM Ticket #9554 (Crash in event loop) closed by pett: can't reproduce
2:33 PM Ticket #9553 (Crash using File→Open dialog on Windows and/or returning from function) closed by pett: can't reproduce: 1.3
2:32 PM Ticket #9552 (Crash in event loop) closed by pett: can't reproduce
2:31 PM Ticket #9551 (Crash in event loop) closed by pett: can't reproduce
2:05 PM 2023-8-10 edited by Tom Goddard: (diff)
2:03 PM Selina_Aug_10_2023.pdf attached to 2023-8-10 by Tom Goddard: Selina's slides for August 10, 2023 group meeting.
1:18 PM Ticket #9549 (Crash in garbage collection) closed by pett: can't reproduce: Hi Peter, Thanks for reporting this problem. Unfortunately, there is …
12:50 PM 2023-8-10 edited by Tom Goddard: (diff)
10:48 AM Ticket #9560 (Possibly of interest: new Chemical Components Dictionary tool from PDBe) created by Tristan Croll: […]
10:43 AM Ticket #9559 (DICOM Segmentations 2D views should show overlay of active ...) created by Elaine Meng: The slice views of the image with segmentations currently show …
8:51 AM Ticket #9558 (Crash in event loop) created by chimerax-bug-report@…: […]
8:49 AM Ticket #9557 (Registration server unavailable) created by carl.carruthers@…: […]
8:32 AM Ticket #9556 (KeyError writing Mol2 file) created by egg08832@…: […]
8:23 AM Ticket #9555 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…: […]
7:45 AM Ticket #9554 (Crash in event loop) created by chimerax-bug-report@…: […]
7:11 AM Ticket #9553 (Crash using File→Open dialog on Windows and/or returning from function) created by chimerax-bug-report@…: […]
4:20 AM Ticket #9552 (Crash in event loop) created by chimerax-bug-report@…: […]
2:52 AM Ticket #9551 (Crash in event loop) created by chimerax-bug-report@…: […]
12:22 AM Ticket #9550 (Side view expose event: glDrawBuffer: invalid operation) created by chimerax-bug-report@…: […]

Aug 9, 2023:

7:18 PM Ticket #9549 (Crash in garbage collection) created by carlton.petermark.3v@…: […]
3:00 PM Ticket #9470 (traceback restoring session saved after using Segmentations tool) closed by Zach Pearson: fixed: DICOM segmentations were being saved with the wrong numpy value type, …
2:36 PM Ticket #9547 (Drawing map: cannot select an axis to squeeze out which has size not ...) closed by Tom Goddard: can't reproduce: It appears the hdf reader returned an array for a single plane that …
2:05 PM Ticket #9548 (Change color-by-chain toolbar icon so blue color (chain A) is on left, ...) closed by Tom Goddard: fixed: Ok. I'm surprised you paid attention to the order. I agree it is …
2:02 PM Ticket #9548 (Change color-by-chain toolbar icon so blue color (chain A) is on left, ...) created by ah-ram_kim@…: Copied from ticket #9534. Hi, Thank you very much for quick fix! I …
1:50 PM Ticket #9539 (DICOM not readable on Windows) closed by Zach Pearson: fixed: Added code to ignore files starting with '._'
12:14 PM Ticket #9526 (DICOM Segmentations: include SEG models opened from DICOM in the list ...) closed by Zach Pearson: fixed: [https://github.com/RBVI/ChimeraX/commit/864fbd826898a4ca0f39b1ec081565 …
11:08 AM Ticket #9546 (Error with saving mol2 file) closed by pett: fixed: Hi Elizabeth, Thanks for reporting this problem. It was a simple …
10:52 AM Ticket #9545 (Crash using File→Open on Windows and/or in return statement) closed by pett: can't reproduce: 1.2.5
10:44 AM Ticket #9543 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by pett: duplicate
8:44 AM Ticket #9547 (Drawing map: cannot select an axis to squeeze out which has size not ...) created by chimerax-bug-report@…: […]
7:27 AM Ticket #9546 (Error with saving mol2 file) created by Elizabeth.Gazaway@…: […]
6:22 AM Ticket #9545 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…: […]

Aug 8, 2023:

9:38 PM Ticket #9544 (Phenix mmCIF secondary structure problems) created by cpf@…: […] When opening CIF files generated by Phenix refine, the …
5:54 PM Ticket #9543 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…: […]
5:25 PM Ticket #9542 (meeting start: encode_vr_room_position: Cannot cast ufunc output) closed by Tom Goddard: fixed: Fixed. The numpy.clip() function now gives an error when trying to …
2:56 PM Ticket #9542 (meeting start: encode_vr_room_position: Cannot cast ufunc output) created by phil.cruz@…: […]
2:44 PM Ticket #9534 (mouse wheel-based zoom is not working) closed by Tom Goddard: fixed: Fixed in tonight's daily build (dated August 8, 2023). The Mac …
12:55 PM Dev2023-8-14 edited by Tom Goddard: (diff)
12:55 PM 2023-8-10 created by Tom Goddard
12:54 PM Dev2023-8-14 created by Tom Goddard
12:53 PM DeveloperMeetings edited by Tom Goddard: (diff)
11:00 AM Ticket #9541 (MemoryError open mmCIF) closed by pett: duplicate
10:55 AM Ticket #9540 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by pett: duplicate: Hi Tarhan, Thanks for reporting this problem. We believe it happens …
10:48 AM Ticket #9524 (DICOM Segmentations: going to different slice doesn't remove overlay) closed by Zach Pearson: worksforme: Seems to work on today's daily build (2023-08-08)
10:29 AM Ticket #9537 (Crash adding trigger handler) closed by pett: can't reproduce
10:28 AM Ticket #9541 (MemoryError open mmCIF) created by chimerax-bug-report@…: […]
10:27 AM Ticket #9536 (MemoryError open mmCIF) closed by pett: duplicate
10:25 AM Ticket #9535 (Crash using Mac color panel) closed by pett: can't reproduce
10:17 AM Ticket #9540 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by tei19@…: […]
9:42 AM Ticket #9539 (DICOM not readable on Windows) created by phil.cruz@…: […]
9:42 AM Ticket #9538 ('ChimeraX-ISOLDE' custom initialization failed: Clipper distribution ...) created by chimerax-bug-report@…: […]
2:05 AM Ticket #9537 (Crash adding trigger handler) created by chimerax-bug-report@…: […]

Aug 7, 2023:

8:33 PM Ticket #9533 ("view" includes hidden elements) closed by Tom Goddard: fixed: Fixed. The view command was using all atoms and bonds of a residue if …
6:57 PM Ticket #9536 (MemoryError open mmCIF) created by chimerax-bug-report@…: […]
3:42 PM Dev2023-8-7 edited by Tom Goddard: (diff)
2:02 PM Ticket #9535 (Crash using Mac color panel) created by chimerax-bug-report@…: […]
1:22 PM Ticket #9397 (Segmentations (SEG) models should not appear in choices of ...) closed by Zach Pearson: fixed
1:18 PM Ticket #9534 (mouse wheel-based zoom is not working) created by ah-ram_kim@…: […]
1:18 PM Dev2023-8-7 edited by Tom Goddard: (diff)
1:05 PM Ticket #9515 (Tried to add model with the same id as another model) closed by Tom Goddard: can't reproduce: Does not look like the user was reporting the error where restoring a …
12:54 PM Ticket #9530 (Crash in garbage collection while drawing volume histogram after ...) closed by Tom Goddard: can't reproduce: Probably a reference count bug. Log had several hundred commands …
12:03 PM Ticket #9529 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by pett: duplicate
11:55 AM Ticket #9527 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by pett: duplicate
11:30 AM Ticket #9519 (Load Toolshed cache: 'list' object has no attribute 'split') closed by pett: can't reproduce: 0.8!
10:46 AM Ticket #9517 (Crash using Save dialog) closed by pett: can't reproduce
10:45 AM Ticket #9533 ("view" includes hidden elements) created by pett: […]
10:37 AM Ticket #9516 (Truncated HIS residue) closed by pett: duplicate
10:24 AM Ticket #9532 (Zero-height help window) created by pett: […]

Aug 6, 2023:

12:37 AM Ticket #9531 (MemoryError opening mmCIF) created by dipikasharma303@…: […]

Aug 5, 2023:

10:23 AM Ticket #9530 (Crash in garbage collection while drawing volume histogram after ...) created by chimerax-bug-report@…: […]
4:29 AM Ticket #9529 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…: […]

Aug 4, 2023:

9:37 PM Ticket #9528 (Crash in event loop) created by eopech@…: […]
6:27 PM Ticket #9527 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…: […]
5:18 PM Ticket #9526 (DICOM Segmentations: include SEG models opened from DICOM in the list ...) created by Elaine Meng: was mentioned in #9397 but is really a separate thing. Would be nice …
5:08 PM Ticket #9525 (DICOM Segmentations: hard to resize cursor using touchpad Shift-scroll) created by Elaine Meng: I don't understand how this Shift-scroll is supposed to work on a …
4:58 PM Ticket #9524 (DICOM Segmentations: going to different slice doesn't remove overlay) created by Elaine Meng: I do see the nice overlay showing the segmented part of a slice. But …
2:01 PM Ticket #9523 (ISOLDE ResidueStepper holding reference to dead structure) created by jheld@…: […]
1:21 PM Ticket #9522 (Interfaces/NetworkX: libbz2.so.1.0: cannot open shared object file: No ...) created by pradip.singh@…: […]
1:08 PM Ticket #9521 ("make install" for a bundle on Windows very slow) created by Tom Goddard: If I do "make install" in the vive bundle directory on Windows …
9:19 AM Ticket #9520 (MemoryError opening mmCIF) created by m.daghan.okur@…: […]
5:33 AM Ticket #9519 (Load Toolshed cache: 'list' object has no attribute 'split') created by chimerax-bug-report@…: […]
2:57 AM Ticket #9518 (Crash using Save dialog) created by jens.luders@…: […]
2:52 AM Ticket #9517 (Crash using Save dialog) created by chimerax-bug-report@…: […]
1:27 AM Ticket #9516 (Truncated HIS residue) created by chimerax-bug-report@…: […]

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