Timeline



Jul 18, 2022:

5:55 PM Ticket #7297 (glClear: invalid framebuffer operation) closed by Tom Goddard
can't reproduce: OpenGL error drawing status line. Reporter says they are using …
5:20 PM Ticket #7298 ("help renumber" not working) created by Elaine Meng
[…]
4:06 PM ChangeLog edited by Tom Goddard
(diff)
4:05 PM ChangeLog edited by Tom Goddard
(diff)
3:46 PM ChangeLog edited by Elaine Meng
(diff)
3:38 PM Dev2022-7-18 edited by Tom Goddard
(diff)
3:00 PM Ticket #7297 (glClear: invalid framebuffer operation) created by chimerax-bug-report@…
[…]
1:34 PM Ticket #7294 (Pseudobond reader not bulletproof to loop pseudobonds) reopened by pett
1:33 PM Ticket #7294 (Pseudobond reader not bulletproof to loop pseudobonds) closed by pett
can't reproduce: I can't reproduce this just by trying to form a loop pseudobond. Nor …
12:22 PM Ticket #7293 (Graphics crash, macOS 12.3.1, Intel Iris Plus Graphics) closed by Tom Goddard
nonchimerax: Intel Mac graphics driver crash.
11:44 AM Ticket #7296 (Crash loading dylib) created by sijie.huang@…
[…]
11:14 AM Ticket #7295 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: 1.3
11:07 AM Ticket #7292 (No space left on device) closed by pett
nonchimerax
11:06 AM Ticket #7291 (No space left on device) closed by pett
nonchimerax
11:02 AM Ticket #7289 (Crash in event loop) closed by pett
can't reproduce
10:25 AM Ticket #7236 (AlphaFold RFE: don't minimize by default) closed by Tom Goddard
fixed: Done. I changed the AlphaFold prediction energy minimization option …
10:22 AM Ticket #7260 (Change AlphaFold prediction to use ColabFold for 5x faster runs) closed by Tom Goddard
fixed
8:26 AM Ticket #7295 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
8:23 AM Ticket #7294 (Pseudobond reader not bulletproof to loop pseudobonds) created by andrew.plested@…
[…]

Jul 17, 2022:

12:52 PM Ticket #7293 (Graphics crash, macOS 12.3.1, Intel Iris Plus Graphics) created by chimerax-bug-report@…
[…]

Jul 16, 2022:

12:42 PM Ticket #7292 (No space left on device) created by chimerax-bug-report@…
[…]
12:41 PM Ticket #7291 (No space left on device) created by chimerax-bug-report@…
[…]
10:35 AM Ticket #7290 (Crash loading dylib) created by gustwe@…
[…]
8:54 AM Ticket #7289 (Crash in event loop) created by chimerax-bug-report@…
[…]
5:27 AM Ticket #7288 (Bad sequence pointer) created by chimerax-bug-report@…
[…]

Jul 15, 2022:

9:33 PM DeveloperMeetings edited by Zach Pearson
(diff)
9:32 PM Dev2022-7-18 edited by Zach Pearson
(diff)
9:32 PM Dev2022-7-18 edited by Zach Pearson
(diff)
9:32 PM Dev2022-7-18 created by Zach Pearson
7:31 PM Ticket #7199 (Can't import libGLU.so.1) closed by Greg Couch
nonchimerax: Missing libGLU. Needs to be installed on the system. Presumably this …
11:40 AM Ticket #7287 (KeyError deleting 2D arrow) created by chimerax-bug-report@…
[…]
11:24 AM Ticket #7281 (ViewDockX saving session: 'QEventLoop' object has no attribute 'exec_') closed by Zach Pearson
fixed: [https://github.com/RBVI/ChimeraX/commit/446ac4d81258d1d5e651f40867d2b4
11:24 AM Ticket #7201 (ViewDockX saving session: 'QEventLoop' object has no attribute 'exec_') closed by Zach Pearson
fixed: [https://github.com/RBVI/ChimeraX/commit/446ac4d81258d1d5e651f40867d2b4
11:06 AM Ticket #7284 (Crash in event loop after volume command) closed by Tom Goddard
can't reproduce: Bug report has no clues about what caused this crash. Was in the Qt …
10:16 AM Ticket #7285 (Unknown crash) closed by pett
can't reproduce
10:06 AM Ticket #7283 (Disconnected ribbon) closed by pett
not a bug: Hi Qinglong, The 8OG residue seems to have a spurious OP3 atom that …
4:30 AM Ticket #7286 (Unknown crash) created by chimerax-bug-report@…
[…]
3:33 AM Ticket #7285 (Unknown crash) created by chimerax-bug-report@…
[…]
3:15 AM Ticket #7284 (Crash in event loop after volume command) created by p.shah.lab@…
[…]

Jul 14, 2022:

3:44 PM 2022-7-14 edited by Tom Goddard
(diff)
3:43 PM 2022-7-14 edited by Tom Goddard
(diff)
2:51 PM Ticket #7283 (Disconnected ribbon) created by Qinglong.You@…
[…] …
1:01 PM Ticket #7282 (Crash in event loop) created by richard_walsh@…
[…]
1:01 PM Ticket #7280 (Crash creating QWebEngineProfile at startup and/or running AlphaFold ...) closed by pett
can't reproduce
12:58 PM Ticket #7279 (Attempt to draw dead arrow) closed by pett
duplicate: Hi Abhilash, Thanks for reporting this problem. It was fixed about 4 …
12:42 PM Ticket #7281 (ViewDockX saving session: 'QEventLoop' object has no attribute 'exec_') created by thomas.knight.21@…
[…]
12:38 PM Ticket #7280 (Crash creating QWebEngineProfile at startup and/or running AlphaFold ...) created by chimerax-bug-report@…
[…]
11:12 AM Ticket #7279 (Attempt to draw dead arrow) created by apadavannil@…
[…]
10:21 AM Ticket #5088 (Github Actions: Ubuntu 20.04 build fails on first curl) closed by Zach Pearson
worksforme: Over the last few days I've tried many cloud builds, each one either …
9:48 AM Ticket #7278 (ImageJ hyperstack shape and axes do not match) closed by Tom Goddard
duplicate: Fixed about 6 months ago.
9:13 AM Ticket #7277 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: 1.3
9:08 AM Ticket #7275 (Crash in fork) closed by pett
limitation: Was using 8.7GB at the time and was forking off a local Modeller process.
7:35 AM Ticket #7278 (ImageJ hyperstack shape and axes do not match) created by chimerax-bug-report@…
[…]

Jul 13, 2022:

8:29 PM Ticket #7277 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
6:20 PM Ticket #7276 (MemoryError saving session) created by chimerax-bug-report@…
[…]
3:54 PM Ticket #7275 (Crash in fork) created by chimerax-bug-report@…
[…]
2:19 PM Ticket #7274 (Make Mac distribution dmg file smaller using LZMA compression) created by Tom Goddard
Zach observed that the Mac distribution dmg file (.dmg) can be made …
1:43 PM Ticket #7273 (Crash in fork) closed by pett
limitation: Was using 8.7GB at the time. No crash log or Python traceback.
12:27 PM Ticket #7273 (Crash in fork) created by chimerax-bug-report@…
[…]
10:35 AM Ticket #7271 (Opening new session in old ChimeraX) closed by pett
not a bug: Current code throws RestoreError instead of TypeError
7:45 AM Ticket #7272 (Shader does not have uniform variable "num_clip_planes") created by tmalla@…
[…]
4:59 AM Ticket #7271 (Opening new session in old ChimeraX) created by chimerax-bug-report@…
[…]

Jul 12, 2022:

9:22 PM Ticket #7270 (ISOLDE: sim_manager is None) created by isaphan@…
[…]
5:43 PM Ticket #7256 (Crash in swapaa) closed by pett
fixed: Hi Amanda, I have committed a fix for this and the fix will be in the …
1:30 PM Ticket #7269 (downloading and saving maps from EMDB) closed by pett
not a bug: Redirected to chimerax-users list, since it is really a usage question.
1:24 PM Ticket #7267 (Crash showing Rapid Access at startup) closed by pett
can't reproduce
1:17 PM Ticket #7263 (Long atom spec crashes ChimeraX) closed by pett
duplicate: Hi Kavita, I think the rule of thumb to try to sidestep this …
11:06 AM Ticket #7265 (QMainWindowLayout::tabPosition called with out-of-bounds value '0') closed by pett
can't reproduce
11:05 AM Ticket #7264 (Crash showing Rapid Access at startup) closed by pett
can't reproduce
10:48 AM Ticket #7007 (Long atom spec crashes ChimeraX) closed by pett
duplicate: Adding reporter to cc list for main version of this ticket
10:43 AM Ticket #7262 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: 1.3
10:40 AM Ticket #7261 (Crash in fork) closed by pett
can't reproduce: Was using 9.2GB at the time somehow -- after opening just one …
10:28 AM Ticket #7257 (Callback to dead color button) closed by pett
fixed
10:03 AM Ticket #7269 (downloading and saving maps from EMDB) created by nxb318@…
[…]
10:02 AM Ticket #7268 (Problem with session file) created by ral357@…
[…] Capsid.cxs
9:50 AM Ticket #7267 (Crash showing Rapid Access at startup) created by chimerax-bug-report@…
[…]
9:35 AM 2022-7-14 created by Tom Goddard
9:33 AM DeveloperMeetings edited by Tom Goddard
(diff)
9:31 AM Ticket #7266 (Renew Windows code signing certificate, expires July 29, 2022) created by Tom Goddard
The daily build email says the Windows code signing certificate …
8:08 AM Ticket #7265 (QMainWindowLayout::tabPosition called with out-of-bounds value '0') created by chimerax-bug-report@…
[…]
8:00 AM Ticket #7264 (Crash showing Rapid Access at startup) created by chimerax-bug-report@…
[…]
7:56 AM Ticket #7263 (Long atom spec crashes ChimeraX) created by kavita.iyer@…
[…]

Jul 11, 2022:

9:20 PM Ticket #7262 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
6:45 PM Dev2022-7-11 edited by Tom Goddard
(diff)
6:37 PM Ticket #7261 (Crash in fork) created by chimerax-bug-report@…
[…]
5:55 PM Ticket #7260 (Change AlphaFold prediction to use ColabFold for 5x faster runs) created by Tom Goddard
The ColabFold google colab page for running AlphaFold jobs uses a …
5:44 PM Ticket #7259 (Opening PDB mmcif as coordset gives disconnected residues) closed by Tom Goddard
duplicate
5:34 PM Ticket #7258 (Make AlphaFold prediction handle energy minimization failure) closed by Tom Goddard
fixed: Done. Return unrelaxed structure prediction and warn when …
5:14 PM Ticket #7259 (Opening PDB mmcif as coordset gives disconnected residues) created by goddard@…
[…]
4:52 PM Ticket #7258 (Make AlphaFold prediction handle energy minimization failure) created by Tom Goddard
AlphaFold prediction fails about 5% of the time with an OpenMM energy …
4:30 PM Ticket #7257 (Callback to dead color button) created by chimerax-bug-report@…
[…]
1:24 PM Ticket #7256 (Crash in swapaa) created by afrance2@…
[…]
1:16 PM ChangeLog edited by Elaine Meng
(diff)
1:11 PM Dev2022-7-11 edited by Zach Pearson
(diff)
1:11 PM DeveloperMeetings edited by Zach Pearson
(diff)
1:10 PM Dev2022-7-11 edited by Zach Pearson
(diff)
1:09 PM Dev2022-7-11 created by Zach Pearson
11:17 AM Ticket #7255 (Crash in event loop) closed by pett
can't reproduce
11:05 AM Ticket #7251 (Windows fatal exception in mouse_pause_tracking) closed by Tom Goddard
can't reproduce: It appears ChimeraX crashed while it was trying to figure out what …
10:39 AM Ticket #7253 (Crash using File→Open on Windows) closed by pett
can't reproduce: 1.4, pre-3.9.11
10:37 AM Ticket #7252 (Crash creating QWebEngineProfile at startup) closed by pett
duplicate
10:11 AM Ticket #7255 (Crash in event loop) created by chimerax-bug-report@…
[…]

Jul 10, 2022:

1:34 PM Ticket #7254 (Use arbitrary folder with cxcmd link) created by Tristan Croll
[…]
9:53 AM Ticket #7253 (Crash using File→Open on Windows) created by chimerax-bug-report@…
[…]
6:36 AM Ticket #7252 (Crash creating QWebEngineProfile at startup) created by chimerax-bug-report@…
[…]
2:33 AM Ticket #7251 (Windows fatal exception in mouse_pause_tracking) created by scsu15@…
[…]

Jul 9, 2022:

10:51 AM Ticket #7250 (Cloud builds) created by Zach Pearson
We want the ability to build ChimeraX in the cloud, download the …
7:32 AM Ticket #7249 (Unable to restore "SchemesManager" object) created by matthew.kraushar@…
[…]

Jul 8, 2022:

7:26 PM Ticket #6619 (In AlphaFold PAE plot show multimer chain boundaries) closed by Tom Goddard
fixed: This was added a few months ago.
6:15 PM Ticket #7211 (Bad curly-brackets label fouls up subsequent label attempts) closed by pett
fixed: The badly labeled residues will continue to show no labels and throw …
6:00 PM ChangeLog edited by pett
(diff)
2:48 PM Ticket #7248 (Crash saving atomic session state) closed by pett
duplicate: Basically the same as #7247, though this time using 26.4 GB.
2:44 PM Ticket #7247 (Crash saving atomic session state) closed by pett
can't reproduce: Seems to somehow be a lack of memory issue. Was using 13.6 GB at the …
12:27 PM Ticket #7248 (Crash saving atomic session state) created by chimerax-bug-report@…
[…]
12:10 PM Ticket #7247 (Crash saving atomic session state) created by chimerax-bug-report@…
[…]
11:36 AM Ticket #7246 (Make PAE plots work on trimmed AlphaFold structures) closed by Tom Goddard
fixed: Done. If the AlphaFold model has multiple chains and whole chains are …
11:31 AM Ticket #7246 (Make PAE plots work on trimmed AlphaFold structures) created by phil.cruz@…
Currently predicted aligned error plots can only be shown with the …
10:08 AM Ticket #7245 ("spacings" is empty) created by jrubenstein@…
[…]
9:13 AM Ticket #7244 (Crash in event loop) closed by pett
can't reproduce
9:10 AM Ticket #7243 (MD Viewer: Values array length does not match objects array length) closed by pett
duplicate
9:08 AM Ticket #7242 (MD Viewer: Values array length does not match objects array length) closed by pett
duplicate
9:04 AM Ticket #7241 (open/save commands not logged) closed by pett
fixed: Hi Utz, No, that is a bug. The open/save commands use a more …
8:37 AM Ticket #7211 (Bad curly-brackets label fouls up subsequent label attempts) reopened by pett
Upon further reflection, it would be better to treat objects lacking …
6:05 AM Ticket #7244 (Crash in event loop) created by chimerax-bug-report@…
[…]
2:50 AM Ticket #7243 (MD Viewer: Values array length does not match objects array length) created by chimerax-bug-report@…
[…]
2:50 AM Ticket #7242 (MD Viewer: Values array length does not match objects array length) created by chimerax-bug-report@…
[…]
2:08 AM Ticket #7241 (open/save commands not logged) created by ermel@…
[…]

Jul 7, 2022:

5:32 PM Ticket #7238 (Added trim option to AlphaFold panel) closed by Tom Goddard
fixed: Done. I added an option to the AlphaFold user interface "Trim fetched …
5:31 PM Ticket #7240 (Allow BLAST to use a trim option when opening AlphaFold results) created by Tom Goddard
I'd like to be able to pass the BLAST tool a database-specific option …
3:56 PM Ticket #7237 (colormapOnGpu shader error) closed by Tom Goddard
fixed: Fixed in tonight's daily builds (dated July 8). The error was from …
3:05 PM Ticket #7239 (Log link to associated EMDB entry when PDB model opened) created by Tom Goddard
Would be useful when opening a PDB model that was solved from a map in …
2:55 PM Ticket #7238 (Added trim option to AlphaFold panel) created by phil.cruz@…
Phil would like to be able to turn off trimming when fetching …
2:51 PM 2022-7-7 edited by Tom Goddard
(diff)
2:26 PM Ticket #7233 (Segger infinite loop making surfaces) closed by Tom Goddard
duplicate: This was fixed 4 months ago and the fix is in ChimeraX 1.4. You are …
2:08 PM NIAID2022 edited by Elaine Meng
(diff)
2:03 PM NIAID2022 edited by Elaine Meng
(diff)
2:01 PM NIAID2022 edited by Elaine Meng
(diff)
1:46 PM NIAID2022 edited by Elaine Meng
(diff)
1:23 PM NIAID2022 edited by Elaine Meng
(diff)
11:00 AM ChangeLog edited by Elaine Meng
(diff)
10:56 AM ChangeLog edited by Elaine Meng
(diff)
6:17 AM Ticket #7237 (colormapOnGpu shader error) created by ermel@…
[…]
3:17 AM Ticket #7236 (AlphaFold RFE: don't minimize by default) created by Tristan Croll
[…]

Jul 6, 2022:

10:18 PM Ticket #7235 (Crash using color panel) created by ichcharisma@…
[…]
6:45 PM FAI edited by Tom Goddard
(diff)
6:43 PM Ticket #7234 (Apple notarization altool command will be discontinued Fall 2023) created by Tom Goddard
A command that the ChimeraX Mac notarization script uses to notarize …
2:24 PM Ticket #7233 (Segger infinite loop making surfaces) created by goran.bajic@…
[…]
12:18 PM Ticket #7232 (RFE: CASTp pocket browser) created by Elaine Meng
The Chimera GUI that lists the pockets and can be sorted by volume, …
12:00 PM Ticket #7231 (update MUSCLE seq align webservice from version 3 to 5) created by Elaine Meng
According to the MUSCLE website <https://drive5.com/muscle/>, version …
11:52 AM Ticket #7229 (Crash in Qt on exit) closed by pett
duplicate
11:46 AM Ticket #7230 ("toolshed reload" screws up commands) created by pett
[…]
11:37 AM Ticket #7229 (Crash in Qt on exit) created by chimerax-bug-report@…
[…]
9:32 AM Ticket #7228 (Graphics crash, macOS 10.15.7, Intel Iris Plus Graphics) closed by Tom Goddard
nonchimerax: Apple graphics driver crash.
8:47 AM Ticket #7227 (Crash in Qt handling mouse event) closed by pett
can't reproduce: No Python stack trace.
8:44 AM Ticket #7226 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: Hi Francesco, Thanks for reporting this problem. We believe it is …
8:41 AM Ticket #7225 (Crash creating QWebEngineProfile at startup) closed by pett
duplicate
8:40 AM Ticket #7223 (Crash in fork) closed by pett
can't reproduce: Was using 10.3GB. Last command was "movie encode", so was probably …
8:32 AM Ticket #7228 (Graphics crash, macOS 10.15.7, Intel Iris Plus Graphics) created by chimerax-bug-report@…
[…]
7:55 AM Ticket #7227 (Crash in Qt handling mouse event) created by chimerax-bug-report@…
[…]
5:42 AM Ticket #7226 (Crash using File→Open on Windows and/or in return statement) created by francesco.musiani@…
[…]
2:21 AM Ticket #7225 (Crash creating QWebEngineProfile at startup) created by chimerax-bug-report@…
[…]
12:01 AM Ticket #7224 (REST server key file contains private key on Mac ARM64) created by Tom Goddard
The rest_server bundles generates a server.pem self-signed certificate …

Jul 5, 2022:

11:04 PM Ticket #7223 (Crash in fork) created by chimerax-bug-report@…
[…]
10:42 PM Ticket #7222 (Make universal Intel/ARM Mac distribution) created by Tom Goddard
We'd like to distribute Mac ChimeraX as a single Intel / ARM64 …
6:25 PM Ticket #7221 (Build from scratch fails due to older core wheels) closed by Zach Pearson
fixed: [https://github.com/RBVI/ChimeraX/commit/96125f931888d06840429e4ee8907c
5:49 PM Ticket #7218 (PickedModel has no drawing() method) closed by pett
fixed: Okay, made the three changes that were being discussed.
5:30 PM Ticket #7211 (Bad curly-brackets label fouls up subsequent label attempts) closed by pett
not a bug: Well, this is just kind of how things work. You are allowed to …
5:25 PM Ticket #7221 (Build from scratch fails due to older core wheels) created by Tom Goddard
"make build-from-scratch" fails perhaps because core has multiple …
4:00 PM 2022-6-30 edited by Zach Pearson
(diff)
1:55 PM Ticket #7215 (Graphics crash, macOS 10.15.4, Intel Iris Plus Graphics 645) closed by Tom Goddard
nonchimerax: Apple graphics driver crash.
1:12 PM Ticket #7220 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: 1.3
1:11 PM Ticket #7219 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
1:01 PM Ticket #7217 (Crash in Qt cleanup during garbage collection) closed by pett
can't reproduce
12:59 PM Ticket #7216 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: 1.3
12:58 PM 2022-6-30 edited by Tom Goddard
(diff)
12:43 PM 2022-7-7 created by Tom Goddard
12:43 PM DeveloperMeetings edited by Tom Goddard
(diff)
12:32 PM Ticket #7220 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
11:59 AM Ticket #7214 (crosslinks histogram: AttributeError: 'QMouseEvent' object has no ...) closed by pett
duplicate
11:58 AM Ticket #7213 (crosslinks histogtam: AttributeError: 'QMouseEvent' object has no ...) closed by pett
duplicate: Duplicate of #6891
11:55 AM Ticket #7212 ('DefaultApi' object has no attribute 'newer_versions') closed by pett
duplicate
11:48 AM Ticket #7210 (Crash in fork) closed by pett
limitation: Was using 8.9GB at the time
11:46 AM Ticket #7208 (Crash in fork) closed by pett
limitation: Was using 8.6GB at the time
11:44 AM Ticket #7207 (Crash in event loop) closed by pett
can't reproduce
11:42 AM Ticket #7206 (Volume not in Surface Color volume menu) closed by pett
can't reproduce
11:17 AM Ticket #7204 (Web service access denial) closed by pett
nonchimerax: Hi David, It looks like your site uses Blue Coat Web Filter to proxy …
11:08 AM Ticket #7203 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: 1.3
11:02 AM Ticket #7202 (ViewDockX saving session: 'QEventLoop' object has no attribute 'exec_') closed by pett
duplicate
10:48 AM Ticket #7200 (QMainWindowLayout::tabPosition called with out-of-bounds value '0') closed by pett
can't reproduce: '0' means NoDockWidgetArea, which makes no sense to use with …
10:29 AM Ticket #7198 (Crash in fork) closed by pett
limitation: Was using 8.2GB at the time
10:26 AM Ticket #7197 (Crash creating QWebEngineProfile at startup) closed by pett
duplicate

Jul 4, 2022:

7:46 PM Ticket #7219 (Crash using File→Open on Windows and/or in return statement) created by solli@…
[…]
2:19 PM Ticket #7218 (PickedModel has no drawing() method) created by chimerax-bug-report@…
[…]
10:12 AM Ticket #7217 (Crash in Qt cleanup during garbage collection) created by chimerax-bug-report@…
[…]
7:20 AM Ticket #7216 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]

Jul 3, 2022:

5:05 PM Ticket #7215 (Graphics crash, macOS 10.15.4, Intel Iris Plus Graphics 645) created by chimerax-bug-report@…
[…]

Jul 2, 2022:

7:42 PM Ticket #7214 (crosslinks histogram: AttributeError: 'QMouseEvent' object has no ...) created by chimerax-bug-report@…
[…]
7:13 PM Ticket #7213 (crosslinks histogtam: AttributeError: 'QMouseEvent' object has no ...) created by chimerax-bug-report@…
[…]
4:46 PM Ticket #7212 ('DefaultApi' object has no attribute 'newer_versions') created by chimerax-bug-report@…
[…]
4:31 AM Ticket #7211 (Bad curly-brackets label fouls up subsequent label attempts) created by Tristan Croll
[…]

Jul 1, 2022:

3:49 PM Ticket #7210 (Crash in fork) created by chimerax-bug-report@…
[…]
3:42 PM Ticket #7209 (Mac notarization fails about 1/4 of the time: "A timestamp was ...) created by Tom Goddard
Our nightly builds on the Mac often fail because of a notarization …
8:37 AM Ticket #7208 (Crash in fork) created by chimerax-bug-report@…
[…]
1:48 AM Ticket #7207 (Crash in event loop) created by chimerax-bug-report@…
[…]

Jun 30, 2022:

5:08 PM Ticket #7206 (Volume not in Surface Color volume menu) created by chimerax-bug-report@…
[…]
1:49 PM Ticket #7205 (Morph: index out of bounds) created by nxb318@…
[…]
12:47 PM Ticket #7204 (Web service access denial) created by seoh@…
[…]
12:45 PM Ticket #7203 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
10:56 AM Ticket #7195 (Crash creating QWebEngineProfile at startup) closed by pett
can't reproduce: Again, some commands in log despite this being a startup crash.
9:36 AM Ticket #7202 (ViewDockX saving session: 'QEventLoop' object has no attribute 'exec_') created by wkweigel@…
[…]
9:35 AM Ticket #7201 (ViewDockX saving session: 'QEventLoop' object has no attribute 'exec_') created by wweigel@…
[…]
8:50 AM Ticket #7200 (QMainWindowLayout::tabPosition called with out-of-bounds value '0') created by chimerax-bug-report@…
[…]
2:54 AM Ticket #7199 (Can't import libGLU.so.1) created by chimerax-bug-report@…
[…]
2:22 AM Ticket #7198 (Crash in fork) created by chimerax-bug-report@…
[…]

Jun 29, 2022:

9:19 PM Ticket #7197 (Crash creating QWebEngineProfile at startup) created by chimerax-bug-report@…
[…]
8:43 PM Ticket #7196 (Crash during drag/drop) created by ichcharisma@…
[…]
6:33 PM Ticket #7195 (Crash creating QWebEngineProfile at startup) created by chimerax-bug-report@…
[…]
10:53 AM Ticket #7194 (Crash using File→Open on Windows) closed by pett
can't reproduce: 1.3
10:25 AM Ticket #7194 (Crash using File→Open on Windows) created by chimerax-bug-report@…
[…]
10:04 AM Ticket #7193 (Install cruft) created by Tristan Croll
[…]
9:24 AM Ticket #7192 (Crash creating QWebEngineProfile at startup) closed by pett
can't reproduce: Don't know how there could be "volume" commands in the log since it …
9:22 AM Ticket #7191 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: 1.3
5:35 AM Ticket #7192 (Crash creating QWebEngineProfile at startup) created by chimerax-bug-report@…
[…]
2:16 AM Ticket #7191 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]

Jun 28, 2022:

10:59 PM Ticket #7159 (Bump setuptools) closed by Zach Pearson
fixed: Tested on Linux and Windows. Using the new pip bundle, I was able to …
10:47 AM Ticket #7190 (Various Windows 11 problems) closed by Tom Goddard
nonchimerax: The most likely cause of the blank graphics in ChimeraX is that your …
10:38 AM Ticket #7188 (WSL2: Attempt to retrieve context when no valid context) closed by Tom Goddard
limitation: WSL2 not supported.
10:36 AM Ticket #7187 (Crosslink histogram: 'QMouseEvent' object has no attribute 'x') closed by Tom Goddard
duplicate: This was fixed months ago and the fix is in ChimeraX 1.4.
10:33 AM Ticket #7186 (WSL2: Attempt to retrieve context when no valid context) closed by Tom Goddard
limitation: ChimeraX does not work in Windows System for Linux 2 using Wayland, …
10:32 AM Ticket #7184 (Crash in Qt event loop running AlphaFold prediction) closed by Tom Goddard
can't reproduce: Probable crash related to Qt html widget used by AlphaFold. There are …
10:15 AM 2022-6-30 created by Tom Goddard
10:14 AM DeveloperMeetings edited by Tom Goddard
(diff)
9:09 AM Ticket #7189 (Coulombic: No module named 'chimerax.atom_search_lib') closed by pett
fixed: Fixed a week after this build.
9:00 AM Ticket #7185 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: 1.3
8:32 AM Ticket #7190 (Various Windows 11 problems) created by jxwang@…
[…] Screenshot.png
8:13 AM Ticket #7189 (Coulombic: No module named 'chimerax.atom_search_lib') created by chimerax-bug-report@…
[…]
7:06 AM Ticket #7188 (WSL2: Attempt to retrieve context when no valid context) created by chimerax-bug-report@…
[…]
5:18 AM Ticket #7187 (Crosslink histogram: 'QMouseEvent' object has no attribute 'x') created by andrea.graziadei@…
[…]
4:45 AM Ticket #7186 (WSL2: Attempt to retrieve context when no valid context) created by chimerax-bug-report@…
[…]
1:15 AM Ticket #7180 (ISOLDE restrain distances: ffi_prep_cif_var failed) closed by Tristan Croll
fixed: Great! While I'm still (a) really surprised that ctypes didn't throw …

Jun 27, 2022:

10:14 PM Ticket #4762 (Install PyPi packages with a ChimeraX command) closed by Zach Pearson
fixed: Added a 'devel pip' alias
6:12 PM Ticket #7185 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
5:07 PM Ticket #7184 (Crash in Qt event loop running AlphaFold prediction) created by chimerax-bug-report@…
[…]
3:36 PM Ticket #1745 (Error opening DICOM with lossless JPEG image encoding) closed by Zach Pearson
wontfix: After the developers meeting, the agreed upon resolution was not to …
3:34 PM Dev2022-6-27 edited by Tom Goddard
(diff)
11:34 AM Ticket #7183 (Restore session: _pickle.UnpicklingError: invalid load key) closed by pett
duplicate
10:57 AM Ticket #7179 (Crash making OpenGL context current during window resize) closed by Tom Goddard
can't reproduce: Access violation. Seems like a Qt bug.
10:39 AM Ticket #7183 (Restore session: _pickle.UnpicklingError: invalid load key) created by chimerax-bug-report@…
[…]
9:28 AM Ticket #7182 (Out of disk space writing command history) closed by pett
nonchimerax: Hi Edoardo, The issue is that one of your disks is out of space, and …
9:13 AM Ticket #7181 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: 1.3
9:09 AM Ticket #7178 (Cannot restore session: invalid load key, '\x04') closed by pett
duplicate: Hi Lu, You can't restore sessions saved by newer versions of ChimeraX …
9:07 AM Ticket #7177 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: 1.3
9:05 AM Ticket #7176 (Unknown crash) closed by pett
can't reproduce
9:04 AM Ticket #7175 (Crash running garbage collection after closing tool) closed by pett
can't reproduce: Possibly the XMAS tool
9:01 AM Ticket #7174 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: 1.3
8:59 AM Ticket #7171 (Tristan cannot log into Trac) closed by pett
fixed
6:59 AM Ticket #7182 (Out of disk space writing command history) created by edoardo.dimprima@…
[…]
3:40 AM Ticket #7181 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
2:42 AM Ticket #7180 (ISOLDE restrain distances: ffi_prep_cif_var failed) created by sean.connell@…
[…]

Jun 26, 2022:

3:19 PM Ticket #7179 (Crash making OpenGL context current during window resize) created by chimerax-bug-report@…
[…]
9:56 AM Ticket #7178 (Cannot restore session: invalid load key, '\x04') created by lu.yang@…
[…]
8:40 AM Ticket #7177 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]

Jun 25, 2022:

10:30 PM Ticket #7176 (Unknown crash) created by chimerax-bug-report@…
[…]
5:14 PM Ticket #7169 (ISOLDE installed into incompatible ChimeraX) closed by Greg Couch
fixed: I've patched this by hand by changing the dependency shown by the …
9:53 AM Ticket #7175 (Crash running garbage collection after closing tool) created by chimerax-bug-report@…
[…]
1:39 AM Ticket #7174 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]

Jun 24, 2022:

5:52 PM Ticket #6700 (Crash using File→Open on Windows and/or in return statement if folder ...) closed by pett
can't reproduce: The "stack overflow" could be an artifact of problems with the Windows …
4:40 PM Ticket #7172 (Allow substituting arguments in a .cxc file command script) closed by Tom Goddard
fixed: I made the runscript command accept .cxc files (or .py as before). …
2:54 PM Dev2022-6-27 edited by Tom Goddard
(diff)
2:46 PM Ticket #1745 (Error opening DICOM with lossless JPEG image encoding) reopened by Zach Pearson
2:08 PM Ticket #7173 (RFE: Get optional dependencies from the Toolshed and/or pip) created by Zach Pearson
Tom notes that the ChimeraX distribution is growing large. I don't …
12:39 PM Ticket #7172 (Allow substituting arguments in a .cxc file command script) created by p.shah.lab@…
Pranav Shah asked how to use two filename arguments to a *.cxc command …
11:51 AM Ticket #7164 (RFE: "pae" arguent to "alphafold match") closed by Tom Goddard
fixed: Done. I added a "pae" option (default false) to the alphafold match …
11:27 AM Ticket #7171 (Tristan cannot log into Trac) created by Tristan Croll
Hi all, Trac seems to have stopped accepting my login credentials. …
11:03 AM Ticket #6921 (RFE: Flatten the namespace package in the source code, somehow) closed by Zach Pearson
fixed: Moved core down to bundles.
10:52 AM Ticket #7163 (RFE: AlphaFoldPAE public matrix attribute) closed by Tom Goddard
fixed: Done. Added pae_matrix property to AlphaFoldPAE.
10:45 AM Ticket #7170 (Session restore: decompression failure) created by ykulathu@…
[…]
10:26 AM Ticket #7156 (AlphaFold Error Plot: local variable 'path' referenced before assignment) closed by Tom Goddard
fixed: Fixed in tomorrow's daily build. This error using the Browse button …
9:40 AM Ticket #7169 (ISOLDE installed into incompatible ChimeraX) created by chimerax-bug-report@…
[…]
9:31 AM Ticket #7167 (Crash using File→Open on Windows and/or in return statement) closed by pett
duplicate
9:18 AM Ticket #7162 (Crash using File→Open on Windows) closed by pett
can't reproduce: 1.4, but before the Python upgrade
9:14 AM Ticket #7161 (Restore new session in old version) closed by pett
not a bug: Not sure how the message could be clearer than "update your version of …
9:09 AM Ticket #7160 (QObject::~QObject: Timers cannot be stopped from another thread) closed by pett
can't reproduce
9:03 AM Ticket #7157 (AlphaFold Error Plot: local variable 'path' referenced before assignment) closed by pett
duplicate
9:00 AM Ticket #7155 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: 1.3
8:29 AM Ticket #7168 (ISOLDE/OpenMM: fitting Ramachandran outliers: Particle coordinate is nan) created by dkuntz@…
[…]
5:01 AM Ticket #7167 (Crash using File→Open on Windows and/or in return statement) created by xiyong.song@…
[…]
5:00 AM Ticket #7166 (Crash using File→Open on Windows and/or in return statement) created by xiyong.song@…
[…]
2:41 AM Ticket #7165 (Crash using File→Open on Windows) created by lucas.tafurpetrozzi@…
[…]
1:46 AM Ticket #7164 (RFE: "pae" arguent to "alphafold match") created by Tristan Croll
[…]
1:45 AM Ticket #7163 (RFE: AlphaFoldPAE public matrix attribute) created by Tristan Croll
[…]

Jun 23, 2022:

10:52 PM Ticket #7162 (Crash using File→Open on Windows) created by chimerax-bug-report@…
[…]
7:13 PM Ticket #7161 (Restore new session in old version) created by chimerax-bug-report@…
[…]
6:49 PM Ticket #7160 (QObject::~QObject: Timers cannot be stopped from another thread) created by chimerax-bug-report@…
[…]
5:36 PM Ticket #7159 (Bump setuptools) created by Zach Pearson
Now that we no longer depend on suds, we're in a position where we can …
4:26 PM Ticket #7067 (Save dialog enhancement) closed by pett
limitation: Glad that works for you! --Eric
3:33 PM Dev2022-6-23 edited by Tom Goddard
(diff)
2:09 PM Dev2022-6-23 edited by Zach Pearson
(diff)
1:52 PM Dev2022-6-23 edited by Tom Goddard
(diff)
1:43 PM phenix-5-4-22 edited by pett
(diff)
1:41 PM 2022-6-23 edited by pett
(diff)
1:12 PM Ticket #7158 (Make a GUI panel for volume surface and mesh options) created by wangc@…
Begin forwarded message: From: 王超 via ChimeraX-users …
12:18 PM 2022-6-23 edited by Tom Goddard
(diff)
12:03 PM DeveloperMeetings edited by Zach Pearson
(diff)
12:03 PM Dev2022-6-23 created by Zach Pearson
11:48 AM phenix-6-23-22 edited by pett
(diff)
4:52 AM Ticket #7157 (AlphaFold Error Plot: local variable 'path' referenced before assignment) created by hzauzsmj@…
[…]
4:39 AM Ticket #7156 (AlphaFold Error Plot: local variable 'path' referenced before assignment) created by hzauzsmj@…
[…]

Jun 22, 2022:

11:59 PM Ticket #4754 (bz2 missing) closed by Greg Couch
fixed: This was fixed on 12 January 2022. So it is in the 1.4 release.
11:55 PM Ticket #4847 (Windows 10 VM) closed by Greg Couch
limitation: Just to follow up on this ticket. This has been discussed in the …
11:43 PM Ticket #2750 (Certificate error fetching EDS map on some platforms) closed by Greg Couch
fixed: Linux works.
11:40 PM Ticket #3355 (Open ticket with UCSF IT to open up pre-release toolshed to outside ...) closed by Greg Couch
limitation: This has not proved to be an issue in practice. The toolshed preview …
11:37 PM Ticket #5003 (Unable to open ChimeraX) closed by Greg Couch
fixed: Glad to hear that you got ChimeraX working. One last thought. Maybe …
11:25 PM Ticket #7096 (ChimeraX 1.4 update panel link gets generic Linux version instead of ...) closed by Greg Couch
fixed
11:20 PM Ticket #7155 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
6:43 PM Ticket #7154 (Crash during fork) created by yue.wang@…
[…]
6:14 PM Dev2022-6-27 edited by Zach Pearson
(diff)
5:58 PM Ticket #3758 (Update gdcm dicom library for Python 3.8) closed by Zach Pearson
fixed
5:58 PM Ticket #1745 (Error opening DICOM with lossless JPEG image encoding) closed by Zach Pearson
fixed: (Same resolution as #3758) Added python-gdcm==3.0.12 to …
5:58 PM phenix-6-23-22 edited by pett
(diff)
5:27 PM Ticket #7149 (Status bar: Attempt to retrieve context when no valid context) closed by Greg Couch
duplicate: Fixed in in daily build.
5:26 PM Ticket #7150 (Remove Ubuntu 16 and 18 daily builds from web page) closed by Greg Couch
fixed: Done.
4:59 PM Ticket #7153 (Crash in event loop) created by cco121@…
[…]
4:31 PM Ticket #7105 (Menus are truncated at the bottom on Windows 11) closed by Zach Pearson
can't reproduce: Installed 1.4 and a 1.5 daily build onto my Windows 11 machine. …
4:16 PM Ticket #7152 (Make toolshed update notification only appear if user has used an ...) created by Tom Goddard
In ticket #7123 Zach was interested in putting an updated version of …
4:10 PM Ticket #7151 (ChimeraX crashes opening cif file on WSL2) closed by Greg Couch
limitation: Thank you for reporting this. It is not something I would have tried …
4:01 PM Ticket #6032 (Error restoring session: blastprotein: __init__() missing 1 required ...) closed by Zach Pearson
fixed: Superseded by ChimeraX 1.4.
3:50 PM Ticket #7114 (Draw status bar: Attempt to retrieve context when no valid context) closed by Tom Goddard
fixed: The original OpenGL error was fixed by using a daily build. I made a …
3:45 PM Ticket #7151 (ChimeraX crashes opening cif file on WSL2) created by kamadak@…
In ticket #7114 Kama is trying to run ChimeraX daily build (June 22, …
3:38 PM Ticket #7150 (Remove Ubuntu 16 and 18 daily builds from web page) created by Tom Goddard
The download page is showing very old Ubuntu 16 and 18 daily builds. …
3:32 PM Ticket #7123 (Basic Actions saving session: 'QEventLoop' object has no attribute 'exec_') closed by Zach Pearson
fixed: That did fix session saving/restoring. We might put the new version on …
1:31 PM phenix-6-23-22 edited by pett
(diff)
1:29 PM Ticket #5223 (Replace Opal web services) closed by pett
fixed: Muscle/Clustal-Omega services ported.
11:30 AM phenix-6-23-22 edited by pett
(diff)
11:30 AM phenix-6-23-22 edited by pett
(diff)
11:24 AM phenix-6-23-22 edited by pett
(diff)
11:19 AM phenix-6-23-22 edited by pett
(diff)
11:15 AM phenix-6-23-22 edited by pett
(diff)
11:11 AM phenix-6-23-22 edited by pett
(diff)
10:45 AM phenix-6-23-22 created by pett
10:44 AM Features edited by pett
(diff)
10:14 AM Ticket #7148 (Graphics crash, macOS 12.4, Intel Iris Plus Graphics) closed by Tom Goddard
nonchimerax: Apple Intel graphics driver crash.
9:26 AM Ticket #7149 (Status bar: Attempt to retrieve context when no valid context) created by chimerax-bug-report@…
[…]
9:24 AM Ticket #7146 (Crash in event loop) closed by pett
can't reproduce: And there have been many bug fixes and improvements since the 1.2.5 …
9:16 AM Ticket #7147 (Crash showing Rapid Access at startup) closed by pett
can't reproduce
9:12 AM Ticket #7145 (Crash in event loop on Mac in NSTextInputContext) closed by pett
can't reproduce: Apparently just after startup
9:09 AM Ticket #7144 (Crash in garbage collection after tool destruction) closed by pett
can't reproduce: I understand _what's_ happening (garbage collection is being called to …
7:53 AM Ticket #7148 (Graphics crash, macOS 12.4, Intel Iris Plus Graphics) created by chimerax-bug-report@…
[…]
6:17 AM Ticket #7147 (Crash showing Rapid Access at startup) created by chimerax-bug-report@…
[…]

Jun 21, 2022:

8:34 PM Ticket #7146 (Crash in event loop) created by magicairben6@…
[…]
8:10 PM Ticket #7145 (Crash in event loop on Mac in NSTextInputContext) created by chimerax-bug-report@…
[…]
5:15 PM Ticket #7144 (Crash in garbage collection after tool destruction) created by chimerax-bug-report@…
[…]
11:39 AM Ticket #7143 (RFE: ortho/perspective control on Side View GUI) created by Elaine Meng
What do you think about having an option in the Side View to switch …
11:33 AM Ticket #7122 (FindHBond: atom unexpectedly has no neighbors) closed by pett
fixed
11:11 AM Ticket #7141 (Crash running AlphaFold prediction) closed by Tom Goddard
can't reproduce: Probable crash in Qt html panel for AlphaFold.
10:38 AM Ticket #7130 (Crash setting volume level?) closed by Tom Goddard
can't reproduce: Could be a graphics driver crash. Does not make sense that the log …
10:30 AM Ticket #7128 (Crash saving STL) closed by Tom Goddard
can't reproduce: The last command before the crash was saving an STL file. But the Mac …
10:18 AM Ticket #7124 (glTexImage2D: out of memory) closed by Tom Goddard
can't reproduce: ChimeraX produced an OpenGL graphics error at startup trying to draw …
9:50 AM Ticket #7142 (Crash showing Rapid Access at startup) closed by pett
can't reproduce
9:46 AM Ticket #7139 (Crash in QMainWindow::removeDockWidget) closed by pett
can't reproduce
9:44 AM Ticket #7138 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: 1.3
9:43 AM Ticket #7137 (Crash while user closing window) closed by pett
can't reproduce
9:40 AM Ticket #7136 (Crash deleting some tool's interface) closed by pett
can't reproduce: Possibly the XMAS tool
8:53 AM Ticket #7142 (Crash showing Rapid Access at startup) created by chimerax-bug-report@…
[…]
12:44 AM Ticket #7141 (Crash running AlphaFold prediction) created by chimerax-bug-report@…
[…]

Jun 20, 2022:

8:21 PM Ticket #7140 (Problems with the display of cyclic peptides) created by chen_mangkun0101@…
[…] [[Image(...)]]
6:58 PM Ticket #7139 (Crash in QMainWindow::removeDockWidget) created by chimerax-bug-report@…
[…]
6:04 PM Ticket #7138 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
3:48 PM Ticket #7137 (Crash while user closing window) created by chimerax-bug-report@…
[…]
1:56 PM Ticket #7127 (problem running AlfaFold Prediction) closed by Tom Goddard
fixed: I just fixed a problem running AlphaFold predictions in ChimeraX …
1:44 PM Ticket #7135 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: 1.3
1:43 PM Ticket #7134 (XMAS: crash in event loop) closed by pett
can't reproduce
1:42 PM Ticket #7133 (Crash in event loop) closed by pett
can't reproduce
1:41 PM Ticket #7132 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce
1:39 PM Ticket #7131 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: 1.3
10:53 AM Ticket #7136 (Crash deleting some tool's interface) created by chimerax-bug-report@…
[…]
9:03 AM Ticket #7126 (Unknown crash) closed by pett
can't reproduce
9:02 AM Ticket #7125 (Crash in Qt on exit) closed by pett
can't reproduce
8:13 AM Ticket #7135 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
8:08 AM Ticket #7134 (XMAS: crash in event loop) created by chimerax-bug-report@…
[…]
7:57 AM Ticket #7133 (Crash in event loop) created by chimerax-bug-report@…
[…]
7:50 AM Ticket #7132 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
6:50 AM Ticket #7131 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
5:44 AM Ticket #7130 (Crash setting volume level?) created by chimerax-bug-report@…
[…]
1:51 AM Ticket #7129 (Crash forking process) created by jongseopark@…
[…]

Jun 19, 2022:

2:15 PM Ticket #7128 (Crash saving STL) created by j.kenkel@…
[…] 7x2f.pdb
7:52 AM Ticket #7127 (problem running AlfaFold Prediction) created by rubinjr@…
[…]
5:58 AM Ticket #7126 (Unknown crash) created by chimerax-bug-report@…
[…]

Jun 18, 2022:

10:54 PM Ticket #7125 (Crash in Qt on exit) created by chimerax-bug-report@…
[…]
9:16 PM Ticket #7124 (glTexImage2D: out of memory) created by 196891@…
[…]
9:53 AM Ticket #7123 (Basic Actions saving session: 'QEventLoop' object has no attribute 'exec_') created by marta.carroni@…
[…]
Note: See TracTimeline for information about the timeline view.