Timeline



Jul 26, 2024:

6:14 PM Ticket #15690 (Avoid red-green color scheme in Foldseek sequences plot, worst choice ...) closed by Tom Goddard
fixed: Fixed. Switched to a bluish-yellowish scheme suggested by this web …
6:12 PM Ticket #15691 (Crash running open-file dialog) created by chimerax-bug-report@…
[…]
6:01 PM Ticket #15666 (Deleting chain B of 3h7s leads to a crash) closed by Eric Pettersen
fixed: Fixed. Fix: …
5:38 PM Ticket #15690 (Avoid red-green color scheme in Foldseek sequences plot, worst choice ...) created by goddard@…
[…]
5:27 PM Ticket #15684 (foldseek ligands warns of about a dozen sequence mismatch problems) closed by Tom Goddard
fixed: Fixed. All of the sequence mismatches observed with foldseek query …
5:24 PM Ticket #15681 (Foldseek loading mmCIF files slows after hundreds already in session) closed by Tom Goddard
fixed: Fixed. The problem was in the foldseek code which was trimming the …
5:19 PM Ticket #15668 (Foldseek excludes residues missing backbone N, e.g. PDB 7w7g /B:654) closed by Tom Goddard
fixed: Fixed. I made ChimeraX foldseek code use …
3:31 PM Ticket #15688 (Improve speed of foldseek ligands command) closed by Tom Goddard
fixed: Fixed. Improved speed finding ligands of 845 hits from 500 seconds …
2:37 PM Ticket #15682 (Combine command is not copying altloc coordinates correctly) closed by Eric Pettersen
fixed: Fix: …
1:31 PM Ticket #15689 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
12:08 PM Ticket #15688 (Improve speed of foldseek ligands command) created by goddard@…
[…]
11:37 AM Ticket #15687 (Crash floating window on Mac) closed by Tom Goddard
can't reproduce: Seems like a Qt bug. The last lines of the stack have lots of …
11:06 AM Ticket #15686 (Crash in event loop) closed by Eric Pettersen
can't reproduce
11:05 AM Ticket #15685 (Crash in event loop) closed by Eric Pettersen
can't reproduce
10:50 AM Ticket #15680 (Crash in chem_group.find_group) closed by Eric Pettersen
can't reproduce: Crashed in threaded C++ implementation of find_group. Not too much …
8:11 AM Ticket #15687 (Crash floating window on Mac) created by chimerax-bug-report@…
[…]
6:51 AM Ticket #15686 (Crash in event loop) created by chimerax-bug-report@…
[…]
12:57 AM Ticket #15685 (Crash in event loop) created by chimerax-bug-report@…
[…]

Jul 25, 2024:

6:21 PM Ticket #15684 (foldseek ligands warns of about a dozen sequence mismatch problems) created by goddard@…
[…]
5:58 PM Ticket #15683 (Foldseek ligands does not dock all altlocs to query) closed by Tom Goddard
fixed: Fixed. I made foldseek ligands keep only one altloc for each ligand …
5:47 PM Ticket #15683 (Foldseek ligands does not dock all altlocs to query) created by goddard@…
[…]
5:38 PM Ticket #15682 (Combine command is not copying altloc coordinates correctly) created by goddard@…
[…]
4:34 PM Ticket #15681 (Foldseek loading mmCIF files slows after hundreds already in session) created by goddard@…
[…]
4:29 PM Ticket #15670 (Foldseek ligands uses illegal chain id character "_") closed by Tom Goddard
wontfix
4:21 PM Ticket #15680 (Crash in chem_group.find_group) created by chimerax-bug-report@…
[…]
4:18 PM Ticket #15679 (Foldseek panel expands to full window width) closed by Tom Goddard
fixed: Fixed. Eric does not observe this problem, and I did not encounter it …
4:15 PM Ticket #15679 (Foldseek panel expands to full window width) created by goddard@…
[…]
3:57 PM Ticket #15677 (Foldseek does not delete old results table when new results open) closed by Tom Goddard
fixed: Fixed. I was calling the QTableView destroy() method which is …
3:10 PM Ticket #15678 (Missing structure labels make opening PDB 8jnb not focus view on full model) created by goddard@…
[…]
2:23 PM Ticket #15669 (module 'xr' has no attribute 'GraphicsBindingOpenGLWin32KHR') closed by Tom Goddard
not a bug: Hi Colin, The ChimeraX xr command uses OpenXR which in theory works …
2:09 PM Ticket #15673 (Qt fatal error: QEventDispatcherUNIXPrivate(): Cannot continue without ...) closed by Tom Goddard
can't reproduce: Qt crashed when Save dialog shown. QEventDispatcherUNIXPrivate(): …
1:51 PM Ticket #15663 (glDrawBuffer: invalid operation) closed by Tom Goddard
duplicate: Linux OpenGL invalid operation error glDrawBuffer(GL_BACK). Have seen …
1:48 PM Ticket #15671 (Crash waking Mac up from sleep) closed by Tom Goddard
duplicate: ChimeraX crashed due to a bug in the Qt window toolkit. The crash can …
1:42 PM Ticket #15677 (Foldseek does not delete old results table when new results open) created by goddard@…
[…]
1:01 PM 2024-7-25 edited by Tom Goddard
(diff)
12:46 PM Ticket #15676 (Crash in garbage collection) closed by Eric Pettersen
duplicate
12:45 PM Ticket #15675 (Crash in garbage collection) closed by Eric Pettersen
duplicate
10:58 AM Ticket #15674 (Restore new session in old ChimeraX) closed by Eric Pettersen
limitation: Hi Christoph, The session your collaborator sent you needs to be …
10:46 AM Ticket #15672 (Crash showing/running open-file dialog) closed by Eric Pettersen
can't reproduce
10:08 AM Ticket #15662 (Crash in garbage collection) closed by Eric Pettersen
duplicate
8:22 AM Ticket #15676 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
7:53 AM Ticket #15675 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
6:28 AM Ticket #15674 (Restore new session in old ChimeraX) created by chkaiser@…
[…]
2:59 AM Ticket #15673 (Qt fatal error: QEventDispatcherUNIXPrivate(): Cannot continue without ...) created by chimerax-bug-report@…
[…]
2:08 AM Ticket #15672 (Crash showing/running open-file dialog) created by chimerax-bug-report@…
[…]

Jul 24, 2024:

10:09 PM Ticket #15671 (Crash waking Mac up from sleep) created by shruthiv@…
[…]
8:29 PM Ticket #15670 (Foldseek ligands uses illegal chain id character "_") created by goddard@…
[…]
6:39 PM Ticket #15669 (module 'xr' has no attribute 'GraphicsBindingOpenGLWin32KHR') created by colingauvin@…
[…]
4:45 PM Ticket #15668 (Foldseek excludes residues missing backbone N, e.g. PDB 7w7g /B:654) created by goddard@…
[…]
4:14 PM Ticket #15667 (Foldseek sequence length mismatch PDB 5v5h_B) closed by Tom Goddard
fixed: Fixed. The terminal lysine residue did not have a CA. Made ChimeraX …
4:09 PM Ticket #15667 (Foldseek sequence length mismatch PDB 5v5h_B) created by goddard@…
[…]
3:50 PM Ticket #15665 (Foldseek opening 3h7s crashes) closed by Tom Goddard
duplicate: Made a simpler version of this crash that does not involve Foldseek, …
3:44 PM Ticket #15666 (Deleting chain B of 3h7s leads to a crash) created by goddard@…
[…]
3:25 PM Ticket #15665 (Foldseek opening 3h7s crashes) created by goddard@…
[…]
2:42 PM Ticket #15664 (Foldseek fails opening 6xhb_B with query 8jnb) closed by Tom Goddard
fixed: Fixed. Turns out foldseek code has another shorter list of accepted …
2:38 PM Ticket #15664 (Foldseek fails opening 6xhb_B with query 8jnb) created by goddard@…
[…]
1:40 PM Ticket #15663 (glDrawBuffer: invalid operation) created by chimerax-bug-report@…
[…]
1:26 PM Ticket #15662 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
10:01 AM Ticket #15661 (Crash running modal dialog) closed by Eric Pettersen
can't reproduce
10:00 AM Ticket #15660 (Crash in garbage collection) closed by Eric Pettersen
can't reproduce: Hi Peter, Thanks for reporting this problem. The crash occurred in …
9:54 AM Ticket #15659 (Crash in event loop) closed by Eric Pettersen
can't reproduce
9:53 AM Ticket #15658 (Crash calculating contour surface) closed by Eric Pettersen
can't reproduce
6:59 AM Ticket #15661 (Crash running modal dialog) created by chimerax-bug-report@…
[…]
1:05 AM Ticket #15660 (Crash in garbage collection) created by carlton.petermark.3v@…
[…]
12:19 AM Ticket #15659 (Crash in event loop) created by chimerax-bug-report@…
[…]

Jul 23, 2024:

9:57 PM Ticket #15658 (Crash calculating contour surface) created by chimerax-bug-report@…
[…]
8:01 PM Ticket #15655 (Use/offer official AlphaFold color palette) closed by Tom Goddard
wontfix: This was discussed on the ChimeraX mailing list in May 2024 …
6:06 PM Ticket #15654 (Residue 1-letter code reported as X while PDB reports it as K) closed by Greg Couch
fixed: Add prefetching of all residue templates so one-letter code is known …
4:53 PM Ticket #15657 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by chimerax-bug-report@…
[…]
3:48 PM ChangeLog edited by Elaine Meng
(diff)
10:03 AM 2024-7-25 created by Tom Goddard
10:02 AM DeveloperMeetings edited by Tom Goddard
(diff)
10:00 AM Ticket #15651 (Crash waking Mac from sleep) closed by Tom Goddard
duplicate: Qt 6.6 bug, crashes in _NSViewHierarchyDidChangeBackingProperties …
1:20 AM Ticket #15656 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by chimerax-bug-report@…
[…]
12:49 AM Ticket #15655 (Use/offer official AlphaFold color palette) created by 419434238@…
[…] 屏幕截图 2024-07-20 233927.png​

Jul 22, 2024:

8:26 PM Ticket #15522 (Mismatch of crosslink positions when loading structures from PDB-Dev) closed by Tom Goddard
fixed: Fixed. Merged Ben's pull request #44 which switches to using …
8:12 PM Ticket #15653 (ChimeraX reports an X while foldseek reports a K in PDB 6uyy chain A ...) closed by Tom Goddard
fixed: Fixed. I made the ChimeraX Foldseek code not report sequence …
8:04 PM Ticket #15652 (Error opening a foldseek hit that contains an X residue) closed by Tom Goddard
fixed
7:54 PM Ticket #15654 (Residue 1-letter code reported as X while PDB reports it as K) created by goddard@…
[…]
7:49 PM Ticket #15653 (ChimeraX reports an X while foldseek reports a K in PDB 6uyy chain A ...) created by goddard@…
[…]
6:49 PM Ticket #15652 (Error opening a foldseek hit that contains an X residue) created by goddard@…
[…]
3:16 PM Ticket #15651 (Crash waking Mac from sleep) created by chimerax-bug-report@…
[…]
12:39 PM Ticket #15648 (Restore new session in old ChimeraX) closed by Eric Pettersen
limitation
12:37 PM Ticket #15646 (Crash in garbage collection) closed by Eric Pettersen
duplicate
12:36 PM Ticket #15645 (Crash in garbage collection) closed by Eric Pettersen
duplicate
12:35 PM Ticket #15643 (Crash in garbage collection) closed by Eric Pettersen
duplicate
12:29 PM Ticket #15641 (Save MRC file of half map: could not broadcast input array from shape) closed by Tom Goddard
not a bug: When you use ChimeraX command "volume flip #1" and then try to save …
12:13 PM Ticket #15640 (Structure pointer interpreted as base class) closed by Eric Pettersen
can't reproduce: Not sure how this could happen -- possibly related to the …
11:05 AM Ticket #15650 (ChimeraX 1.7 PyPy package import error: ModuleNotFoundError: No module ...) created by Tom Goddard
After installing the missing tinyarray package (ticket #15649) the …
11:02 AM Ticket #15649 (ChimeraX 1.7 PyPi package import error: ModuleNotFoundError: No module ...) created by Tom Goddard
(base) $ python3.11 python3.11 Python 3.11.6 (main, Oct 2 2023, …
10:58 AM Ticket #15648 (Restore new session in old ChimeraX) created by chimerax-bug-report@…
[…]
10:53 AM Ticket #15632 (Crash changing Mac display configuration) closed by Tom Goddard
duplicate
10:48 AM Ticket #15630 (Crash changing Mac display configuration) closed by Tom Goddard
duplicate: Qt 6.6 bug crashing _NSViewHierarchyDidChangeBackingProperties in …
10:46 AM Ticket #15628 (Crash changing Mac display configuration) closed by Tom Goddard
duplicate: This ChimeraX crash is in the Qt window toolkit and we have most often …
10:40 AM Ticket #15647 (Improve PyPi web page ChimeraX description) created by Tom Goddard
The ChimeraX PyPi package web page description seems to be using …
10:14 AM Ticket #15637 (GL.glDrawElementsInstanced: Windows Error) closed by Tom Goddard
can't reproduce: Possibly a Windows graphic driver problem since the traceback was in …
9:50 AM Ticket #15636 (Crash waking Mac from sleep) closed by Tom Goddard
duplicate: Crash in _NSViewHierarchyDidChangeBackingProperties(). Possibly …
9:49 AM Ticket #15635 (Crash waking Mac from sleep) closed by Tom Goddard
duplicate: Same crash, same reporter, as #15634
9:46 AM Ticket #15634 (Crash waking Mac from sleep) closed by Tom Goddard
duplicate: This ChimeraX crash is in the Qt window toolkit and we have most often …

Jul 21, 2024:

7:14 PM Ticket #15646 (Crash in garbage collection) created by chimerax-bug-report@…
[…]

Jul 20, 2024:

6:23 PM Ticket #15645 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
5:04 PM Ticket #15644 (Bundle builder should tell cython correct deployment target by setting ...) created by Zach Pearson
10:52 AM Ticket #15643 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
1:47 AM Ticket #15642 (MD Viewer: 'close' during playback produce traceback) created by chimerax-bug-report@…
[…]

Jul 19, 2024:

3:21 PM Ticket #15641 (Save MRC file of half map: could not broadcast input array from shape) created by ebillin@…
[…]
2:55 PM Ticket #15640 (Structure pointer interpreted as base class) created by chimerax-bug-report@…
[…]
2:39 PM Ticket #15639 (RFE: depth testing for volumes) created by Zach Pearson
Currently it looks like opaque models are always drawn over volumes, …
10:22 AM Ticket #15638 (RFE: Port the Chimera lighting GUI) created by Zach Pearson
We're closer than ever to releasing our new raycasting rendering mode. …
9:37 AM Ticket #15637 (GL.glDrawElementsInstanced: Windows Error) created by chimerax-bug-report@…
[…]
8:39 AM Ticket #15636 (Crash waking Mac from sleep) created by chimerax-bug-report@…
[…]
8:21 AM Ticket #15635 (Crash waking Mac from sleep) created by bullitt@…
[…]
6:34 AM Ticket #15634 (Crash waking Mac from sleep) created by bullitt@…
[…]

Jul 18, 2024:

3:53 PM Ticket #15631 (Crash at startup) closed by Greg Couch
worksforme: Please update to ChimeraX 1.8 and let us if it happens again. Thank you.
2:59 PM Ticket #15577 (non-printable surface missing coulombic coloring) closed by Eric Pettersen
can't reproduce: Okay! :-)
2:58 PM Ticket #15633 (Restore new session in old ChimeraX) closed by Eric Pettersen
limitation
2:52 PM Ticket #15629 (ArtiaX/pandas vs. numpy) closed by Eric Pettersen
limitation: Hi Robin, I think you need to upgrade both ChimeraX and ArtiaX to …
1:34 PM NIAID2024 edited by Elaine Meng
(diff)
12:50 PM Ticket #15633 (Restore new session in old ChimeraX) created by chimerax-bug-report@…
[…]
10:28 AM Ticket #15624 (ui view fourup: ZeroDivisionError) closed by Zach Pearson
duplicate: Duplicate of ​https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15343 …
9:55 AM Ticket #15627 (MemoryError opening mmCIF files) closed by Eric Pettersen
duplicate
9:54 AM Ticket #15626 (MemoryError opening mmCIF files) closed by Eric Pettersen
duplicate: Hi Raj, Thanks for reporting this problem. It has been fixed in …
6:50 AM Ticket #15632 (Crash changing Mac display configuration) created by andreapellegrini6698@…
[…]
5:34 AM Ticket #15631 (Crash at startup) created by vivek.singh@…
[…]
2:11 AM Ticket #15630 (Crash changing Mac display configuration) created by chimerax-bug-report@…
[…]
1:24 AM Ticket #15629 (ArtiaX/pandas vs. numpy) created by robinbenjamineberle@…
[…]
12:27 AM Ticket #15628 (Crash changing Mac display configuration) created by jean.millet@…
[…]

Jul 17, 2024:

11:14 PM Ticket #15627 (MemoryError opening mmCIF files) created by rohits22@…
[…]
11:14 PM Ticket #15626 (MemoryError opening mmCIF files) created by rohits22@…
[…]
1:32 PM Ticket #15625 (Dark mode changes broke command-line error reporting) created by Eric Pettersen
[…]
12:38 PM Ticket #15624 (ui view fourup: ZeroDivisionError) created by chimerax-bug-report@…
[…]
10:42 AM Ticket #15620 (Wrl outputs have bleeding color) closed by Tom Goddard
nonchimerax: Glad you have a lead on the problem. Let me know if other issues …
8:47 AM Ticket #15623 (Crash processing atom spec) closed by Eric Pettersen
duplicate
3:57 AM Ticket #15623 (Crash processing atom spec) created by chimerax-bug-report@…
[…]

Jul 16, 2024:

10:34 PM Ticket #15615 (Crash changing display configuration on Mac) closed by Tom Goddard
duplicate: ChimeraX crashed unplugging or plugging in an external display. This …
10:30 PM Ticket #15614 (Crash changing display configuration on Mac) closed by Tom Goddard
duplicate: Mac Qt 6.6 crash probably from unplugging or plugging in external display.
5:01 PM Ticket #15621 (Crash in garbage collection) closed by Eric Pettersen
duplicate
4:56 PM Ticket #15619 (Crash processing atom spec) closed by Eric Pettersen
duplicate
4:56 PM Ticket #15618 (Crash processing atom spec) closed by Eric Pettersen
duplicate
4:55 PM Ticket #15617 ('pwd' failure when working directory removed) closed by Eric Pettersen
duplicate
4:44 PM Ticket #15622 (MatchMaker: assign RMSDs without opening sequence viewers) created by Daphne.Chen@…
Either with 'rmsd' boolean keyword or 'rmsd' arg-less keyword.
2:29 PM Ticket #15616 ('pwd' failure when working directory removed) closed by Eric Pettersen
fixed
9:17 AM Ticket #15621 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
7:51 AM Ticket #15620 (Wrl outputs have bleeding color) created by kristen.browne@…
[…] [[Image(...)]] [[Image(...)]]
7:39 AM Ticket #15619 (Crash processing atom spec) created by chimerax-bug-report@…
[…]
7:30 AM Ticket #15618 (Crash processing atom spec) created by chimerax-bug-report@…
[…]
4:17 AM Ticket #15617 ('pwd' failure when working directory removed) created by chimerax-bug-report@…
[…]
4:15 AM Ticket #15616 ('pwd' failure when working directory removed) created by chimerax-bug-report@…
[…]
2:29 AM Ticket #15615 (Crash changing display configuration on Mac) created by jean.millet@…
[…]

Jul 15, 2024:

4:17 PM Ticket #15614 (Crash changing display configuration on Mac) created by chimerax-bug-report@…
[…]
3:30 PM Dev2024-7-15 edited by Tom Goddard
(diff)
11:27 AM Ticket #15604 (ItemTable.scroll_to(item) does not scroll the table) closed by Eric Pettersen
fixed: scroll_to() wasn't accounting for table sorting fix: …
11:05 AM Ticket #15606 (Memory shortage repainting windows) closed by Tom Goddard
can't reproduce: ChimeraX crashed in Apple's Intel graphics driver. It might have been …
10:49 AM Ticket #15613 (Crash in garbage collection) closed by Eric Pettersen
duplicate: Hi Guilherme, Thanks for reporting this problem. It has been fixed …
10:31 AM Ticket #15609 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by Eric Pettersen
duplicate: Hi Tianyi, Thanks for reporting this problem. It is a bug with the Qt …
10:27 AM Ticket #15608 (Histogram widget: operands could not be broadcast together with shapes) closed by Eric Pettersen
duplicate
10:26 AM Ticket #15607 (Histogram widget: operands could not be broadcast together with shapes) closed by Eric Pettersen
duplicate
10:19 AM Ticket #15605 (MemoryError opening mmCIF files) closed by Eric Pettersen
duplicate
10:18 AM Ticket #15613 (Crash in garbage collection) created by guiolive@…
[…]
10:18 AM Ticket #15603 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by Eric Pettersen
duplicate: Hi Wiliam, Thanks for reporting this problem. It is a bug with the …
10:15 AM Ticket #15602 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by Eric Pettersen
duplicate
8:39 AM Ticket #15612 (PAE surf output problem) created by kristen.browne@…
[…] [[Image(...)]]
8:12 AM Ticket #15611 (Missing outputs) created by kristen.browne@…
[…] expected_ChimeraX_annotated.xlsx​
2:50 AM Ticket #15610 (glTexImage3D: out of memory) created by chimerax-bug-report@…
[…]

Jul 14, 2024:

11:22 PM Ticket #15609 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by zhangtia22@…
[…]
3:59 PM Ticket #15608 (Histogram widget: operands could not be broadcast together with shapes) created by chimerax-bug-report@…
[…]
3:59 PM Ticket #15607 (Histogram widget: operands could not be broadcast together with shapes) created by chimerax-bug-report@…
[…]
12:06 PM Ticket #15606 (Memory shortage repainting windows) created by daphne.chen@…
[…] error.txt​
5:16 AM Ticket #15605 (MemoryError opening mmCIF files) created by chimerax-bug-report@…
[…]

Jul 13, 2024:

10:49 PM Ticket #15604 (ItemTable.scroll_to(item) does not scroll the table) created by goddard@…
[…]
6:43 AM Ticket #15603 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by whale6@…
[…]

Jul 12, 2024:

11:21 AM Ticket #15602 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…
[…]
11:18 AM Ticket #15599 (Render by Attribute: 'MarkedHistogram' object has no attribute '_min_val') closed by Eric Pettersen
fixed
9:42 AM Ticket #15601 (Non-ASCII PDB file) closed by Eric Pettersen
can't reproduce: Gave a good error the first time. Seems to be SQLite output!
9:34 AM Ticket #15598 (MemoryError opening mmCIF files) closed by Eric Pettersen
duplicate
9:33 AM Ticket #15597 (Crash in QDialog.exec()) closed by Eric Pettersen
can't reproduce
9:30 AM Ticket #15601 (Non-ASCII PDB file) created by chimerax-bug-report@…
[…]
5:56 AM Ticket #15600 (RFE: fetch map for session if appropriate) created by Tristan Croll
[…]
5:46 AM Ticket #15599 (Render by Attribute: 'MarkedHistogram' object has no attribute '_min_val') created by chimerax-bug-report@…
[…]
5:29 AM Ticket #15598 (MemoryError opening mmCIF files) created by chimerax-bug-report@…
[…]

Jul 11, 2024:

4:50 PM Ticket #15597 (Crash in QDialog.exec()) created by chimerax-bug-report@…
[…]
3:14 PM Ticket #15596 (Toolshed can't find ArtiaX bundle) created by johutchings@…
[…]
1:56 PM 2024-7-11 edited by Tom Goddard
(diff)
1:53 PM 2024-7-11 edited by Zach Pearson
(diff)
10:58 AM Ticket #15595 (Generic chooser widget: argument of type 'NoneType' is not iterable) closed by Eric Pettersen
fixed: Fix: …
10:39 AM Ticket #15593 (Crash unplugging Mac external monitor) closed by Tom Goddard
duplicate: Thanks for the report. Unfortunately the Qt window toolkit version …
10:33 AM Ticket #15590 (Crash changing Mac display configuration) closed by Tom Goddard
duplicate: Plugging in or unplugging a display on Mac …
10:13 AM Ticket #15594 (MemoryError opening mmCIF files) closed by Eric Pettersen
duplicate

Jul 10, 2024:

10:15 PM Ticket #15595 (Generic chooser widget: argument of type 'NoneType' is not iterable) created by chimerax-bug-report@…
[…]
7:32 PM Ticket #15594 (MemoryError opening mmCIF files) created by chimerax-bug-report@…
[…]
4:15 PM Ticket #15592 (Save mmCIF files with unix line endings instead of DOS line endings) closed by Greg Couch
fixed: Agreed. I found a commit, ceebbe884ecca01a634193df961fee0a58584aba, …
2:09 PM Ticket #15593 (Crash unplugging Mac external monitor) created by psauer@…
[…]
1:01 PM Ticket #15592 (Save mmCIF files with unix line endings instead of DOS line endings) created by goddard@…
[…]
12:02 PM Ticket #15591 (Add Foldseek structure similarity search) created by Tom Goddard
Martin Steinegger asked if we could add a Foldseek search tool to …
11:42 AM Ticket #15587 (Crash either moving window or changing display) closed by Tom Goddard
can't reproduce: The [NSWindow _windowMovedToRect:dueToMoveEvent] entry in the stack …
11:28 AM Dev2024-7-15 edited by Eric Pettersen
(diff)
11:15 AM Ticket #15590 (Crash changing Mac display configuration) created by chimerax-bug-report@…
[…]
9:18 AM Ticket #15589 (Color Actions: can only concatenate str (not "NoneType") to str) closed by Eric Pettersen
duplicate
9:02 AM Ticket #15586 (Crash in garbage collection) closed by Eric Pettersen
duplicate
6:37 AM Ticket #15589 (Color Actions: can only concatenate str (not "NoneType") to str) created by chimerax-bug-report@…
[…]
3:00 AM Ticket #15588 (Maestro: KeyError: 'i_m_residue_number') created by Tim.Hoermann@…
[…]

Jul 9, 2024:

3:14 PM Ticket #15587 (Crash either moving window or changing display) created by chimerax-bug-report@…
[…]
2:46 PM Ticket #15586 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
11:50 AM Ticket #15585 (Select..Contacts not completely working) closed by Eric Pettersen
fixed: Fix: …
10:38 AM Dev2024-7-15 created by Tom Goddard
10:37 AM 2024-6-27 edited by Tom Goddard
(diff)
10:37 AM 2024-7-11 created by Tom Goddard
10:36 AM DeveloperMeetings edited by Tom Goddard
(diff)
9:01 AM Ticket #15583 (Crash in garbage collection) closed by Eric Pettersen
duplicate
9:00 AM Ticket #15582 (Save command history: No space left on device) closed by Eric Pettersen
nonchimerax
8:59 AM Ticket #15581 (Restore new session in old ChimeraX) closed by Eric Pettersen
limitation
8:13 AM Ticket #15585 (Select..Contacts not completely working) created by Elaine Meng
[…]
5:53 AM Ticket #15584 (Permission denied writing setting/history files) created by chimerax-bug-report@…
[…]
2:45 AM Ticket #15583 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
2:35 AM Ticket #15582 (Save command history: No space left on device) created by chimerax-bug-report@…
[…]
2:02 AM Ticket #15581 (Restore new session in old ChimeraX) created by chimerax-bug-report@…
[…]

Jul 8, 2024:

6:28 PM Ticket #15575 (fitmap: self.data is None fitting atomic model into simulated map) closed by Tom Goddard
wontfix: While it would be desirable to fix this, the case of fitting an atomic …
6:16 PM Ticket #15579 (Error opening foldseek results with AlphaFold fragment structure) closed by Tom Goddard
fixed: Fixed. Made parsing of alphafold hit names handle fragment specifier. …
5:12 PM Ticket #15578 (AlphaFold JSON: Expecting ',' delimiter) closed by Tom Goddard
nonchimerax: User tried to open a file called alphafold_database.json that did not …
4:40 PM Ticket #15567 (MatchMaker: no 'structure' attr in bring-models filter) closed by Eric Pettersen
fixed: Fix: …
4:13 PM Dev2024-7-8 edited by Tom Goddard
(diff)
3:06 PM Dev2024-7-8 edited by Tom Goddard
(diff)
3:01 PM Dev2024-7-8 edited by Tom Goddard
(diff)
2:43 PM Ticket #15580 ('close' with segmentation tool opened tries to reset mouse bindings ...) created by Zach Pearson
2:38 PM Ticket #15570 (Context menu: self.bundle_info is None) closed by Eric Pettersen
fixed: Hi Kelvin, Thanks for reporting this problem. We think it was fixed …
2:02 PM Ticket #15579 (Error opening foldseek results with AlphaFold fragment structure) created by Elaine Meng
[…]
1:17 PM Ticket #15574 (Crash waking Mac up from sleep in displayConfigFinalizedProc, ATI graphics) closed by Tom Goddard
duplicate: Crash plugging in or unplugging an external display. Work-around code …
1:17 PM Ticket #15578 (AlphaFold JSON: Expecting ',' delimiter) created by chimerax-bug-report@…
[…]
1:13 PM Ticket #15572 (libopenvr incompatible) closed by Tom Goddard
limitation: VR is not supported on Mac computers. I've improved the code so it …
1:03 PM Ticket #15569 (lookingglass errors) closed by Tom Goddard
can't reproduce: The error message says it failed to find a LookingGlass display. The …
1:00 PM Ticket #15577 (non-printable surface missing coulombic coloring) created by kristen.browne@…
[…] 8vel-mol-surf-lowres-coulombic.glb​ …
12:54 PM Ticket #15566 (Error in custom "lattice" command) closed by Tom Goddard
fixed
12:54 PM Ticket #15566 (Error in custom "lattice" command) reopened by Tom Goddard
12:52 PM Ticket #15576 (Crash closing lung data) created by Elaine Meng
[…]
12:49 PM Ticket #15564 (Fitmap: Tried to get the position of deleted drawing) closed by Tom Goddard
fixed: Fixed. Fit search code that prevented trying to position a deleted …
11:01 AM Ticket #15575 (fitmap: self.data is None fitting atomic model into simulated map) created by goddard@…
[…]
10:56 AM Ticket #15571 (PermissionError saving settings on Windows) closed by Eric Pettersen
can't reproduce: Hi Prakash, Thanks for reporting this problems. There have been some …
10:48 AM Ticket #15568 (MemoryError opening mmCIF files) closed by Eric Pettersen
duplicate
10:44 AM Ticket #15566 (Error in custom "lattice" command) closed by Eric Pettersen
can't reproduce: Maybe for light-sheet microscopy?
10:37 AM Ticket #15565 (Crash in garbage collection) closed by Eric Pettersen
duplicate
10:32 AM Ticket #15563 (MemoryError opening mmCIF files) closed by Eric Pettersen
duplicate: Hi Baturay, Thanks for reporting this problem. It has been fixed in …
10:26 AM Ticket #15574 (Crash waking Mac up from sleep in displayConfigFinalizedProc, ATI graphics) created by chimerax-bug-report@…
[…]

Jul 7, 2024:

10:47 PM Ticket #15573 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by chimerax-bug-report@…
[…]
10:47 PM Ticket #15572 (libopenvr incompatible) created by hijikata@…
[…]
10:13 PM Ticket #15571 (PermissionError saving settings on Windows) created by prakash.shukla@…
[…]
9:50 PM Ticket #15570 (Context menu: self.bundle_info is None) created by wh-kelvin.chung@…
[…]
1:03 PM Ticket #15569 (lookingglass errors) created by chimerax-bug-report@…
[…]
10:46 AM Ticket #15568 (MemoryError opening mmCIF files) created by chimerax-bug-report@…
[…]
3:01 AM Ticket #15567 (MatchMaker: no 'structure' attr in bring-models filter) created by chimerax-bug-report@…
[…]
2:36 AM Ticket #15566 (Error in custom "lattice" command) created by chimerax-bug-report@…
[…]

Jul 6, 2024:

11:06 AM Ticket #15565 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
10:13 AM Ticket #15564 (Fitmap: Tried to get the position of deleted drawing) created by um18fa@…
[…]
5:01 AM Ticket #15563 (MemoryError opening mmCIF files) created by B.altay@…
[…]

Jul 5, 2024:

4:56 PM Ticket #6988 (RFE: have warnings reveal log if tabbed) closed by Eric Pettersen
fixed: Fix: …
3:54 PM Ticket #15551 (problems with seq-structure association dialog) closed by Eric Pettersen
fixed: The list widget was comparing the old selected item text with the new …
1:30 PM Ticket #15562 (Crash in garbage collection) closed by Eric Pettersen
duplicate
1:23 PM Ticket #15560 (Crash in event loop) closed by Eric Pettersen
can't reproduce
1:02 PM Ticket #15562 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
12:33 PM Ticket #15561 (Crash in event loop) created by pk8@…
[…]
11:55 AM Ticket #15560 (Crash in event loop) created by chimerax-bug-report@…
[…]
11:55 AM Ticket #15552 (surface shown for hidden model when coulombic used in trajectory playback) closed by Eric Pettersen
fixed: Making coulombic not ask for H-bond-guided hydrogens fixed both …
9:34 AM Ticket #15558 (Crash in check_for_changes during running simulation) closed by Eric Pettersen
can't reproduce
9:29 AM Ticket #15556 (Crash in garbage collection) closed by Eric Pettersen
duplicate
9:25 AM Ticket #15555 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by Eric Pettersen
duplicate
9:22 AM Ticket #15554 (Crash showing open-file dialog) closed by Eric Pettersen
can't reproduce
9:12 AM Ticket #15550 (MemoryError opening mmCIF files) closed by Eric Pettersen
duplicate
9:10 AM Ticket #15549 (Crash in garbage collection) closed by Eric Pettersen
duplicate: Hi, Thanks for reporting this problem. It has been fixed in the 1.8 …
7:57 AM Ticket #15559 (Crash opening mmCIF) created by r.xie@…
[…]
7:04 AM Ticket #15558 (Crash in check_for_changes during running simulation) created by chimerax-bug-report@…
[…]
6:09 AM Ticket #15557 (mmcif.find_template_residue() fails on Mac for template names ...) created by Tristan Croll
Reported by Yang Lee, just confirmed by me in ChimeraX 1.8. In …
5:53 AM Ticket #15556 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
4:43 AM Ticket #15555 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…
[…]
2:56 AM Ticket #15554 (Crash showing open-file dialog) created by chimerax-bug-report@…
[…]

Jul 4, 2024:

9:38 PM Ticket #15553 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by chimerax-bug-report@…
[…]
4:37 PM Ticket #15552 (surface shown for hidden model when coulombic used in trajectory playback) created by Elaine Meng
Maybe it's two problems. Test case setup: open 2gbp open 2fw0 mm …
1:43 PM Ticket #15551 (problems with seq-structure association dialog) created by Elaine Meng
[…]
7:17 AM Ticket #15550 (MemoryError opening mmCIF files) created by chimerax-bug-report@…
[…]

Jul 3, 2024:

8:25 PM Ticket #15549 (Crash in garbage collection) created by paulpku@…
[…]
1:22 PM Ticket #15444 (More alphafold updates) closed by Eric Pettersen
fixed: Added the printable versions of the outputs to the pipeline script as …
10:06 AM Ticket #15543 (Intel Mac image save artifacts with silhouette edges) closed by Tom Goddard
nonchimerax: Those artifacts are a defect in Apple's Intel graphics driver. It is …
9:40 AM Ticket #15547 (MemoryError opening mmCIF files) closed by Eric Pettersen
duplicate
9:39 AM Ticket #15546 (Color Actions: can only concatenate str (not "NoneType") to str) closed by Eric Pettersen
duplicate: Was fixed 8 days later
9:36 AM Ticket #15545 (Crash in event loop) closed by Eric Pettersen
can't reproduce
4:03 AM Ticket #15548 (Crash in python_instances_of_class) created by chimerax-bug-report@…
[…]
1:16 AM Ticket #15547 (MemoryError opening mmCIF files) created by chimerax-bug-report@…
[…]
12:01 AM Ticket #15546 (Color Actions: can only concatenate str (not "NoneType") to str) created by chimerax-bug-report@…
[…]

Jul 2, 2024:

10:21 PM Ticket #15545 (Crash in event loop) created by chimerax-bug-report@…
[…]
10:00 PM Ticket #15544 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by chimerax-bug-report@…
[…]
12:40 PM DeveloperMeetings edited by Tom Goddard
(diff)
12:39 PM Dev2024-7-8 edited by Tom Goddard
(diff)
12:39 PM Dev2024-7-8 created by Tom Goddard
12:37 PM Dev2024-7-1 edited by Tom Goddard
(diff)
12:37 PM DeveloperMeetings edited by Tom Goddard
(diff)
12:34 PM Ticket #15543 (Intel Mac image save artifacts with silhouette edges) created by tommycottle@…
[…] heme_coord_model.png​
12:33 PM Ticket #15542 (Qt could not get OpenGL context, Linux, ancient graphics card) closed by Tom Goddard
nonchimerax: Qt could not get an opengl context for the user interface. Graphics …
9:05 AM Ticket #15541 (Crash in python_instances_of_class) closed by Eric Pettersen
can't reproduce
8:55 AM Ticket #15540 (Crash in garbage collection) closed by Eric Pettersen
duplicate: Hi Sana, Thanks for reporting this problem. This was fixed in the …
8:53 AM Ticket #15539 (Crash in garbage collection) closed by Eric Pettersen
duplicate
8:51 AM Ticket #15537 (MemoryError opening mmCIF files) closed by Eric Pettersen
duplicate
8:18 AM Ticket #15542 (Qt could not get OpenGL context, Linux, ancient graphics card) created by chimerax-bug-report@…
[…]
5:21 AM Ticket #15541 (Crash in python_instances_of_class) created by chimerax-bug-report@…
[…]
4:33 AM Ticket #15540 (Crash in garbage collection) created by sana2000@…
[…]

Jul 1, 2024:

11:33 PM Ticket #15539 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
4:28 PM Ticket #15538 (Install/uninstall issue) created by lptwomey@…
[…]
1:34 PM Ticket #15537 (MemoryError opening mmCIF files) created by chimerax-bug-report@…
[…]
12:28 PM Ticket #14934 (Daily build "developer cannot be verified") closed by Eric Pettersen
fixed: Still having problems getting AmberTools to run, but it's not causing …
12:22 PM Ticket #15523 (Crash in event loop) closed by Eric Pettersen
can't reproduce: Thanks for the info. Perhaps your graphics card got into a bad state …
12:15 PM Ticket #15536 (ui view fourup: division by zero) created by chimerax-bug-report@…
[…]
11:32 AM Ticket #15535 (Crash in Linux Mesa NVD7 graphics driver) closed by Tom Goddard
duplicate: Same graphics driver crash as #15531 and same reporter.
11:29 AM Ticket #15532 (Unclipped submodels not selectable) closed by Tom Goddard
fixed: Mostly fixed. Picking atoms in a submodel that had clipping disabled …
11:21 AM Ticket #15535 (Crash in Linux Mesa NVD7 graphics driver) created by chimerax-bug-report@…
[…]
11:20 AM Ticket #15534 (Crash on exit) closed by Eric Pettersen
can't reproduce
11:19 AM Ticket #15531 (Crash in Linux Mesa NVD7 graphics driver) closed by Tom Goddard
nonchimerax: Crashed in graphics driver showing a couple atomic models OpenGL …
11:18 AM Ticket #15534 (Crash on exit) created by chimerax-bug-report@…
[…]
11:17 AM Ticket #15533 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by chimerax-bug-report@…
[…]
11:14 AM Ticket #15532 (Unclipped submodels not selectable) created by Tristan Croll
[…]
11:12 AM Ticket #15531 (Crash in Linux Mesa NVD7 graphics driver) created by chimerax-bug-report@…
[…]
11:10 AM Ticket #15530 (Crash painting newly exposed widget(?)) closed by Eric Pettersen
can't reproduce
11:10 AM Ticket #15527 (glDrawBuffer: invalid operation) closed by Tom Goddard
duplicate: This is a somewhat common Linux problem glDrawBuffer(GL_BACK) fails. …
11:03 AM Ticket #15528 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by Eric Pettersen
duplicate
10:54 AM Ticket #15525 (PermissionError matching PAE file) closed by Tom Goddard
nonchimerax: Appears the user denied access to the Desktop for ChimeraX so it …
10:20 AM Ticket #15521 (Crash in Mac display reconfiguration) closed by Tom Goddard
duplicate: Duplicate of #15413. This ticket is the same as a crash I had on my …
9:51 AM Ticket #15520 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by Eric Pettersen
duplicate
9:50 AM Ticket #15519 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by Eric Pettersen
duplicate
9:47 AM Ticket #15526 (chimerax.ui.ask failure with Qt 6.7) closed by Eric Pettersen
duplicate: Duplicate of #15498
9:43 AM ChangeLog edited by Elaine Meng
(diff)
9:22 AM Ticket #15530 (Crash painting newly exposed widget(?)) created by chimerax-bug-report@…
[…]
8:47 AM Ticket #15529 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by celia.plisson-chastang@…
[…]

Jun 30, 2024:

1:22 AM Ticket #15528 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…
[…]

Jun 29, 2024:

9:28 PM Ticket #15527 (glDrawBuffer: invalid operation) created by chimerax-bug-report@…
[…]
1:49 PM Ticket #15526 (chimerax.ui.ask failure with Qt 6.7) created by Zach Pearson
{{{Traceback (most recent call last): File …

Jun 28, 2024:

6:36 PM Ticket #15525 (PermissionError matching PAE file) created by chimerax-bug-report@…
[…]
4:41 PM Ticket #15524 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by vsreddy@…
[…]
12:31 PM Ticket #15523 (Crash in event loop) created by victor.tobiasson@…
[…]
4:02 AM Ticket #15522 (Mismatch of crosslink positions when loading structures from PDB-Dev) created by Georg.Kempf@…
[…]
2:27 AM Ticket #15521 (Crash in Mac display reconfiguration) created by chimerax-bug-report@…
[…]
2:20 AM Ticket #15520 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…
[…]
12:52 AM Ticket #15519 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…
[…]

Jun 27, 2024:

5:58 PM Ticket #15428 (problem with viruses bychain outputs in flows) closed by Eric Pettersen
fixed: The updated bundle is on the toolshed, and the pipeline script has …
5:34 PM Ticket #15517 (Crash changing Mac display configuration) closed by Tom Goddard
can't reproduce: Did this ChimeraX crash happen after you unplugged an external display …
5:26 PM Ticket #15514 (Collection slices incorrectly updated) closed by Tom Goddard
fixed: Fixed. Made slicing collections copy the numpy array of C++ pointers.
5:22 PM Ticket #15513 (Graphics crash, macOS 10.15.7, NVIDIA GeForce GT 755M) closed by Tom Goddard
nonchimerax: Apple Nvidia graphics driver crash.
2:49 PM Ticket #15515 (Crash adding hydrogens for Dock Prep) closed by Eric Pettersen
can't reproduce: The log doesn't show anything being opened before Dock Prep, yet Dock …
2:42 PM Ticket #15512 (Crash showing save dialog) closed by Eric Pettersen
can't reproduce
2:39 PM Ticket #15511 (Crash in garbage collection) closed by Eric Pettersen
duplicate
2:38 PM Ticket #15510 (Crash in garbage collection) closed by Eric Pettersen
duplicate
2:36 PM Ticket #15509 (Test) closed by Eric Pettersen
not a bug
2:34 PM Ticket #15508 (Crash in garbage collection) closed by Eric Pettersen
duplicate: Duplicate of #15507
2:31 PM Ticket #15518 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by chimerax-bug-report@…
[…]
2:29 PM Ticket #15517 (Crash changing Mac display configuration) created by psauer@…
[…]
2:29 PM Ticket #15516 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by chimerax-bug-report@…
[…]
2:28 PM Ticket #15515 (Crash adding hydrogens for Dock Prep) created by chimerax-bug-report@…
[…]
2:27 PM Ticket #15514 (Collection slices incorrectly updated) created by goddard@…
[…]
2:27 PM Ticket #15513 (Graphics crash, macOS 10.15.7, NVIDIA GeForce GT 755M) created by chimerax-bug-report@…
[…]
2:26 PM Ticket #15512 (Crash showing save dialog) created by chimerax-bug-report@…
[…]
2:08 PM Ticket #15511 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
2:01 PM Ticket #15505 (Attempt to retrieve context when no valid context) closed by Tom Goddard
can't reproduce: ChimeraX 1.6 on startup on Linux calls make current on the Qt …
1:48 PM Ticket #15510 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
1:14 PM Ticket #15509 (Test) created by Eric Pettersen
[…]
1:11 PM Ticket #5407 (Display HTML within table) closed by Eric Pettersen
fixed: Table columns initialized with "is_html=True" will support HTML markup …

Jun 26, 2024:

6:23 PM Ticket #15508 (Crash in garbage collection) created by sana2000@…
[…]
6:12 PM Ticket #15507 (Crash in garbage collection) closed by Eric Pettersen
duplicate: Hi Sana, Thanks for reporting this problem. I would recommend …
6:09 PM Ticket #15506 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by Eric Pettersen
duplicate
6:07 PM Ticket #15507 (Crash in garbage collection) created by sana2000@…
[…]
3:58 PM Ticket #15506 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…
[…]
1:52 PM Ticket #15498 (chimerax.ui.ask failure with Qt 6.7) closed by Eric Pettersen
fixed: Fix available in next daily build. Fix: …
12:37 PM Ticket #15505 (Attempt to retrieve context when no valid context) created by saverio.lemme@…
[…]
11:38 AM Ticket #15504 (Stack overflow processing atom spec) created by gk351@…
[…]
11:25 AM Ticket #15503 (Crash in garbage collection) closed by Eric Pettersen
duplicate
11:18 AM Ticket #15500 (Open PDB file: invalid map<K, T> key) closed by Eric Pettersen
wontfix: Seems like a functional duplicate of #15309; probably terrible …