Timeline



Nov 11, 2021:

5:33 PM Ticket #5588 (Log blank) created by nimendozam@…
[…] Bug in resent view and no log shown with pwd.png
3:52 PM Ticket #5587 (Cannot reshow Distances tool) created by kimsk@…
[…]
3:15 PM Ticket #5586 (Crash in Qt on exit) created by chimerax-bug-report@…
[…]
9:51 AM Ticket #5585 (Problem opening file hyperlinked in Excel in ChimeraX) created by jribeiro@…
[…]
5:41 AM Ticket #5584 (wrapped C/C++ object of type QScreen has been deleted) created by chimerax-bug-report@…
[…]

Nov 10, 2021:

9:58 PM Ticket #5583 (Crash firing selection-changed trigger after opening Alphafold model) created by chimerax-bug-report@…
[…]
9:57 PM Ticket #5582 (Startup error on Windows 7) created by chimerax-bug-report@…
[…]
9:53 PM Ticket #5581 (Modeller: not enough args for format string) created by yen-li.li@…
[…]
8:20 PM Ticket #5580 (Alphafold search blast results: 'NoneType' object has no attribute 'split') created by chimerax-bug-report@…
[…]
3:06 PM Ticket #5579 (Alphafold search blast results: 'NoneType' object has no attribute 'split') created by chung-han.tsai@…
[…]
11:58 AM Ticket #5578 (Run AlphaFold on UCSF Wynton cluster) created by Tom Goddard
Would like to allow ChimeraX to submit AlphaFold jobs to the UCSF …
11:48 AM Ticket #5427 (Read EMAN format: cannot load .dylibs/libhdf5.200.dylib) closed by Tom Goddard
fixed: Presumed fixed. Tested on macOS Big Sur but not tested on macOS Catalina.
11:46 AM Ticket #5450 (crash taking sqrt()?!?) closed by Tom Goddard
can't reproduce
10:16 AM Ticket #5575 (Crash in Qt event loop after changing transparency, access violation) closed by Tom Goddard
can't reproduce: Crashed in the Qt event loop. Probably not related to the last …
9:50 AM Ticket #5577 (Crash in set_sseq_chain_id) closed by pett
can't reproduce
9:00 AM Ticket #5577 (Crash in set_sseq_chain_id) created by chimerax-bug-report@…
[…]
1:19 AM Ticket #5576 (Update coordinates: OpenMM: RuntimeError: Release Object) created by chimerax-bug-report@…
[…]

Nov 9, 2021:

5:35 PM Training edited by Tom Goddard
(diff)
12:30 PM Ticket #5575 (Crash in Qt event loop after changing transparency, access violation) created by chimerax-bug-report@…
[…]
12:15 PM Ticket #5572 (Blast results: invalid literal for int() with base 10) closed by Zach Pearson
fixed
11:19 AM Ticket #5564 (Build Structure: cannot change rotamer library) closed by pett
fixed: Hi Charisma, Thanks for reporting this problem. I have fixed it now …
11:18 AM DeveloperMeetings edited by Tom Goddard
(diff)
11:16 AM Ticket #5574 (devel install does not replace previous bundle) created by jingrou.zeng18@…
The devel install command should replace the existing installed bundle …
11:12 AM Ticket #5568 (glGetFramebufferAttachmentParameteriv: invalid enumerant) closed by Tom Goddard
nonchimerax: Graphics driver bug, fails to start, ATI FirePro 2260 gpu (circa 2008).
11:10 AM Ticket #5567 (Disconnected screen crash) closed by Tom Goddard
duplicate: This ChimeraX crash is caused by removing an external screen on macOS …
11:04 AM Ticket #5566 (Crash in alphafold predict) closed by Tom Goddard
can't reproduce: I see ChimeraX crash sometime after you started an AlphaFold
11:01 AM Ticket #5563 (vseries slider: list index out of range) closed by Tom Goddard
duplicate: Fixed several months ago after 1.2.5 release. User created vseries …
10:53 AM Ticket #5562 (Status bar destruction: wrapped C/C++ object of type QScreen has been ...) closed by Tom Goddard
duplicate: Fixed several months ago.
10:34 AM Ticket #5573 (Crash showing rapid access at startup) closed by pett
can't reproduce
10:33 AM Ticket #5573 (Crash showing rapid access at startup) created by chimerax-bug-report@…
[…]
9:35 AM Ticket #5572 (Blast results: invalid literal for int() with base 10) created by Elaine Meng
[…]
8:59 AM Ticket #5571 (Blast: not enough values to unpack) closed by pett
duplicate
8:55 AM Ticket #5571 (Blast: not enough values to unpack) created by chimerax-bug-report@…
[…]
8:47 AM Ticket #5570 (Crash submitting Blast job) closed by pett
can't reproduce
8:46 AM Ticket #5569 (glGetFramebufferAttachmentParameteriv: invalid enumerant) closed by pett
duplicate
7:49 AM Ticket #5570 (Crash submitting Blast job) created by chimerax-bug-report@…
[…]
7:18 AM Ticket #5569 (glGetFramebufferAttachmentParameteriv: invalid enumerant) created by chimerax-bug-report@…
[…]
7:11 AM Ticket #5568 (glGetFramebufferAttachmentParameteriv: invalid enumerant) created by chimerax-bug-report@…
[…]
7:04 AM Ticket #5567 (Disconnected screen crash) created by jflecken@…
[…]
4:58 AM Ticket #5566 (Crash in alphafold predict) created by hamine.oliveira@…
[…]
3:54 AM Ticket #5565 (Lone '~' expands to ~ribbon) created by Tristan Croll
[…]

Nov 8, 2021:

11:59 PM Ticket #5561 (include query model name in Blast results window) closed by Zach Pearson
fixed: Should be fixed in …
11:11 PM Ticket #5564 (Build Structure: cannot change rotamer library) created by ichcharisma@…
[…] Screen Shot 2021-11-09 at 16.11.12.png
9:14 PM Ticket #5563 (vseries slider: list index out of range) created by chimerax-bug-report@…
[…]
4:55 PM Ticket #5562 (Status bar destruction: wrapped C/C++ object of type QScreen has been ...) created by chimerax-bug-report@…
[…]
4:53 PM Ticket #5519 (Out of memory fetching/opening mmCIFs) closed by Greg Couch
can't reproduce: The exact same set of commands works for me and the Windows Task …
4:28 PM Ticket #5540 (Question marks used for gaps instead of dashes) closed by pett
fixed: Matchmaker is supposed to rectify those sequences to their normal …
10:42 AM Ticket #5558 (Graphics driver crash, macOS 11.6, Intel Iris Plus Graphics 645, ...) closed by Tom Goddard
nonchimerax: Apple graphics driver crash.
10:34 AM Ticket #5557 (Crash opening session) closed by pett
can't reproduce
10:11 AM Ticket #5555 (failed starting of .exe file) closed by Greg Couch
nonchimerax: Nothing is blocking the download on our end. If you can view the …
10:08 AM Ticket #5556 (Crash showing selection on alphafold model (swap buffers?)) closed by Tom Goddard
nonchimerax: It looks like the crash (access violation) was in OpenGL …
7:46 AM Ticket #5561 (include query model name in Blast results window) created by Elaine Meng
From: Elaine Meng <meng@…> Date: November 3, 2021 at …
7:00 AM Ticket #5560 (Alignment headers somehow being directly saved in sessions) created by devonjboland@…
[…]

Nov 7, 2021:

8:50 PM Ticket #5559 (Blast Protein: wrapped C/C++ object of type QProgressBar has been deleted) created by chimerax-bug-report@…
[…]
11:34 AM Ticket #5558 (Graphics driver crash, macOS 11.6, Intel Iris Plus Graphics 645, ...) created by chimerax-bug-report@…
[…]
9:42 AM Ticket #5557 (Crash opening session) created by chimerax-bug-report@…
[…]
7:44 AM Ticket #5556 (Crash showing selection on alphafold model (swap buffers?)) created by chimerax-bug-report@…
[…]

Nov 6, 2021:

7:18 PM Ticket #5555 (failed starting of .exe file) created by ronald.clarke@…
[…] failed.docx
1:57 AM Ticket #5554 (Crash drawing side view) created by chimerax-bug-report@…
[…]
1:33 AM Ticket #5553 (Version check bug) closed by Greg Couch
fixed: Remove debug code that got checked in.

Nov 5, 2021:

5:14 PM Ticket #5552 (morph same true: Execution of 'Structure' object's 'coordset_size' ...) closed by Tom Goddard
duplicate: This error saving a session is fixed in the current ChimeraX 1.3 …
2:42 PM Ticket #5553 (Version check bug) created by chimerax-bug-report@…
[…]
10:09 AM Ticket #5550 (Alphafold match: 'Structure' object has no attribute ...) closed by Tom Goddard
fixed: Fixed in 1.3 and 1.4. When alignment of alphafold model to an …
9:45 AM Ticket #5548 (Windows 7 graphics error) closed by Tom Goddard
nonchimerax: ChimeraX does not support Windows 7, only Windows 10 as shown on the …
9:43 AM Ticket #5547 (Crash disconnecting screen) closed by Tom Goddard
duplicate: Qt bug fixed in Qt 5.15 used in current ChimeraX. This crash has been …
9:37 AM Ticket #5546 (Crash saving session including maps) closed by Tom Goddard
can't reproduce: Looks like it crashed getting the attribute of an atomic structure, …
9:13 AM Ticket #5552 (morph same true: Execution of 'Structure' object's 'coordset_size' ...) created by am2837@…
[…]
8:53 AM Ticket #5551 (unhashable type: 'Color') closed by pett
duplicate: Hi Juliana, Thanks for reporting this problem. It was fixed in the …
8:48 AM Ticket #5549 (Access violation on Windows in Qt event loop) closed by pett
can't reproduce
8:14 AM Ticket #5545 (Error in toolshed error message) closed by pett
duplicate: Hi Matthew, The toolshed is trying to tell you that the Clipper …
7:42 AM Ticket #5551 (unhashable type: 'Color') created by jglavina@…
[…]
4:07 AM Ticket #5550 (Alphafold match: 'Structure' object has no attribute ...) created by Tristan Croll
[…]
1:35 AM Ticket #5549 (Access violation on Windows in Qt event loop) created by chimerax-bug-report@…
[…]
1:34 AM Ticket #5548 (Windows 7 graphics error) created by urban@…
[…]
12:30 AM Ticket #5547 (Crash disconnecting screen) created by chimerax-bug-report@…
[…]

Nov 4, 2021:

10:20 PM Ticket #5546 (Crash saving session including maps) created by joewang@…
[…]
8:27 PM Ticket #5545 (Error in toolshed error message) created by mjw100@…
[…]
8:22 PM Ticket #5544 (Allow EMDB fetch command to choose europe/japan/china/us and ftp/https) closed by Tom Goddard
fixed: Added the extra EMDB fetch options in ChimeraX 1.3 and 1.4.
8:18 PM Ticket #5544 (Allow EMDB fetch command to choose europe/japan/china/us and ftp/https) created by philip.macmenamin@…
The NIH 3D pipeline would like to fetch EMDB maps from the US mirror …
4:38 PM NTTData edited by Elaine Meng
(diff)
2:22 PM NTTData edited by Elaine Meng
(diff)
2:09 PM NTTData edited by Elaine Meng
(diff)
2:07 PM NTTData edited by Elaine Meng
(diff)
1:35 PM NTTData edited by Elaine Meng
(diff)
12:49 PM 2021-11-4 edited by Tom Goddard
(diff)
12:22 PM Ticket #5542 (VR crash in openvr waitGetPoses()) closed by Tom Goddard
can't reproduce: Crash in OpenVR waitGetPoses(). Interesting to see VR use on Linux. …
12:09 PM 2021-11-4 edited by Tom Goddard
(diff)
12:07 PM 2021-11-4 edited by Tom Goddard
(diff)
12:04 PM 2021-11-4 edited by Tom Goddard
(diff)
11:48 AM 2021-11-4 edited by Tom Goddard
(diff)
11:22 AM 2021-11-4 edited by Tom Goddard
(diff)
11:18 AM 2021-11-4 edited by Tom Goddard
(diff)
11:17 AM 2021-11-4 edited by Tom Goddard
(diff)
11:03 AM Ticket #5543 (VR crash in drawing) closed by pett
duplicate
11:01 AM Ticket #5541 (Crash showing rapid access at startup, Linux ChimeraX 1.2.5) closed by pett
can't reproduce
10:50 AM Ticket #5543 (VR crash in drawing) created by chimerax-bug-report@…
[…]
10:49 AM Ticket #5542 (VR crash in openvr waitGetPoses()) created by chimerax-bug-report@…
[…]
10:45 AM Ticket #5541 (Crash showing rapid access at startup, Linux ChimeraX 1.2.5) created by chimerax-bug-report@…
[…]
10:12 AM Ticket #5539 (Crash showing rapid access at startup, Linux ChimeraX 1.2.5) closed by pett
can't reproduce
10:10 AM Ticket #5538 (Region bound checking using None) closed by pett
duplicate
9:16 AM Ticket #5540 (Question marks used for gaps instead of dashes) created by Elaine Meng
[…] questionmarks.cxs
6:31 AM Ticket #5539 (Crash showing rapid access at startup, Linux ChimeraX 1.2.5) created by chimerax-bug-report@…
[…]

Nov 3, 2021:

9:55 PM Ticket #5538 (Region bound checking using None) created by ichcharisma@…
[…] Screen Shot 2021-11-04 at 13.54.19.png
5:50 PM Ticket #5537 (Add tool to measure pocket volumes) created by meng@…
Begin forwarded message: From: Elaine Meng Subject: Re: …
1:50 PM Ticket #5536 (Duplicate pseudobond depiction) created by slange001@…
[…] ChimeraX_pbond_bug_report.png
1:27 PM Dev2021-11-11 edited by Tom Goddard
(diff)
1:27 PM ChangeLog edited by Elaine Meng
(diff)
1:25 PM Ticket #5530 (Write GLTF: index 1 is out of bounds for axis 0 with size 1) closed by Tom Goddard
duplicate: Fixed 5 months ago. Ticket #4788
1:23 PM Dev2021-11-11 created by Tom Goddard
1:21 PM DeveloperMeetings edited by Tom Goddard
(diff)
1:15 PM Ticket #5534 (Unknown crash) closed by Tom Goddard
can't reproduce: It is puzzling that none of the commands in the log enable clipping. …
12:02 PM Ticket #5527 (Atomic structures with all atoms deleted are not closed in Python) closed by pett
fixed: I tested out having the structure live on with zero atoms and …
10:52 AM Ticket #5532 (Region bound checking using None) closed by pett
fixed
10:12 AM Ticket #5535 (Matchmaker: 'NoneType' object has no attribute 'setChecked') closed by pett
duplicate: Duplicate of #5207
9:58 AM Ticket #5533 (Unknown crash) closed by pett
can't reproduce: Hundreds of open-dialog "fatal" errors. The Python log ended open …
8:43 AM Ticket #5535 (Matchmaker: 'NoneType' object has no attribute 'setChecked') created by chimerax-bug-report@…
[…]
8:22 AM Ticket #5534 (Unknown crash) created by chimerax-bug-report@…
[…]
7:11 AM Ticket #5533 (Unknown crash) created by chimerax-bug-report@…
[…]
3:31 AM Ticket #5532 (Region bound checking using None) created by chimerax-bug-report@…
[…]
2:18 AM Ticket #5531 (Problems connecting with Visual Studio Code) created by Tristan Croll
[…] pyvsc-run-isolated.py

Nov 2, 2021:

11:43 PM Ticket #5529 (Remove lineprofiler from prereqs) closed by Tom Goddard
fixed: Removed prereqs/lineprofiler.
11:30 PM Ticket #5530 (Write GLTF: index 1 is out of bounds for axis 0 with size 1) created by chimerax-bug-report@…
[…]
8:08 PM Ticket #5529 (Remove lineprofiler from prereqs) created by Tom Goddard
I think we can git remove the prereqs/lineprofiler directory. It is …
7:22 PM Ticket #5528 (Remove pywin32 and wmi dependencies used by bug reporter on Windows) created by Tom Goddard
We've been getting github security warnings about pywin32 in ChimeraX. …
3:21 PM Ticket #5527 (Atomic structures with all atoms deleted are not closed in Python) created by Tom Goddard
The atomic structure C++ code deletes the C++ structure automatically …
2:59 PM Ticket #5525 (Morph problem) closed by Tom Goddard
fixed: Fixed in ChimeraX 1.3 and 1.4 daily build. Morph code was checking …
2:20 PM Training edited by Tom Goddard
(diff)
11:46 AM Ticket #5526 (Probably garbage collection crash) closed by pett
duplicate
11:09 AM Ticket #5524 (Modeller failure) closed by pett
fixed: Hi Deepesh, Thanks for reporting this problem. It turns out that our …
10:45 AM Ticket #5526 (Probably garbage collection crash) created by chimerax-bug-report@…
[…]
10:20 AM Ticket #5525 (Morph problem) created by am2837@…
[…]
10:08 AM Ticket #5523 (Unknown crash) closed by pett
can't reproduce
9:42 AM 2021-11-4 created by Tom Goddard
9:41 AM DeveloperMeetings edited by Tom Goddard
(diff)
9:35 AM Ticket #5524 (Modeller failure) created by dstnt@…
[…]
2:39 AM Ticket #5523 (Unknown crash) created by chimerax-bug-report@…
[…]

Nov 1, 2021:

10:26 PM Ticket #5522 (Clashes syntax error) created by ichcharisma@…
[…]
4:59 PM Ticket #5520 (Unknown crash with unformatted stack trace) closed by Tom Goddard
can't reproduce: Thanks for the report. The crash stack trace gives no indication of …
11:57 AM Ticket #5518 (Graphics crash, macOS 10.15, Intel Iris Graphics 6100) closed by Tom Goddard
nonchimerax: Apple graphics driver crash.
11:43 AM Ticket #5514 (volume erase: out of memory) closed by Tom Goddard
duplicate: OpenGL out of memory, duplicate of #5384, error message has been …
10:54 AM Ticket #5521 (Add Charge: bad hydrogen name) closed by pett
duplicate
10:38 AM Ticket #5516 (Unknown crash) closed by pett
can't reproduce
10:18 AM Ticket #5515 (Qt crash during exit) closed by pett
can't reproduce
10:15 AM Ticket #5513 (Crash clicking close button of dock widget) closed by pett
can't reproduce
10:12 AM Ticket #5512 (Download page incorrect in Chrome) closed by pett
fixed
10:09 AM Ticket #5511 (Assertion failed: (backingScaleFactor > 0.f), function ...) closed by pett
can't reproduce: Seems to be a problem with dragging/dropping a color from/to the color …
9:52 AM Ticket #5521 (Add Charge: bad hydrogen name) created by chimerax-bug-report@…
[…]
8:02 AM Ticket #5520 (Unknown crash with unformatted stack trace) created by semchonok@…
[…]

Oct 31, 2021:

12:42 PM Ticket #5519 (Out of memory fetching/opening mmCIFs) created by chimerax-bug-report@…
[…]
12:33 AM Ticket #5518 (Graphics crash, macOS 10.15, Intel Iris Graphics 6100) created by chimerax-bug-report@…
[…]
12:30 AM Ticket #5517 (Unknown crash) created by luyuchao_2006@…
[…]
12:18 AM Ticket #5516 (Unknown crash) created by chimerax-bug-report@…
[…]

Oct 30, 2021:

9:31 AM Ticket #5515 (Qt crash during exit) created by chimerax-bug-report@…
[…]
9:22 AM Ticket #5514 (volume erase: out of memory) created by chimerax-bug-report@…
[…]
3:37 AM Ticket #5499 (MD template error) closed by Tristan Croll
fixed: Updated template in ISOLDE's DB, and sent a copy to the user.
2:10 AM Ticket #5513 (Crash clicking close button of dock widget) created by chimerax-bug-report@…
[…]

Oct 29, 2021:

9:28 PM Ticket #5314 (Movie encode on Redhat Enterprise Linux 8 fails to find libbz2.so) closed by Greg Couch
fixed: Fixed by compiling ffmpeg separately for CentOS. Ubuntu has ffmpeg in …
9:24 PM Ticket #5247 (Make download and older releases pages easier to maintain) closed by Greg Couch
fixed: Added script to generate JSON files for current candidate, daily, and …
9:08 PM ChangeLog edited by Greg Couch
(diff)
6:21 PM Ticket #5512 (Download page incorrect in Chrome) created by agarrubio@…
[…]
3:02 PM Ticket #5511 (Assertion failed: (backingScaleFactor > 0.f), function ...) created by chimerax-bug-report@…
[…]
12:22 PM Ticket #5501 (Cannot save session: bytes object is too large) closed by Tom Goddard
fixed: Added error message that explain 4Gb limit and suggests saving map in …
11:35 AM Ticket #5509 (glGetFramebufferAttachmentParameteriv: invalid enumerant) closed by Tom Goddard
nonchimerax: Windows 7 is not supported. Error appears to be a graphics driver problem.
11:34 AM Ticket #5508 (Graphics driver crash, macOS 11.6, Intel UHD Graphics 617, report 2) closed by Tom Goddard
duplicate: Same user as #5496 reported yesterday. Using 9 Gbytes of memory on a …
11:30 AM Ticket #5510 (add charge failure) closed by pett
fixed
11:29 AM Ticket #5507 (Crash updating file history) closed by Tom Goddard
nonchimerax: Setting html for the file history Qt html widget crashed. It was …
11:14 AM Ticket #5510 (add charge failure) created by chimerax-bug-report@…
[…]
11:00 AM Ticket #5509 (glGetFramebufferAttachmentParameteriv: invalid enumerant) created by chimerax-bug-report@…
[…]
10:59 AM Ticket #5508 (Graphics driver crash, macOS 11.6, Intel UHD Graphics 617, report 2) created by chimerax-bug-report@…
[…]
10:57 AM Ticket #5507 (Crash updating file history) created by chimerax-bug-report@…
[…]
10:35 AM Ticket #5505 (Read PDB as .gro) closed by pett
not a bug: Cannot read a PDB file as a .gro
10:30 AM Ticket #5503 (Cannot save session: bytes object is too large) closed by pett
duplicate
10:29 AM Ticket #5502 (Cannot save session: bytes object is too large) closed by pett
duplicate
9:58 AM Ticket #5506 (ChimeraX - Color by seq_conservation fails in tutorial) created by Sean.Moore@…
[…]

Oct 28, 2021:

8:23 PM Ticket #5505 (Read PDB as .gro) created by chimerax-bug-report@…
[…]
6:28 PM Ticket #5504 (Python shell broken with PyQt 6.2) created by goddard@…
[…]
6:22 PM Ticket #5503 (Cannot save session: bytes object is too large) created by chimerax-bug-report@…
[…]
6:04 PM Ticket #5502 (Cannot save session: bytes object is too large) created by chimerax-bug-report@…
[…]
4:15 PM Ticket #5501 (Cannot save session: bytes object is too large) created by chimerax-bug-report@…
[…]
4:04 PM Ticket #5497 (Graphics presets don't reset depthJump) closed by Tom Goddard
fixed: Thanks for catching that. I made the lighting presets simple, …
3:49 PM Ticket #5495 (Model tiling: 'NoneType' object is not iterable) closed by Tom Goddard
fixed: Fixed tile command when no model specifier given. Actual bug reported …
2:26 PM Dev2021-10-28 edited by Tom Goddard
(diff)
2:05 PM Ticket #5500 (stop bothering me) created by Greg Couch
Add way to turn off being reminded that there is a ChimeraX update
12:22 PM 2021-10-28 edited by Tom Goddard
(diff)
12:14 PM Ticket #5499 (MD template error) created by jopark@…
[…]
10:49 AM Ticket #5498 (Discontinuous secondary structure) closed by pett
not a bug: Hi Andrea, In order to handle the case where a structure has adjacent …
10:38 AM Ticket #5498 (Discontinuous secondary structure) created by andrea.foote@…
[…] Screen Shot 2021-10-28 at 1.36.09 PM.png
10:32 AM Ticket #5490 (Conflicting attr registration) closed by pett
fixed
10:05 AM Ticket #5496 (Graphics driver crash, macOS 11.6, Intel UHD Graphics 617) closed by Tom Goddard
nonchimerax: Apple graphics driver crash.
9:51 AM Ticket #5488 (wrapped C/C++ object of type QScreen has been deleted) closed by Tom Goddard
duplicate: Fixed 6 months ago, not in 1.2.5, #4538.
9:41 AM Ticket #5494 (Modeller: not enough args for format string) closed by pett
fixed
8:58 AM Ticket #5497 (Graphics presets don't reset depthJump) created by jrf296@…
[…]
8:51 AM Ticket #5492 (Unknown crash) closed by pett
can't reproduce: The "stack overflow" is different though.
8:48 AM Ticket #5491 (Crash in garbage collection during new-object allocation) closed by pett
duplicate
8:44 AM Ticket #5489 (Unknown crash) closed by pett
can't reproduce
5:07 AM Ticket #5496 (Graphics driver crash, macOS 11.6, Intel UHD Graphics 617) created by chimerax-bug-report@…
[…]
4:24 AM Ticket #5495 (Model tiling: 'NoneType' object is not iterable) created by chimerax-bug-report@…
[…]
3:30 AM Ticket #5494 (Modeller: not enough args for format string) created by chimerax-bug-report@…
[…]
2:48 AM Ticket #5493 (H-bonds nowhere near nucleic acid depictions) created by vishal.sahu@…
[…] double-helix-interaction-issue.png
2:24 AM Ticket #5492 (Unknown crash) created by chimerax-bug-report@…
[…]

Oct 27, 2021:

9:18 PM Ticket #5491 (Crash in garbage collection during new-object allocation) created by chimerax-bug-report@…
[…]
5:47 PM Ticket #5490 (Conflicting attr registration) created by Elaine Meng
[…]
2:24 PM Ticket #5489 (Unknown crash) created by chimerax-bug-report@…
[…]
2:10 PM Ticket #5484 (Chain IDs not written consistently) closed by pett
fixed: The code to put spaces around short residue names was wrong. Not …
1:38 PM Ticket #5488 (wrapped C/C++ object of type QScreen has been deleted) created by chimerax-bug-report@…
[…]
1:16 PM Ticket #5485 (Color button accessed after C++ deleted) closed by pett
fixed: Instead of relying on __del__ (which doesn't get called for the …
11:03 AM Ticket #5487 (Graphics driver crash, macOS 10.5.7, Intel Iris Plus Graphics) closed by Tom Goddard
nonchimerax: Apple graphics driver crash.
11:01 AM Ticket #5481 (Graphics driver crash, macOS 11.6, Intel Iris Plus Graphics) closed by Tom Goddard
nonchimerax: Apple graphics driver crash.
10:59 AM Ticket #5479 (Crash changing silhouettes) closed by Tom Goddard
can't reproduce: We've seen this crash Windows fatal exception: access violation …
10:24 AM Ticket #5486 (Crash in garbage collection) closed by pett
duplicate: Hi, Thanks for reporting this problem. We believe it is fixed in the …
10:07 AM Ticket #5483 (Show CAs only) closed by pett
not a bug: As this is a usage question, forwarded it to chimerax-users mailing list
10:01 AM Ticket #5482 (Cannot save PDB) closed by pett
duplicate
9:35 AM Ticket #5480 (Can't bond an atom to itself) closed by pett
duplicate: Hi Allen, Could you upgrade your ChimeraX to the latest version and …
9:18 AM Ticket #5478 (All atoms for zone mask must be from a single model) closed by Tristan Croll
fixed: I've already reworked this to throw a UserError here (and also to …
9:01 AM Ticket #5477 (Cannot restore session: _pickle.UnpicklingError: invalid load key) closed by pett
duplicate: Hi Kate, You need a newer version of ChimeraX in order to restore …
8:20 AM Ticket #5487 (Graphics driver crash, macOS 10.5.7, Intel Iris Plus Graphics) created by chimerax-bug-report@…
[…]
7:57 AM Ticket #5486 (Crash in garbage collection) created by jso1@…
[…]
6:34 AM Ticket #5485 (Color button accessed after C++ deleted) created by chimerax-bug-report@…
[…]
4:35 AM Ticket #5484 (Chain IDs not written consistently) created by Tristan Croll
[…] chains_renamed.pdb
4:25 AM Ticket #5483 (Show CAs only) created by bssfh@…
[…]
3:11 AM Ticket #5482 (Cannot save PDB) created by chimerax-bug-report@…
[…]
2:53 AM Ticket #5481 (Graphics driver crash, macOS 11.6, Intel Iris Plus Graphics) created by chimerax-bug-report@…
[…]
12:48 AM Ticket #5480 (Can't bond an atom to itself) created by allenwu1991@…
[…]

Oct 26, 2021:

11:16 PM Ticket #5479 (Crash changing silhouettes) created by chimerax-bug-report@…
[…]
5:57 PM Ticket #5478 (All atoms for zone mask must be from a single model) created by chimerax-bug-report@…
[…]
5:10 PM Ticket #5477 (Cannot restore session: _pickle.UnpicklingError: invalid load key) created by kimsk@…
[…]
11:52 AM Ticket #5474 (Hangs reading PDB) closed by pett
can't reproduce: Disturbing, but okay -- will close for now.
11:49 AM Ticket #5476 (1.3 release candidate cannot read 1.4 sessions) closed by pett
fixed: Added code to release candidate to read 1.4 custom-attribute session info.
11:27 AM Ticket #5475 (Out of memory saving large image) closed by Tom Goddard
limitation: ChimeraX is not able to render an image as large as you requested with …
11:21 AM Ticket #5473 (toolshed python package parsing cannot handle quotes) closed by Greg Couch
fixed: This will be fixed in the next daily build and the 1.3 release …
11:14 AM Ticket #5476 (1.3 release candidate cannot read 1.4 sessions) created by Elaine Meng
[…] modelloops.cxs
10:49 AM Ticket #5475 (Out of memory saving large image) created by elzbieta.wator@…
[…]
10:37 AM Dev2021-10-28 created by Tom Goddard
10:32 AM 2021-10-28 edited by Tom Goddard
(diff)
10:31 AM 2021-10-28 created by Tom Goddard
10:30 AM DeveloperMeetings edited by Tom Goddard
(diff)
10:27 AM Ticket #5471 (Crash after hiding atomic model, Windows) closed by Tom Goddard
can't reproduce: Not enough information in the crash report to debug this. The Python …
9:39 AM Ticket #5472 (Crash in atomstruct::Atom::default_radius()) closed by pett
duplicate: Duplicate of
8:19 AM Ticket #5474 (Hangs reading PDB) created by phil.cruz@…
[…]
8:09 AM Ticket #5473 (toolshed python package parsing cannot handle quotes) created by wolfgang.lugmayr@…
[…]
4:51 AM Ticket #5469 (Request for help in debugging) closed by Tristan Croll
fixed: Looks like the problem is in passing the std::vector by const …
12:54 AM Ticket #5472 (Crash in atomstruct::Atom::default_radius()) created by muhammad.obk@…
[…]

Oct 25, 2021:

7:52 PM Ticket #5471 (Crash after hiding atomic model, Windows) created by yen-li.li@…
[…]
4:06 PM Ticket #5438 (Build frequently breaks installing cxservices) closed by Zach Pearson
fixed: I made the distclean target that gets called by …
2:42 PM Ticket #5463 (Structure.delete_alt_locs() failing) closed by pett
fixed: alt loc ANISOU info was being used after the altloc map had been …
2:31 PM Ticket #5470 (Crash in atomstruct::Atom::default_radius()) created by muhammad.obk@…
[…]
12:20 PM Ticket #5469 (Request for help in debugging) created by Tristan Croll
[…]
11:53 AM Ticket #5468 (Cannot restore session: _pickle.UnpicklingError: invalid load key) closed by pett
not a bug: Hi Nitesh, We believe this error occurs when you try to restore a …
11:52 AM Ticket #5468 (Cannot restore session: _pickle.UnpicklingError: invalid load key) created by nkkhandelwal@…
The following bug report has been submitted: Platform: …
11:35 AM Ticket #5467 (Allow reading Amira version 3.0 volume data) created by deng.luo@…
[…]
11:23 AM Ticket #5466 (Crash showing rapid access at startup) closed by pett
duplicate
11:21 AM Ticket #5466 (Crash showing rapid access at startup) created by chimerax-bug-report@…
[…]
11:00 AM Ticket #5465 (Unknown crash) closed by pett
can't reproduce
10:51 AM Ticket #5461 (Graphics driver crash, macOS 11.6, Intel UHD Graphics 617) closed by Tom Goddard
nonchimerax: Apple graphics driver crash.
10:08 AM Ticket #5462 (Crash with largely trashed stack) closed by pett
can't reproduce
10:04 AM Ticket #5460 (problem with displaying secondary structures) closed by pett
not a bug: Forwarded to chimerax-users list and answered there.
9:37 AM Ticket #5458 (Unknown crash) closed by pett
can't reproduce
9:20 AM Ticket #5465 (Unknown crash) created by chimerax-bug-report@…
[…]
7:27 AM Ticket #5464 (better template residue support) created by Tristan Croll
[…]
5:45 AM Ticket #5463 (Structure.delete_alt_locs() failing) created by Tristan Croll
[…]

Oct 24, 2021:

6:36 PM Ticket #5462 (Crash with largely trashed stack) created by chimerax-bug-report@…
[…]

Oct 23, 2021:

5:01 PM Ticket #5461 (Graphics driver crash, macOS 11.6, Intel UHD Graphics 617) created by chimerax-bug-report@…
[…]
3:06 PM Ticket #5460 (problem with displaying secondary structures) created by elzbieta.wator@…
[…] [[Image(...)]]
12:19 AM Ticket #5459 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) created by chimerax-bug-report@…
[…]

Oct 22, 2021:

6:02 PM Ticket #5458 (Unknown crash) created by chimerax-bug-report@…
[…]
4:09 PM Ticket #5453 (Problem saving blast table info in session) closed by pett
fixed: Fixed in the latest daily build.
3:58 PM Ticket #5446 (Modeller residue indices wrong) closed by pett
fixed: Okay, even *more* fixed now! :-)
3:42 PM Ticket #5441 (Crash with Qt 6.2 showing Shell tool) closed by Tom Goddard
fixed: Closing this ticket since the crash is now avoided. Will add the …
2:36 PM Ticket #5456 (Graphics driver crash, macOS 11.6, Intel Iris Plus Graphics 655) closed by Tom Goddard
nonchimerax: Apple graphics driver crash. Unfortunately Apple graphics drivers are …
2:17 PM Ticket #5455 (Difficulty panning/zooming) closed by Tom Goddard
duplicate: Follow up to #5454. Since the loss of multitouch trackpad events …
1:02 PM Ticket #5457 (Mac multitouch rotation does not work after Log undocked) created by goddard@…
[…]
11:03 AM Ticket #5446 (Modeller residue indices wrong) reopened by pett
For the UniProt sequence it remodels well past the point it should, …
10:23 AM Dev2021-10-14 edited by pett
(diff)
5:45 AM Ticket #5456 (Graphics driver crash, macOS 11.6, Intel Iris Plus Graphics 655) created by spencer.bliven@…
[…]
4:46 AM Ticket #5455 (Difficulty panning/zooming) created by ruggero.gabbrielli@…
[…]
4:42 AM Ticket #5454 (Difficulty panning/zooming) created by ruggero.gabbrielli@…
[…]
12:22 AM Ticket #5453 (Problem saving blast table info in session) created by nishaj@…
[…]

Oct 21, 2021:

7:06 PM 2021-10-21 edited by Tom Goddard
(diff)
6:42 PM Ticket #5451 (Crash in ctypes) closed by Tom Goddard
duplicate: Yep, looks like garbage collection crash. Still don't have any leads …
6:30 PM Ticket #5448 (Check if EMDB maps can be fetched by https instead of ftp) closed by Tom Goddard
fixed: Made EMDB fetch use Japan mirror if hostname ends in ".jp".
6:08 PM Ticket #5452 (Crash in garbage collection during new-object allocation) closed by pett
duplicate
6:00 PM Ticket #5452 (Crash in garbage collection during new-object allocation) created by chimerax-bug-report@…
[…]
5:57 PM Ticket #5445 (coordination number does not match sum of ligand denticity) closed by pett
not a bug: Hi Tony, Sorry to waste a bunch of your time, but this report was …
5:55 PM Ticket #5451 (Crash in ctypes) created by chimerax-bug-report@…
[…]
5:53 PM Ticket #5449 (Will NIH 3D pipeline script work with new EMDB metadata format?) closed by pett
not a bug
5:26 PM Ticket #5446 (Modeller residue indices wrong) closed by pett
fixed
5:05 PM Ticket #5447 (Crash after AlphaFold prediction finishes) closed by Tom Goddard
can't reproduce: Oh, I see. So they were rather indirectly AlphaFold related, just …
4:50 PM Ticket #5450 (crash taking sqrt()?!?) created by chimerax-bug-report@…
[…]
4:33 PM Ticket #5432 (Support chain merging in Structure.combine()) closed by pett
limitation: Upon further reflection, preservation of custom attributes depends …
4:12 PM Ticket #5449 (Will NIH 3D pipeline script work with new EMDB metadata format?) created by phil.cruz@…
Will the change to EMDB data model v3 effect how the NIH 3D ChimeraX …
3:25 PM Ticket #5443 (glGetFramebufferAttachmentParameteriv: invalid enumerant) closed by Tom Goddard
nonchimerax: ChimeraX runs on Windows 10. It is not supported on Windows 7. This …
2:18 PM NTTData edited by Elaine Meng
(diff)
2:10 PM NTTData edited by Elaine Meng
(diff)
1:45 PM NTTData edited by Elaine Meng
(diff)
1:39 PM Ticket #5448 (Check if EMDB maps can be fetched by https instead of ftp) created by philip.macmenamin@…
NIH 3D pipeline is fetching EMDB maps by ftp. That is frowned on in …
1:03 PM Ticket #5447 (Crash after AlphaFold prediction finishes) created by chimerax-bug-report@…
[…]
10:29 AM Ticket #5446 (Modeller residue indices wrong) created by Elaine Meng
[…] bloop.cxs
9:57 AM Ticket #5444 (Crash reading PDB file) closed by pett
can't reproduce
8:50 AM GrantAims2 edited by Elaine Meng
(diff)
7:28 AM Ticket #5445 (coordination number does not match sum of ligand denticity) created by chimerax-bug-report@…
[…]
4:03 AM Ticket #5444 (Crash reading PDB file) created by chimerax-bug-report@…
[…]
2:19 AM WikiStart edited by Tom Goddard
(diff)
2:16 AM GrantAims2 edited by Tom Goddard
(diff)
2:15 AM GrantAims2 edited by Tom Goddard
(diff)
2:14 AM GrantAims2 edited by Tom Goddard
(diff)
2:12 AM GrantAims2 edited by Tom Goddard
(diff)
2:05 AM GrantAims2 edited by Tom Goddard
(diff)
2:04 AM GrantAims2 edited by Tom Goddard
(diff)
2:04 AM GrantAims2 edited by Tom Goddard
(diff)
2:01 AM GrantAims2 edited by Tom Goddard
(diff)
1:46 AM GrantAims2 created by Tom Goddard
1:32 AM Grants edited by Tom Goddard
(diff)
1:28 AM Grants edited by Tom Goddard
(diff)
1:26 AM Grants created by Tom Goddard

Oct 20, 2021:

11:06 PM Ticket #5443 (glGetFramebufferAttachmentParameteriv: invalid enumerant) created by zengqh99@…
[…]
5:21 PM Ticket #5249 (RFE: model-restriction widget for clashes/contacts) closed by pett
fixed: Implemented an 'ignoreHiddenModels' option to the command, default …
5:16 PM Ticket #5442 (multiple columns of options) created by Elaine Meng
Currently a set options is constrained to be in a single column. …
12:56 PM Ticket #5433 (Bond connectivity changes don't update ribbon) closed by pett
fixed: Adding chain-forming bond now updates ribbons.
10:31 AM Ticket #5441 (Crash with Qt 6.2 showing Shell tool) created by goddard@…
[…]
10:21 AM Ticket #5436 (peptide ligand not labeled when only cartoon shown) closed by Tom Goddard
wontfix: Bad input data. The PDB should fix this entry so the 5 residues are …
9:37 AM Ticket #5440 (Unknown crash) closed by pett
can't reproduce
9:35 AM Ticket #5439 (Daily build download error) closed by pett
fixed: Hi Guillaume, Thanks for reporting this problem. We believe it is …
9:32 AM Ticket #5435 (Crash reading PDB file) closed by pett
can't reproduce: Possibly duplicate. Would need actual PDB file to debug.
9:08 AM Ticket #5440 (Unknown crash) created by chimerax-bug-report@…
[…]
12:19 AM Ticket #5439 (Daily build download error) created by guillaume.petit@…
[…]

Oct 19, 2021:

6:00 PM 2021-10-21 created by Tom Goddard
5:58 PM DeveloperMeetings edited by Tom Goddard
(diff)
5:51 PM Ticket #5438 (Build frequently breaks installing cxservices) created by Tom Goddard
In recent months my developer builds often break with some problem …
4:07 PM Ticket #5429 (QWindowsWindow::setGeometry: Unable to set geometry) closed by Tom Goddard
can't reproduce: The ChimeraX crash info is not very informative. It looks like it was …
3:30 PM Ticket #5437 (split into chains loses chain info) created by Elaine Meng
If I open a structure and show the sequence of a chain it includes the …
1:45 PM Ticket #5436 (peptide ligand not labeled when only cartoon shown) created by Elaine Meng
Although I can select cartoon on the main protein and label all its …
1:19 PM Ticket #5435 (Crash reading PDB file) created by chimerax-bug-report@…
[…]
11:18 AM Ticket #5431 (Crash showing Rapid access at startup) closed by pett
duplicate
8:54 AM Ticket #5434 (metadata interchange) created by Tristan Croll
[…]
7:37 AM Ticket #5433 (Bond connectivity changes don't update ribbon) created by Tristan Croll
[…]
7:32 AM Ticket #5432 (Support chain merging in Structure.combine()) created by Tristan Croll
[…] test_session.cxs
6:28 AM Ticket #5431 (Crash showing Rapid access at startup) created by chimerax-bug-report@…
[…]
6:10 AM Ticket #5430 (Crash saving session) created by kasperhb@…
[…]
4:40 AM Ticket #5429 (QWindowsWindow::setGeometry: Unable to set geometry) created by peng@…
[…]

Oct 18, 2021:

10:47 PM Ticket #5422 (Installation problems on Debian "Bullseye") closed by Greg Couch
limitation: Unfortunately, we have currently limited our Linux support to Ubuntu …
4:08 PM Ticket #5428 ('measure volume' doesn't return value) closed by Tom Goddard
fixed: Fixed. Made measure volume and measure area return total volume and …
1:31 PM Ticket #5428 ('measure volume' doesn't return value) created by pett
run(session, "measure volume #1") logs the volume, but doesn't return it.
11:54 AM Ticket #5427 (Read EMAN format: cannot load .dylibs/libhdf5.200.dylib) created by peter.kirchweger@…
[…]
11:50 AM Ticket #5425 (no 'contacts' in interfaces.cmd) closed by Tom Goddard
fixed: Fixed. Contacts command was renamed interfaces but programmer docs …
10:41 AM Ticket #5426 (Unknown crash) created by p.albanese@…
[…]
10:41 AM Ticket #5425 (no 'contacts' in interfaces.cmd) created by pett
WARNING: autodoc: failed to import function 'contacts' from module …
10:35 AM Ticket #5424 (Direct model panel editing) created by 2wswer@…
I would like to suggest/request that the "Models" panel should be able …
10:24 AM Ticket #5423 (Unknown crash) closed by pett
can't reproduce
10:21 AM Ticket #5421 (Close event on already closed window) closed by pett
can't reproduce
10:15 AM Ticket #5419 (Bug Reporter failure on Windows) closed by Tom Goddard
nonchimerax: This is a Windows system problem. Online info says "Error Code …
10:03 AM Ticket #5420 (restore session in older ChimeraX) closed by pett
fixed: Hi Ira, As you figured out yourself, ChimeraX 1.2.5 can't restore …
9:38 AM Ticket #5423 (Unknown crash) created by chimerax-bug-report@…
[…]
4:12 AM Ticket #5282 (Ramachandran plot clashes: wrapped C/C++ object of type QComboBox has ...) closed by Tristan Croll
can't reproduce: Thank you very much for sharing the model and structure factors. …
12:59 AM Ticket #5422 (Installation problems on Debian "Bullseye") created by kostrewa@…
[…]

Oct 17, 2021:

9:16 AM Ticket #5421 (Close event on already closed window) created by chimerax-bug-report@…
[…]

Oct 16, 2021:

10:44 AM Ticket #5420 (restore session in older ChimeraX) created by ira.lacdao@…
[…]

Oct 15, 2021:

11:34 PM Ticket #5419 (Bug Reporter failure on Windows) created by chimerax-bug-report@…
[…]
2:26 PM Ticket #5412 (AlphaFold unzipping of results: expected str, bytes or os.PathLike ...) closed by Tom Goddard
fixed: Fixed. In case user manages to start two results.zip downloads before …
9:38 AM Ticket #5418 (Crash "access violation", no traceback) closed by pett
can't reproduce: Though this crash is possibly while using the SEQCROW "Manage Models" …
1:53 AM Ticket #5349 (blast results load/align structure only aligns first model in NMR ensemble) closed by Zach Pearson
fixed: Should be fixed by …

Oct 14, 2021:

6:26 PM Ticket #5418 (Crash "access violation", no traceback) created by chimerax-bug-report@…
[…]
4:52 PM Ticket #5415 (Coulombic coloring fails on 7mjo, sqm on ligand) closed by pett
limitation
4:52 PM Ticket #5414 (Coulombic coloring fails on 7mjo, sqm cannot handle HIS+HIS) closed by pett
limitation
4:45 PM Ticket #5413 (Dual display crash) closed by Tom Goddard
nonchimerax: It appears ChimeraX crashed in the Qt window toolkit when an external …
4:40 PM Ticket #5402 (ctypes access violation) closed by pett
fixed
4:19 PM Dev2021-10-14 edited by Tom Goddard
(diff)
4:19 PM Dev2021-10-14 edited by Tom Goddard
(diff)
4:15 PM Ticket #5417 (Hide Windows installer signing password) created by Tom Goddard
Make Windows build redirect installer build to separate log so …
4:13 PM Ticket #5416 (Put checksums from download page on a separate page) created by Tom Goddard
Put link in Notes field of downloads table to checksums. Want to …
3:49 PM Ticket #5415 (Coulombic coloring fails on 7mjo, sqm on ligand) created by philip.macmenamin@…
[…]
3:42 PM Ticket #5414 (Coulombic coloring fails on 7mjo, sqm cannot handle HIS+HIS) created by philip.macmenamin@…
[…]
3:37 PM Ticket #5411 (Hung saving TIFF?) closed by Tom Goddard
can't reproduce: User typed ctrl-C to the shell (Linux) where ChimeraX started …
3:19 PM 2021-10-14 edited by Tom Goddard
(diff)
1:17 PM Ticket #5404 (Fix residue: Not enough connected atoms to form a dihedral) closed by Tristan Croll
fixed: I *think* everything in here has been taken care of by recent bug-fixes…
12:58 PM Ticket #5403 (debloat Blast input and output dialogs) closed by Zach Pearson
fixed: Great! Fixed in …
12:49 PM Ticket #5410 (Crash report: Permission denied) closed by pett
duplicate
12:48 PM Ticket #5409 (ChimeraX bug report submission) closed by pett
fixed
12:47 PM Ticket #5409 (ChimeraX bug report submission) reopened by pett
12:45 PM Ticket #5408 (Save settings: No such file or directory) closed by pett
duplicate
12:43 PM Ticket #5406 (color byattr: min() arg is an empty sequence) closed by pett
duplicate
12:14 PM 2021-10-14 edited by Tom Goddard
(diff)
12:00 PM 2021-10-14 edited by Tom Goddard
(diff)
11:56 AM 2021-10-14 edited by Tom Goddard
(diff)
11:53 AM 2021-10-14 edited by Tom Goddard
(diff)
11:53 AM Ticket #5413 (Dual display crash) created by hrishikesh.das@…
[…]
11:49 AM 2021-10-14 edited by Tom Goddard
(diff)
11:22 AM 2021-10-14 edited by Tom Goddard
(diff)
11:22 AM 2021-10-14 edited by Tom Goddard
(diff)
11:15 AM Ticket #5412 (AlphaFold unzipping of results: expected str, bytes or os.PathLike ...) created by chimerax-bug-report@…
[…]
9:33 AM Ticket #5409 (ChimeraX bug report submission) closed by Zach Pearson
not a bug: The AlphaFold bundle import was fixed in #5399 yesterday, so on …
7:18 AM Ticket #5411 (Hung saving TIFF?) created by chimerax-bug-report@…
[…]
7:02 AM Ticket #5410 (Crash report: Permission denied) created by chimerax-bug-report@…
[…]
5:56 AM Ticket #5409 (ChimeraX bug report submission) created by Tristan Croll
[…]

Oct 13, 2021:

7:54 PM Ticket #5408 (Save settings: No such file or directory) created by chimerax-bug-report@…
[…]
3:05 PM Ticket #5407 (Display HTML within table) created by Zach Pearson
Involves implementing a QStyledItemDelegate subclass.
2:18 PM Ticket #5398 (hide-dust shortcut: local variable 'maps' referenced before assignment) closed by Tom Goddard
duplicate: Fixed 4 months ago. #4829
2:16 PM Ticket #5406 (color byattr: min() arg is an empty sequence) created by chimerax-bug-report@…
[…]
2:02 PM Ticket #5405 (Problem coloring chains) created by hernando.sosa@…
[…]
1:45 PM Ticket #5404 (Fix residue: Not enough connected atoms to form a dihedral) created by chimerax-bug-report@…
[…]
1:05 PM Ticket #5403 (debloat Blast input and output dialogs) created by Elaine Meng
From: Eric Pettersen <pett@…> Subject: Widget spacing Date: …
12:31 PM Ticket #5402 (ctypes access violation) created by amith.rangarajan@…
[…]
11:30 AM Ticket #5401 (Blast Protein: Ligand Formulas (chemical formulas) hard to read) created by Elaine Meng
The Ligand Formulas (chemical formulas of ligand residues) are hard to …
11:28 AM Ticket #5394 (Blast Protein empty Ligand Symbols column) closed by Zach Pearson
fixed: I had the wrong graphql query, sorry! …
11:15 AM Ticket #5394 (Blast Protein empty Ligand Symbols column) reopened by Elaine Meng
10:22 AM Dev2021-10-14 edited by Zach Pearson
(diff)
9:22 AM Ticket #4963 (residue_graph: edges should be a n x 2 array of unsigned ints) closed by Tristan Croll
fixed: Really sorry for my ridiculously slow response to this - it's been a …
9:12 AM Ticket #5400 (ISOLDE simulation: No compatible CUDA device is available) closed by Tristan Croll
not a bug: Looks like your display driver version is too old. OpenMM uses CUDA …
9:10 AM Ticket #5399 (AlphaFold failure due to blast reorganization) closed by Zach Pearson
fixed: Fixed in …
8:53 AM Ticket #5397 (Crash in Qt on exit) closed by pett
duplicate
8:14 AM Ticket #4964 (residue_graph: edges should be a n x 2 array of unsigned ints) closed by Tristan Croll
fixed: Shouldn't hit this traceback anymore. ISOLDE still won't rebuild …
7:15 AM Ticket #5400 (ISOLDE simulation: No compatible CUDA device is available) created by shabir.najmudin@…
[…]
7:01 AM Ticket #5399 (AlphaFold failure due to blast reorganization) created by juliingaramo.98@…
[…]
6:28 AM Ticket #5398 (hide-dust shortcut: local variable 'maps' referenced before assignment) created by chimerax-bug-report@…
[…]
5:35 AM Ticket #4976 (Possibly fetching 'residues' of dead Structure) closed by Tristan Croll
fixed
5:25 AM Ticket #5026 ('SplitStereoCamera' object has no attribute 'field_width') closed by Tristan Croll
fixed: field width is now only used when the camera is orthographic.
5:22 AM Ticket #5037 (Update ISOLDE rotamers: wrapped C/C++ object of type QTableWidget has ...) closed by Tristan Croll
fixed
5:21 AM Ticket #5085 (ISOLDE: wrapped C/C++ object of type QTableWidget has been deleted) closed by Tristan Croll
fixed
5:21 AM Ticket #5140 (OpenMM: Error initializing CUDA: CUDA_ERROR_UNKNOWN) closed by Tristan Croll
can't reproduce: Actually, looking at where it crashed it's probably not a memory …
5:14 AM Ticket #5236 (Crash in OpenMM finding clashes) closed by Tristan Croll
can't reproduce: Not much to go on here, I'm afraid. Best advice is to update to …
5:11 AM Ticket #5272 (ISOLDE: All atoms for zone mask must be from a single model!) closed by Tristan Croll
fixed
4:02 AM Ticket #5277 (ISOLDE: various dead widgets being accessed) closed by Tristan Croll
duplicate: See my response to #5282 - for now, this can be avoided by not closing …
3:44 AM Ticket #5296 (PEE template incorrect) closed by Tristan Croll
fixed: Will close this as "fixed". The issue of possible out-of-date …
3:42 AM Ticket #5322 (OpenMMException: Error compiling program: nvrtc: error: invalid value ...) closed by Tristan Croll
duplicate: Sorry about the slow response. This problem is caused by the CUDA 11.0 …
2:13 AM Ticket #5397 (Crash in Qt on exit) created by chimerax-bug-report@…
[…]

Oct 12, 2021:

5:35 PM Ticket #5387 (After 'split': 'Sequence' object has no attribute 'structure') closed by pett
fixed: Fixed on both develop and release.
5:21 PM Ticket #5384 (volume style image: graphics out of memory) closed by Tom Goddard
nonchimerax: Improved the error reporting so the OpenGL "out of memory" message …
3:41 PM Ticket #5396 (Renew SSL certificate for vr.ucsf.edu before November 2021) created by Tom Goddard
-------- Forwarded Message -------- Subject: WARNING: Expiration …
2:56 PM Ticket #5390 (Graphics driver crash, macoOS 11.6, Intel Iris Plus Graphics 655) closed by Tom Goddard
nonchimerax: Apple graphics driver crash. Unfortunately Apple OpenGL graphics is …
2:16 PM 2021-10-14 created by Tom Goddard
2:15 PM Ticket #5395 (Create tutorial for putting model on web page) created by Tom Goddard
Maybe export as GLTF and figure out some javascript library that can …
2:09 PM DeveloperMeetings edited by Tom Goddard
(diff)
1:51 PM Ticket #5385 (Sequence Viewer scrollbar does not adjust for change in panel height) closed by pett
fixed: Fixed on develop and 1.3 branch
12:26 PM Ticket #5228 (Blastprotein: Visual fixes) closed by Zach Pearson
fixed: Looks like the last thing to do is the column widths. I spun that off …
12:24 PM Ticket #5394 (Blast Protein empty Ligand Symbols column) closed by Zach Pearson
fixed: Fixed in …
12:24 PM Ticket #5393 (blast command defaults to maxseqs 500, should be 100) closed by Zach Pearson
fixed: Fixed in …
12:06 PM Ticket #5394 (Blast Protein empty Ligand Symbols column) created by Elaine Meng
Seems like something went awry with parsing ligand symbols. E.g. open …
12:03 PM Ticket #5392 (Blast Protein won't start: No module named 'chimerax.blastprotein.tool') closed by Zach Pearson
fixed
11:42 AM Ticket #5393 (blast command defaults to maxseqs 500, should be 100) created by Elaine Meng
Tested in UCSF ChimeraX version: 1.3.dev202110120902 (2021-10-12) …
11:30 AM Ticket #5392 (Blast Protein won't start: No module named 'chimerax.blastprotein.tool') created by Elaine Meng
[…]
10:50 AM Ticket #5391 (Crash in Qt on exit) closed by pett
duplicate
10:06 AM Ticket #5388 (Crash setting style) closed by pett
can't reproduce
9:58 AM Ticket #5391 (Crash in Qt on exit) created by chimerax-bug-report@…
[…]
9:55 AM Ticket #5390 (Graphics driver crash, macoOS 11.6, Intel Iris Plus Graphics 655) created by tobias.starborg@…
[…]
8:38 AM Ticket #5381 (ISOLDE: wrapped C/C++ object of type QTableWidget has been deleted) closed by Tristan Croll
fixed: Forgot to clean up the last selected model's changes trigger on …
7:20 AM Ticket #5389 (Build warnings) created by Tristan Croll
[…]
4:37 AM Ticket #5388 (Crash setting style) created by chimerax-bug-report@…
[…]
Note: See TracTimeline for information about the timeline view.