Timeline



Aug 30, 2021:

6:39 PM Ticket #5130 (Paid AWS account for VR meeting server) created by Tom Goddard
The VR meeting server chimeraxmeeting.net is hosted by an Amazon Web …
5:17 PM Ticket #5129 (Graphics artifacts with silhouettes on Mac) closed by Tom Goddard
nonchimerax
4:49 PM Ticket #5126 ('view' session data is None) closed by Tom Goddard
limitation: Hi Randy, Thanks for checking the session. And thanks Greg, I …
1:45 PM Ticket #5129 (Graphics artifacts with silhouettes on Mac) created by nharper@…
[…] test.png​
1:12 PM Ticket #5128 (Error initializing CUDA: CUDA_ERROR_NO_DEVICE) created by chimerax-bug-report@…
[…]
11:58 AM Ticket #5112 (AlignSeqPairArg gives sequence with incorrect polymer_type PT_NONE) closed by Eric Pettersen
fixed: Copied StructureSeqs weren't copying polymer_type
11:41 AM Ticket #5127 (Qt crash during exit) created by chimerax-bug-report@…
[…]
11:35 AM Ticket #5125 (RFE: scroll contour) closed by Tom Goddard
wontfix: It's a nice idea. But the Volume panel itself scrolls when several …
11:24 AM Ticket #5121 (OpenGL startup errors) closed by Tom Goddard
nonchimerax: ChimeraX cannot start because your Radeon graphics driver is broken. …
10:44 AM Ticket #5126 ('view' session data is None) created by ewatson@…
[…]
10:25 AM Ticket #5119 (Matchmaker: 'NoneType' object has no attribute 'setChecked') closed by Eric Pettersen
can't reproduce: Hi Jonathan, Thanks for reporting this problem. I have tried various …
9:27 AM Ticket #5123 (Dual display crash) closed by Eric Pettersen
duplicate: Qt 5.12
6:55 AM Ticket #5125 (RFE: scroll contour) created by jaremko@…
[…]

Aug 29, 2021:

10:43 PM Ticket #5124 (Crash loading OpenMM plugins) created by Helge.Paternoga@…
[…]
9:36 PM Ticket #5123 (Dual display crash) created by chimerax-bug-report@…
[…]

Aug 27, 2021:

6:02 PM Dev2021-9-2 edited by Tom Goddard
(diff)
5:53 PM Ticket #5122 (Improve Tools menu categories) created by Tom Goddard
The AlphaFold tool does not seem to belong in menu Tools / Structure …
5:40 PM Ticket #5115 (Crash in Python garbage collection while fetching attribute) closed by Tom Goddard
duplicate: This is our old friend the Python garbage collection crash. It is in …
5:24 PM Dev2021-9-2 edited by Tom Goddard
(diff)
5:23 PM Dev2021-9-2 created by Tom Goddard
5:22 PM DeveloperMeetings edited by Tom Goddard
(diff)
4:56 PM Ticket #5121 (OpenGL startup errors) created by ElhaiJ@…
[…]
3:42 PM Ticket #5117 (Modeller results disliked by Coot) closed by Eric Pettersen
nonchimerax: Hi Yen-Li, ChimeraX merely makes it easy to prepare the inputs and …
3:40 PM Ticket #5120 ((Various modules) Malformed docstrings) created by Zach Pearson
While looking at what it would take to tackle this ticket …
1:33 PM 2021-8-26 edited by Tom Goddard
(diff)
1:30 PM Ticket #5119 (Matchmaker: 'NoneType' object has no attribute 'setChecked') created by jonathan.sheehan@…
[…]
1:21 PM Ticket #5111 (Modeller sequence/structure mismatch) closed by Eric Pettersen
fixed: Apparently fixed in the daily build.
1:07 PM ChangeLog edited by Elaine Meng
(diff)
12:47 PM NTTData edited by Elaine Meng
(diff)
12:44 PM NTTData edited by Elaine Meng
(diff)
12:42 PM NTTData edited by Elaine Meng
(diff)
12:42 PM NTTData edited by Elaine Meng
(diff)
12:27 PM Ticket #5118 (ChimeraX hangs if the blastprotein module can't connect) created by goddard@…
During a meeting yesterday (26 August) our infrastructure was down. …
12:24 PM Ticket #5116 (quick question...) closed by Zach Pearson
fixed: Hi Monique, A power outage took our infrastructure out yesterday. …
11:37 AM Ticket #5117 (Modeller results disliked by Coot) created by yen-li.li@…
[…] modeller model in coot.png​
10:01 AM Ticket #5116 (quick question...) created by mrogals@…
[…]

Aug 25, 2021:

7:48 PM Ticket #5115 (Crash in Python garbage collection while fetching attribute) created by goddard@…
[…]
5:57 PM Ticket #5114 (volume maximum not extending map bounds) closed by Tom Goddard
fixed: Fixed. The map combine operation was using Volume.region_grid() and …
5:52 PM Ticket #5114 (volume maximum not extending map bounds) created by goddard@…
[…]
5:46 PM Ticket #5113 (Session depends on atomic bundle when no atomic models opened) created by goddard@…
[…]
4:29 PM Ticket #5112 (AlignSeqPairArg gives sequence with incorrect polymer_type PT_NONE) created by goddard@…
[…]
3:26 PM Ticket #5111 (Modeller sequence/structure mismatch) created by chimerax-bug-report@…
[…]
11:20 AM Ticket #5108 (Crystal Contacts: set model menu to invalid value) closed by Tom Goddard
fixed: Fixed. ChimeraX unit cell tool did not start because a bug where it …
10:48 AM Ticket #5095 (Error closing altloc explorer tool) closed by Eric Pettersen
fixed: Only happens with no structures open.
10:41 AM Ticket #5107 (Boolean attribute test produces traceback) closed by Eric Pettersen
fixed
10:11 AM Ticket #5110 (Crash in set sseq.chain_id) closed by Eric Pettersen
fixed: Hi Caitie, Thanks for getting back to me. I can indeed get 1.0 to …
9:55 AM Ticket #5109 (Crystal Contacts: set model menu to invalid value) closed by Eric Pettersen
duplicate
9:54 AM Ticket #5109 (Crystal Contacts: set model menu to invalid value) reopened by Eric Pettersen
9:28 AM Ticket #5110 (Crash in set sseq.chain_id) created by caitie.mccafferty@…
[…]
8:16 AM Ticket #5109 (Crystal Contacts: set model menu to invalid value) closed by Zach Pearson
duplicate: Duplicate of #5108
4:01 AM Ticket #5109 (Crystal Contacts: set model menu to invalid value) created by chimerax-bug-report@…
[…]
4:00 AM Ticket #5108 (Crystal Contacts: set model menu to invalid value) created by ulrich.baumann@…
[…]

Aug 24, 2021:

5:41 PM Ticket #5104 (Problem destroying in-window status bar during session reset: wrapped ...) closed by Tom Goddard
duplicate: Fixed in daily build, not in 1.2.5. Duplicate #4583.
5:40 PM Ticket #5106 (Crash in sseq.structure) closed by Eric Pettersen
can't reproduce: Need more info, but I just fixed a crash with sseq.structure which …
5:38 PM Ticket #5105 (Problem destroying in-window status bar during session reset: wrapped ...) closed by Eric Pettersen
duplicate
5:38 PM Ticket #5105 (Problem destroying in-window status bar during session reset: wrapped ...) reopened by Eric Pettersen
5:32 PM Ticket #5107 (Boolean attribute test produces traceback) created by Eric Pettersen
[…]
3:12 PM Ticket #5106 (Crash in sseq.structure) created by chimerax-bug-report@…
[…]
12:58 PM Ticket #5105 (Problem destroying in-window status bar during session reset: wrapped ...) closed by Zach Pearson
duplicate: Duplicate of #5104
12:55 PM Ticket #5105 (Problem destroying in-window status bar during session reset: wrapped ...) created by chimerax-bug-report@…
[…]
12:55 PM Ticket #5104 (Problem destroying in-window status bar during session reset: wrapped ...) created by chimerax-bug-report@…
[…]
12:47 PM Ticket #5066 (Replace compiled p7zip with binary package) closed by Zach Pearson
fixed: Closed by …
11:21 AM Ticket #5097 (Crash in sseq.structure) closed by Eric Pettersen
fixed: The "structure sequence" wasn't being properly demoted to plain …
10:10 AM Ticket #5102 (Bundle ChimeraX-mmCIF has no module) closed by Greg Couch
duplicate: Duplicate of #5083
9:42 AM 2021-8-26 created by Tom Goddard
9:41 AM DeveloperMeetings edited by Tom Goddard
(diff)
9:16 AM Ticket #5098 (Crash with bad stack) closed by Tom Goddard
can't reproduce: Crashed in malloc in a ctypes call.
9:01 AM Ticket #5096 (Bad sequence association) closed by Eric Pettersen
can't reproduce: Can't reproduce. The error is possibly the result of bad state due to …
8:59 AM Ticket #5094 (Dual display crash) closed by Eric Pettersen
duplicate: Qt 5.12
6:45 AM Ticket #5103 (Unknown crash) created by oleland@…
[…]
1:26 AM Ticket #5102 (Bundle ChimeraX-mmCIF has no module) created by chimerax-bug-report@…
[…]

Aug 23, 2021:

11:10 PM Ticket #5101 (Crash in Nucletides using weakref set) created by venkatareddy@…
[…]
9:11 PM Ticket #5100 (Crash dismissing registration window) created by manikandan.k@…
[…]
7:06 PM Ticket #5099 (BLAST gui shows wrong database and chain when the blastprotein command ...) created by goddard@…
[…]
5:28 PM Ticket #5098 (Crash with bad stack) created by chimerax-bug-report@…
[…]
5:14 PM Ticket #5097 (Crash in sseq.structure) created by Elaine Meng
[…] mismatch1.cxs​
3:07 PM Ticket #5096 (Bad sequence association) created by Elaine Meng
[…]
2:47 PM Ticket #5095 (Error closing altloc explorer tool) created by goddard@…
[…]
1:37 PM Ticket #5094 (Dual display crash) created by chimerax-bug-report@…
[…]
11:03 AM Ticket #5092 ("Access violation" in swap_buffers drawing status line) closed by Tom Goddard
can't reproduce
11:02 AM Ticket #5093 (Unknown crash) closed by Eric Pettersen
can't reproduce
11:01 AM Ticket #5090 (Graphics crash, macOS 10.15, Geforce GT 650M) closed by Tom Goddard
nonchimerax
3:43 AM Ticket #5093 (Unknown crash) created by chimerax-bug-report@…
[…]
2:14 AM Ticket #5092 ("Access violation" in swap_buffers drawing status line) created by chimerax-bug-report@…
[…]

Aug 22, 2021:

2:04 AM Ticket #5090 (Graphics crash, macOS 10.15, Geforce GT 650M) created by chimerax-bug-report@…
[…]

Aug 21, 2021:

2:34 AM Ticket #5089 (Crash in save dialog) created by chimerax-bug-report@…
[…]

Aug 20, 2021:

6:41 PM Ticket #5087 ("Access violation" filtering Collection) closed by Eric Pettersen
fixed
3:05 PM Ticket #5088 (Github Actions: Ubuntu 20.04 build fails on first curl) created by Zach Pearson
I'm currently testing continuous integration and in the process …
9:14 AM Ticket #5082 (Crash with bad stack) closed by Eric Pettersen
can't reproduce
7:03 AM Ticket #5087 ("Access violation" filtering Collection) created by amith.rangarajan@…
[…]
6:39 AM Ticket #5086 (Improve attribute-registration error reporting) created by chimerax-bug-report@…
[…]
5:16 AM Ticket #5085 (ISOLDE: wrapped C/C++ object of type QTableWidget has been deleted) created by chimerax-bug-report@…
[…]
2:45 AM Ticket #5080 (Show UniProt name in Blast AlphaFold results table) closed by Zach Pearson
fixed
2:30 AM Ticket #5084 (OpenMM 7.6) created by Tristan Croll
[…]
2:25 AM Ticket #5077 ("Access violation" fetching BLAST PDB info) closed by Zach Pearson
fixed: Should be fixed by …
2:03 AM Ticket #5081 (Blast protein: Internal Server Error) closed by Zach Pearson
can't reproduce: Restarted webservices at some point between this being opened and me …

Aug 19, 2021:

10:44 PM Ticket #5083 (Bundle ChimeraX-mmCIF has no module) created by chimerax-bug-report@…
[…]
10:42 PM Ticket #5082 (Crash with bad stack) created by chimerax-bug-report@…
[…]
8:08 PM Ticket #5081 (Blast protein: Internal Server Error) created by goddard@…
[…]
4:36 PM Ticket #5080 (Show UniProt name in Blast AlphaFold results table) created by goddard@…
[…]
3:26 PM Ticket #5077 ("Access violation" fetching BLAST PDB info) reopened by Tom Goddard
2:54 PM Dev2021-8-19 edited by Tom Goddard
(diff)
2:46 PM Dev2021-8-19 edited by Greg Couch
(diff)
2:46 PM Dev2021-8-19 edited by Greg Couch
(diff)
12:13 PM Dev2021-8-19 edited by Tom Goddard
(diff)
12:05 PM 2021-8-19 edited by Tom Goddard
(diff)
12:00 PM 2021-8-19 edited by Tom Goddard
(diff)
11:25 AM 2021-8-19 edited by Tom Goddard
(diff)
11:14 AM 2021-8-19 edited by Tom Goddard
(diff)
9:21 AM Ticket #5079 (Long atom spec crashes ChimeraX) closed by Eric Pettersen
duplicate: Duplicate of #4842
9:17 AM Ticket #5078 ("Access violation" reading PDB file) closed by Eric Pettersen
can't reproduce
9:16 AM Ticket #5077 ("Access violation" fetching BLAST PDB info) closed by Eric Pettersen
can't reproduce
4:36 AM Ticket #5079 (Long atom spec crashes ChimeraX) created by chimerax-bug-report@…
[…]

Aug 18, 2021:

10:15 AM Ticket #5078 ("Access violation" reading PDB file) created by chimerax-bug-report@…
[…]
9:08 AM Ticket #5077 ("Access violation" fetching BLAST PDB info) created by chimerax-bug-report@…
[…]
7:38 AM Ticket #5076 (Startup error on Windows 7) closed by Eric Pettersen
limitation
12:42 AM Ticket #5072 ("Access violation" reading mmCIF in script) closed by Greg Couch
duplicate: Duplicate of #5073.
12:41 AM Ticket #5074 ("Access violation" reading mmCIF in script) closed by Greg Couch
duplicate: Duplicate of #5073.
12:30 AM Ticket #5073 ("Access violation" reading mmCIF 1d3g) closed by Greg Couch
fixed: This bug due to an file reading optimization on Windows that fails …

Aug 17, 2021:

11:50 PM Ticket #5076 (Startup error on Windows 7) created by chimerax-bug-report@…
[…]
6:53 PM Ticket #5075 ("Access violation" getting StructureDatas._graphics_changeds) closed by Tom Goddard
can't reproduce: Same crash is #4530 in ChimeraX 1.1 where it was simply opening an …
2:14 PM Ticket #5071 (AddH stripping protons from water near metal) closed by Eric Pettersen
fixed: Actually search for metal coordinations instead of trusting that …
1:35 PM Ticket #5075 ("Access violation" getting StructureDatas._graphics_changeds) created by chimerax-bug-report@…
[…]
10:30 AM 2021-8-19 edited by Tom Goddard
(diff)
10:29 AM Dev2021-8-19 created by Tom Goddard
10:27 AM 2021-8-19 created by Tom Goddard
10:25 AM DeveloperMeetings edited by Tom Goddard
(diff)
9:13 AM Ticket #5070 (Crash at startup in rapid_access_shown, Linux) closed by Eric Pettersen
can't reproduce
9:12 AM Ticket #5069 (Unable to open file for writing PDB) closed by Eric Pettersen
not a bug
9:09 AM Ticket #5068 (Unknown error) closed by Eric Pettersen
not a bug
9:08 AM Ticket #5067 (Crash in Qt on exit) closed by Eric Pettersen
can't reproduce: Dual displays
9:05 AM Ticket #5065 (Crash in garbage collection during new-object allocation) closed by Eric Pettersen
can't reproduce: Hi Ryan, We have never been able to reproduce this problem, but we …
9:00 AM Ticket #5074 ("Access violation" reading mmCIF in script) created by davidleeming05@…
[…]
7:35 AM Ticket #5073 ("Access violation" reading mmCIF 1d3g) created by davidleeming05@…
[…]
5:33 AM Ticket #5072 ("Access violation" reading mmCIF in script) created by chimerax-bug-report@…
[…]
4:07 AM Ticket #5071 (AddH stripping protons from water near metal) created by Tristan Croll
[…]
3:04 AM Ticket #5070 (Crash at startup in rapid_access_shown, Linux) created by chimerax-bug-report@…
[…]

Aug 16, 2021:

11:42 PM Ticket #5069 (Unable to open file for writing PDB) created by chimerax-bug-report@…
[…]
7:14 PM Ticket #5068 (Unknown error) created by chimerax-bug-report@…
[…]
4:42 PM Ticket #5067 (Crash in Qt on exit) created by chimerax-bug-report@…
[…]
3:27 PM Ticket #5045 (Modeller sequence mismatch failure) closed by Eric Pettersen
fixed: Tomorrow's daily build should work without the delete-chains hocus …
1:56 PM Ticket #5066 (Replace compiled p7zip with binary package) created by Zach Pearson
In upcoming versions of g++ compiling p7zip throws a -Wnarrowing …
1:03 PM Ticket #5065 (Crash in garbage collection during new-object allocation) created by rslack@…
[…]
10:13 AM Ticket #5058 (Graphics crash, macOS 11.4, Intel HD 6000 graphics) closed by Tom Goddard
nonchimerax
9:56 AM Ticket #5061 (Various OpenGL errors) closed by Tom Goddard
duplicate: Duplicate of #5060.
9:54 AM Ticket #5060 (Various OpenGL errors) closed by Tom Goddard
nonchimerax: This ChimeraX error is with your graphics driver. Updating the driver …
9:46 AM Ticket #5064 (Crash in garbage collection during new-object allocation) closed by Eric Pettersen
can't reproduce: Again, Python 3.7
9:38 AM Ticket #5062 (All-numeric residue names) closed by Eric Pettersen
not a bug: Really a usage question -- redirected to chimerax-users
9:36 AM Ticket #5064 (Crash in garbage collection during new-object allocation) created by chimerax-bug-report@…
[…]
9:33 AM Ticket #5059 (Crash showing Open dialog) closed by Eric Pettersen
can't reproduce
7:13 AM Ticket #5063 (color byattr: 'list' object has no attribute 'items') created by rhernan2@…
[…]
7:12 AM Ticket #5062 (All-numeric residue names) created by Tristan Croll
[…]
2:26 AM Ticket #5061 (Various OpenGL errors) created by diva.niru@…
[…]
2:10 AM Ticket #5060 (Various OpenGL errors) created by diva.niru@…
[…]
12:06 AM Ticket #5059 (Crash showing Open dialog) created by chimerax-bug-report@…
[…]

Aug 15, 2021:

10:55 PM Ticket #5058 (Graphics crash, macOS 11.4, Intel HD 6000 graphics) created by chimerax-bug-report@…
[…]

Aug 14, 2021:

11:32 PM Ticket #5057 (Don't produce traceback when unable to restore new session) created by venkatareddy@…
[…]

Aug 13, 2021:

6:58 PM Ticket #5054 (BLAST REST service is down) closed by Zach Pearson
fixed: Should be fixed by cxwebservices commit …
5:39 PM Ticket #5056 (Allow blastprotein command to use a UniProt name or id) created by Tom Goddard
Would be convenient if the blastprotein command could take as the …
5:36 PM Ticket #5055 (Allow BLAST gui to use a sequence viewer id and direct sequence input) created by Tom Goddard
When you make a better BLAST gui it would be nice if it could work …
4:56 PM Ticket #5054 (BLAST REST service is down) created by goddard@…
[…]
1:47 PM Ticket #5053 (Coulombic coloring of combined surface) closed by Eric Pettersen
not a bug: Forwarded to and answered on chimerax-users list
1:02 PM Ticket #5052 (Unknown crash) closed by Eric Pettersen
can't reproduce
12:52 PM Ticket #5053 (Coulombic coloring of combined surface) created by wenxiang.cao@…
[…]
7:29 AM Ticket #5052 (Unknown crash) created by chimerax-bug-report@…
[…]

Aug 12, 2021:

7:50 PM Ticket #4610 ("Show in sequence viewer" error when no hits) closed by Zach Pearson
fixed: Should be fixed in tonight's build by …
6:48 PM Ticket #5051 (Unknown crash) created by marioihdzjr@…
[…]
5:27 PM NTTData edited by Tom Goddard
(diff)
5:10 PM Ticket #5042 (os.getcwd() failure saving map) closed by Tom Goddard
fixed: You denied permission for ChimeraX to access the the Desktop folder. …
4:32 PM Ticket #5050 (colorkey label seems cut off at top) closed by Eric Pettersen
fixed
4:07 PM Ticket #5049 (Crash showing Open dialog) closed by Eric Pettersen
can't reproduce: The error code is "wrong thread". It also looks like somehow it got …
4:03 PM Ticket #5048 (Crash on exit in sip) closed by Eric Pettersen
can't reproduce
4:02 PM Ticket #5047 (Crash on exit in sip) closed by Eric Pettersen
can't reproduce
2:51 PM Ticket #5050 (colorkey label seems cut off at top) created by Elaine Meng
see attached session and PNG image ... dunno if it's my bad graphics …
2:18 PM NTTData edited by Elaine Meng
(diff)
2:13 PM NTTData edited by Elaine Meng
(diff)
2:09 PM Ticket #5049 (Crash showing Open dialog) created by chimerax-bug-report@…
[…]
2:04 PM NTTData edited by Elaine Meng
(diff)
1:38 PM NTTData edited by Elaine Meng
(diff)
1:17 PM Ticket #5048 (Crash on exit in sip) created by chimerax-bug-report@…
[…]
12:17 PM Ticket #5047 (Crash on exit in sip) created by chimerax-bug-report@…
[…]
12:13 PM 2021-8-12 edited by Tom Goddard
(diff)
11:58 AM 2021-8-12 edited by Tom Goddard
(diff)
11:42 AM 2021-8-12 edited by Tom Goddard
(diff)
11:42 AM 2021-8-12 edited by Tom Goddard
(diff)
11:35 AM 2021-8-12 edited by Tom Goddard
(diff)
11:35 AM 2021-8-12 edited by Tom Goddard
(diff)
11:33 AM 2021-8-12 edited by Tom Goddard
(diff)
11:14 AM 2021-8-12 edited by Tom Goddard
(diff)
11:10 AM 2021-8-12 edited by Tom Goddard
(diff)