![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Aug 19, 2021:
- 10:44 PM Ticket #5083 (Bundle ChimeraX-mmCIF has no module) created by
- […]
- 10:42 PM Ticket #5082 (Crash with bad stack) created by
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- 8:08 PM Ticket #5081 (Blast protein: Internal Server Error) created by
- […]
- 4:36 PM Ticket #5080 (Show UniProt name in Blast AlphaFold results table) created by
- […]
- 3:26 PM Ticket #5077 ("Access violation" fetching BLAST PDB info) reopened by
- 2:54 PM Dev2021-8-19 edited by
- (diff)
- 2:46 PM Dev2021-8-19 edited by
- (diff)
- 2:46 PM Dev2021-8-19 edited by
- (diff)
- 12:13 PM Dev2021-8-19 edited by
- (diff)
- 12:05 PM 2021-8-19 edited by
- (diff)
- 12:00 PM 2021-8-19 edited by
- (diff)
- 11:25 AM 2021-8-19 edited by
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- 11:14 AM 2021-8-19 edited by
- (diff)
- 9:21 AM Ticket #5079 (Long atom spec crashes ChimeraX) closed by
- duplicate: Duplicate of #4842
- 9:17 AM Ticket #5078 ("Access violation" reading PDB file) closed by
- can't reproduce
- 9:16 AM Ticket #5077 ("Access violation" fetching BLAST PDB info) closed by
- can't reproduce
- 4:36 AM Ticket #5079 (Long atom spec crashes ChimeraX) created by
- […]
Aug 18, 2021:
- 10:15 AM Ticket #5078 ("Access violation" reading PDB file) created by
- […]
- 9:08 AM Ticket #5077 ("Access violation" fetching BLAST PDB info) created by
- […]
- 7:38 AM Ticket #5076 (Startup error on Windows 7) closed by
- limitation
- 12:42 AM Ticket #5072 ("Access violation" reading mmCIF in script) closed by
- duplicate: Duplicate of #5073.
- 12:41 AM Ticket #5074 ("Access violation" reading mmCIF in script) closed by
- duplicate: Duplicate of #5073.
- 12:30 AM Ticket #5073 ("Access violation" reading mmCIF 1d3g) closed by
- 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
- […]
- 6:53 PM Ticket #5075 ("Access violation" getting StructureDatas._graphics_changeds) closed by
- 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
- fixed: Actually search for metal coordinations instead of trusting that …
- 1:35 PM Ticket #5075 ("Access violation" getting StructureDatas._graphics_changeds) created by
- […]
- 10:30 AM 2021-8-19 edited by
- (diff)
- 10:29 AM Dev2021-8-19 created by
- 10:27 AM 2021-8-19 created by
- 10:25 AM DeveloperMeetings edited by
- (diff)
- 9:13 AM Ticket #5070 (Crash at startup in rapid_access_shown, Linux) closed by
- can't reproduce
- 9:12 AM Ticket #5069 (Unable to open file for writing PDB) closed by
- not a bug
- 9:09 AM Ticket #5068 (Unknown error) closed by
- not a bug
- 9:08 AM Ticket #5067 (Crash in Qt on exit) closed by
- can't reproduce: Dual displays
- 9:05 AM Ticket #5065 (Crash in garbage collection during new-object allocation) closed by
- 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
- […]
- 7:35 AM Ticket #5073 ("Access violation" reading mmCIF 1d3g) created by
- […]
- 5:33 AM Ticket #5072 ("Access violation" reading mmCIF in script) created by
- […]
- 4:07 AM Ticket #5071 (AddH stripping protons from water near metal) created by
- […]
- 3:04 AM Ticket #5070 (Crash at startup in rapid_access_shown, Linux) created by
- […]
Aug 16, 2021:
- 11:42 PM Ticket #5069 (Unable to open file for writing PDB) created by
- […]
- 7:14 PM Ticket #5068 (Unknown error) created by
- […]
- 4:42 PM Ticket #5067 (Crash in Qt on exit) created by
- […]
- 3:27 PM Ticket #5045 (Modeller sequence mismatch failure) closed by
- 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
- 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
- […]
- 10:13 AM Ticket #5058 (Graphics crash, macOS 11.4, Intel HD 6000 graphics) closed by
- nonchimerax
- 9:56 AM Ticket #5061 (Various OpenGL errors) closed by
- duplicate: Duplicate of #5060.
- 9:54 AM Ticket #5060 (Various OpenGL errors) closed by
- 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
- can't reproduce: Again, Python 3.7
- 9:38 AM Ticket #5062 (All-numeric residue names) closed by
- 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
- […]
- 9:33 AM Ticket #5059 (Crash showing Open dialog) closed by
- can't reproduce
- 7:13 AM Ticket #5063 (color byattr: 'list' object has no attribute 'items') created by
- […]
- 7:12 AM Ticket #5062 (All-numeric residue names) created by
- […]
- 2:26 AM Ticket #5061 (Various OpenGL errors) created by
- […]
- 2:10 AM Ticket #5060 (Various OpenGL errors) created by
- […]
- 12:06 AM Ticket #5059 (Crash showing Open dialog) created by
- […]
Aug 15, 2021:
Aug 14, 2021:
Aug 13, 2021:
- 6:58 PM Ticket #5054 (BLAST REST service is down) closed by
- fixed: Should be fixed by cxwebservices commit …
- 5:39 PM Ticket #5056 (Allow blastprotein command to use a UniProt name or id) created by
- 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
- 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
- […]
- 1:47 PM Ticket #5053 (Coulombic coloring of combined surface) closed by
- not a bug: Forwarded to and answered on chimerax-users list
- 1:02 PM Ticket #5052 (Unknown crash) closed by
- can't reproduce
- 12:52 PM Ticket #5053 (Coulombic coloring of combined surface) created by
- […]
- 7:29 AM Ticket #5052 (Unknown crash) created by
- […]
Aug 12, 2021:
- 7:50 PM Ticket #4610 ("Show in sequence viewer" error when no hits) closed by
- fixed: Should be fixed in tonight's build by …
- 6:48 PM Ticket #5051 (Unknown crash) created by
- […]
- 5:27 PM NTTData edited by
- (diff)
- 5:10 PM Ticket #5042 (os.getcwd() failure saving map) closed by
- 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
- fixed
- 4:07 PM Ticket #5049 (Crash showing Open dialog) closed by
- 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
- can't reproduce
- 4:02 PM Ticket #5047 (Crash on exit in sip) closed by
- can't reproduce
- 2:51 PM Ticket #5050 (colorkey label seems cut off at top) created by
- see attached session and PNG image ... dunno if it's my bad graphics …
- 2:18 PM NTTData edited by
- (diff)
- 2:13 PM NTTData edited by
- (diff)
- 2:09 PM Ticket #5049 (Crash showing Open dialog) created by
- […]
- 2:04 PM NTTData edited by
- (diff)
- 1:38 PM NTTData edited by
- (diff)
- 1:17 PM Ticket #5048 (Crash on exit in sip) created by
- […]
- 12:17 PM Ticket #5047 (Crash on exit in sip) created by
- […]
- 12:13 PM 2021-8-12 edited by
- (diff)
- 11:58 AM 2021-8-12 edited by
- (diff)
- 11:42 AM 2021-8-12 edited by
- (diff)
- 11:42 AM 2021-8-12 edited by
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- 11:35 AM 2021-8-12 edited by
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- 11:35 AM 2021-8-12 edited by
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- 11:33 AM 2021-8-12 edited by
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- 11:14 AM 2021-8-12 edited by
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- 11:10 AM 2021-8-12 edited by
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- 11:08 AM 2021-8-12 edited by
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- 11:07 AM 2021-8-12 edited by
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- 11:03 AM 2021-8-12 edited by
- (diff)
- 11:03 AM 2021-8-12 edited by
- (diff)
- 9:13 AM Ticket #5046 (Crash with trashed stack) closed by
- can't reproduce
- 9:09 AM Ticket #5044 (Crash on exit in sip) closed by
- can't reproduce
- 6:20 AM Ticket #5046 (Crash with trashed stack) created by
- […]
- 1:13 AM Ticket #5045 (Modeller sequence mismatch failure) created by
- […] Modeller Comparative Error.png
- 12:39 AM Ticket #5044 (Crash on exit in sip) created by
- […]
Aug 11, 2021:
- 11:32 PM Ticket #5038 (the problem with chimerax install) closed by
- nonchimerax: dxdiag says your graphics card is "Microsoft Basic Display Adapter", …
- 8:17 PM Ticket #4924 (AlphaFold2 in Google Collab notebook) closed by
- duplicate: I made a new ticket #5043 with the more general goal of providing an …
- 8:15 PM Ticket #5043 (Add an AlphaFold structure prediction tool) created by
- Would like the user to be able to specify a sequence and compute a …
- 8:08 PM Ticket #5042 (os.getcwd() failure saving map) created by
- […]
- 6:09 PM Ticket #5041 (Crash in garbage collection during new-object allocation) closed by
- can't reproduce: This may have been a bug in Python. All reports of this crash occur …
- 5:57 PM Ticket #5041 (Crash in garbage collection during new-object allocation) created by
- […]
- 3:55 PM Ticket #4979 (MatchMaker get percent identity from Python) closed by
- fixed: Now also returns the aligned sequences as 'aligned ref seq' and …
- 2:58 PM Ticket #4979 (MatchMaker get percent identity from Python) reopened by
- Thanks! It doesn't quite do what I want. I want the percent identity …
- 12:03 PM Ticket #4979 (MatchMaker get percent identity from Python) closed by
- fixed: Now returns a dict that includes the initial pairings as well. Keep …
- 10:57 AM Ticket #4869 (Treat file suffixes as case independent) closed by
- fixed
- 10:45 AM ChangeLog edited by
- (diff)
- 9:56 AM Ticket #5040 (SSL failure during registration attempt) created by
- […]
- 9:41 AM Ticket #5039 ("sticky" cartoon settings) created by
- […]
- 5:50 AM Ticket #5038 (the problem with chimerax install) created by
- […]
Aug 10, 2021:
- 4:11 PM Ticket #4997 (Graphics slow showing huge structure) closed by
- not a bug: Ok. The temporary solution for saving the CA model is to use mmCIF …
- 4:07 PM ChangeLog edited by
- (diff)
- 3:57 PM Ticket #4343 (PDB writing: issue error/warning for long chain IDs) closed by
- fixed: Now issues warnings when writing atom names, residue names, or chain …
- 12:37 PM Ticket #5037 (Update ISOLDE rotamers: wrapped C/C++ object of type QTableWidget has ...) created by
- […]
- 12:02 PM Ticket #4983 (drag and drop has file: prepended) closed by
- fixed: Have committed a horrible hack to work around this problem. Hoping …
- 11:14 AM Ticket #5036 (Index error showing sequence feature) closed by
- fixed
- 11:01 AM Ticket #5036 (Index error showing sequence feature) created by
- […]
- 10:02 AM Ticket #5033 (Bad session file when maps included) closed by
- duplicate
- 9:59 AM Ticket #5035 (Report sequence identity from MAV) created by
- […]
- 8:59 AM 2021-8-12 created by
- 8:58 AM 2021-8-5 edited by
- (diff)
- 8:57 AM DeveloperMeetings edited by
- (diff)
- 8:46 AM Ticket #5032 (Crash opening PDB file) closed by
- duplicate
- 8:01 AM Ticket #5034 (Error in warning message when alias overridden) created by
- […]
- 7:17 AM Ticket #5033 (Bad session file when maps included) created by
- […]
Aug 9, 2021:
- 6:33 PM Ticket #5019 (Read mmCIF: not enough memory) closed by
- can't reproduce: On my Windows 10 system, albeit with 32GB, it loads just fine in …
- 6:15 PM Ticket #5032 (Crash opening PDB file) created by
- […]
- 6:09 PM Ticket #5030 (Crash opening PDB file) closed by
- duplicate
- 6:00 PM Ticket #5027 (Crash showing Open dialog) closed by
- can't reproduce: Opening from the toolbar. The Windows error code (well one of them, …
- 5:55 PM Ticket #5031 (How to copy a Sequence Viewer subsequence to the clip board) created by
- […]
- 5:07 PM Ticket #5030 (Crash opening PDB file) created by
- […]
- 5:06 PM Ticket #5029 (Crash opening PDB file) created by
- […]
- 4:54 PM Ticket #4501 (Easier import for MD) reopened by
- No option for the series slider yet
- 4:53 PM Ticket #4501 (Easier import for MD) closed by
- fixed: open MD formats now accept start/step/end keyword arguments (starting …
- 4:44 PM Ticket #5028 (cylinder arrowheads) created by
- […]
- 4:36 PM Ticket #5027 (Crash showing Open dialog) created by
- […]
- 2:34 PM Ticket #5025 (Graphics hardware encountered an error and was reset) closed by
- nonchimerax: Apple graphics driver crash, Intel graphics, two displays.
- 2:21 PM Ticket #5023 (Crash rending QGraphicsScene) closed by
- can't reproduce: This is the 6th report of this crash over the past 2 years, searching …
- 2:11 PM Ticket #5015 ('VolumeViewer' object has no attribute 'tool_window') closed by
- can't reproduce: Old version of ChimeraX (1.0). Unlikely this error still is present.
- 12:09 PM Ticket #5024 (Crash setting C++ pointer) closed by
- can't reproduce: If the Python backtrace is to be believed, it crashed in: …
- 11:52 AM Ticket #5022 (Open DICOM: 'MainWindow' object has no attribute 'folder_open_cb') closed by
- duplicate: Hi Yuji, Thanks for reporting this problem. It is fixed in the …
- 11:50 AM Ticket #5021 ('SaveModelOptionWidget' object has no attribute '_name') closed by
- duplicate
- 11:49 AM Ticket #5020 (Crash reading PDB file) closed by
- can't reproduce: Probably due to a non-ASCII character in the PDB file, which is fixed …
- 11:37 AM Ticket #5018 (Crash showing error dialog) closed by
- can't reproduce: Was trying to show the "bug level" error dialog (i.e. with the "Report …
- 11:18 AM Ticket #5016 (Crash closing tool) closed by
- can't reproduce: Crash in self.main_window.removeDockWidget(self.dock_widget). Had …
- 4:01 AM Ticket #5026 ('SplitStereoCamera' object has no attribute 'field_width') created by
- […]
Aug 8, 2021:
- 4:08 PM Ticket #5025 (Graphics hardware encountered an error and was reset) created by
- […]
- 1:19 AM Ticket #5024 (Crash setting C++ pointer) created by
- […]
- 12:28 AM Ticket #5023 (Crash rending QGraphicsScene) created by
- […]
Aug 7, 2021:
- 10:37 PM Ticket #5022 (Open DICOM: 'MainWindow' object has no attribute 'folder_open_cb') created by
- […]
- 9:59 PM Ticket #5021 ('SaveModelOptionWidget' object has no attribute '_name') created by
- […]
- 1:00 AM Ticket #5020 (Crash reading PDB file) created by
- […]
Aug 6, 2021:
- 9:21 PM Ticket #5019 (Read mmCIF: not enough memory) created by
- […]
- 8:56 PM Ticket #5018 (Crash showing error dialog) created by
- […]
- 5:26 PM Ticket #5017 (Matchmaker crash) created by
- […]
- 4:24 PM Ticket #5013 (Crash fetching from Toolshed) closed by
- can't reproduce: Need a person to work with on this.
- 1:02 PM Ticket #5016 (Crash closing tool) created by
- […]
- 12:02 PM Ticket #5015 ('VolumeViewer' object has no attribute 'tool_window') created by
- […]
- 11:05 AM Ticket #4349 (Startup error not reported) closed by
- fixed: The nogui UI class was adding a NoGuiLog to the logger stack very …
- 10:48 AM Ticket #5014 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) closed by
- duplicate
- 9:33 AM Ticket #5014 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) created by
- […]
- 9:25 AM Ticket #5012 (Graphics kernel error / crash in swap_buffers) closed by
- nonchimerax: Crash in Apple graphics driver adjusting volume threshold, Radeon Pro …
- 7:39 AM Ticket #5010 (Simulation doesn't start) closed by
- not a bug: Great to hear it! I'll go ahead and close this ticket as "not a bug" - …
- 5:53 AM Ticket #5013 (Crash fetching from Toolshed) created by
- […]
- 1:42 AM Ticket #5012 (Graphics kernel error / crash in swap_buffers) created by
- […]
Aug 5, 2021:
- 5:44 PM Ticket #4083 (need some way to see association when model color is white) closed by
- fixed: Put faint outline around white color swatch; color swatches react to …
- 3:24 PM 2021-8-5 edited by
- (diff)
- 3:22 PM Dev2021-8-5 edited by
- (diff)
- 3:03 PM Ticket #5009 (Crash in swap_buffers) closed by
- nonchimerax: Crash in Apple Radeon graphics driver.
- 3:01 PM Ticket #5007 (Pick surface(?): index is out of bounds for axis) closed by
- duplicate: Fixed a month ago. #4828
- 1:28 PM Ticket #4994 (AlphaFold fetch in getting attribute structure.chains) closed by
- can't reproduce: Updated my ChimeraX installation, and fetching the AlphaFold models …
- 12:08 PM 2021-8-5 edited by
- (diff)
- 11:50 AM 2021-8-5 edited by
- (diff)
- 11:49 AM 2021-8-5 edited by
- (diff)
- 11:49 AM 2021-8-5 edited by
- (diff)
- 11:48 AM 2021-8-5 edited by
- (diff)
- 11:13 AM 2021-8-5 edited by
- (diff)
- 11:09 AM 2021-8-5 edited by
- (diff)
- 10:46 AM Ticket #5011 (ChimeraX License) closed by
- fixed: Hi Aluisio, Our website is back up now. Please try again. --Eric …
- 10:27 AM Ticket #5011 (ChimeraX License) created by
- […]
- 2:16 AM Ticket #5010 (Simulation doesn't start) created by
- […]
- 1:24 AM Ticket #5009 (Crash in swap_buffers) created by
- […]
Aug 4, 2021:
- 7:58 PM Ticket #5008 (Better error reporting when web services are down) created by
- We should provide good error messages when ChimeraX web services are …
- 4:42 PM Ticket #5006 (Graphics kernel error) closed by
- nonchimerax: Apple graphics driver crash. Same as your previous crash reports …
- 4:29 PM Ticket #5005 (Dual display crash) closed by
- duplicate: Qt 5.12
- 4:09 PM Ticket #5007 (Pick surface(?): index is out of bounds for axis) created by
- […]
- 2:12 PM WikiStart edited by
- (diff)
- 2:01 PM Ticket #5006 (Graphics kernel error) created by
- […]
- 12:51 PM Ticket #5005 (Dual display crash) created by
- […]
- 11:54 AM Ticket #5004 (Sequence-Viewer-generated 'select' command bad if blank chain ID) closed by
- fixed: "concise_residue_spec" routine wasn't handling blank chain IDs correctly
- 11:43 AM Ticket #5004 (Sequence-Viewer-generated 'select' command bad if blank chain ID) created by
- […] blankchain.cxs
- 11:29 AM Ticket #4999 (Color key: ZeroDivisionError: float division by zero) closed by
- fixed: Creating a key with all the values the same failed. Fixed in …
- 10:31 AM Ticket #5001 (Unknown crash) closed by
- can't reproduce: Hi Jozef, Thanks for getting back to me. I tried truncating the N …
- 8:50 AM Ticket #5003 (Unable to open ChimeraX) created by
- […]
- 12:50 AM Ticket #5002 (Problem installing ISOLDE) created by
- […]
- 12:49 AM Ticket #5001 (Unknown crash) created by
- […]
Aug 3, 2021:
- 8:55 PM Ticket #3683 (Startup hangs on Windows when initial size spans two screens) closed by
- nonchimerax: Qt bug.
- 8:54 PM Ticket #3998 (TEMPy does not start with ChimeraX 1.1) closed by
- fixed: Greg Couch made Toolshed not offer Tempy in ChimeraX 1.0 and newer.
- 8:53 PM Ticket #3690 (ChimeraX hangs at startup, white window, two displays, Windows 10) closed by
- nonchimerax: Qt bug.
- 8:52 PM Ticket #3749 (ChimeraX compile fails on macOS 11.0 Big Sur) closed by
- fixed: Fixed. ChimeraX builds now work for macOS Big Sur (11.0) and Monterey …
- 8:50 PM Ticket #3784 (meeting: _decode_socket_message: source code string cannot contain ...) closed by
- can't reproduce: Never saw this error again. Probably requires some special network …
- 8:48 PM Ticket #3834 (Windows crash resizing main window) closed by
- nonchimerax: Qt bug.
- 8:47 PM Ticket #3840 (Font problems) closed by
- nonchimerax: Seems like a font installation problem on the computer and Qt not …
- 8:45 PM Ticket #4000 (SEQCROW uses deprecated PyQt5 imports) closed by
- fixed
- 8:44 PM Ticket #4012 (Error restoring session with embedded maps; text-color issue in bug ...) closed by
- can't reproduce: Do not have an example file that can reproduce this bug.
- 8:41 PM Ticket #4280 (Save movie image files numbered starting at 25 instead of 1) closed by
- not a bug
- 8:38 PM Ticket #4225 (Tomogram fetch hung) closed by
- can't reproduce
- 8:37 PM Ticket #4238 (Selection outline invisible on segmentations) closed by
- fixed
- 8:36 PM Ticket #4235 (RealSense camera interface pyrealsense2 not available for Python 3.8) closed by
- fixed: Python 3.8 and 3.9 versions were made available on PyPi.
- 8:33 PM Ticket #4367 (Startup message "Could not find virtual screen for QCocoaScreen") closed by
- can't reproduce: Have not seen this again.
- 8:28 PM Ticket #4938 (Crash saving image with surface) closed by
- can't reproduce: No response from reporter.
- 8:27 PM Ticket #4925 (Image transparency) closed by
- can't reproduce: No response from reporter.
- 8:24 PM Ticket #4998 (Graphics driver error on startup, Windows, Radeon graphics) closed by
- nonchimerax: The ChimeraX problem is due to a buggy Radeon graphics driver. You …
- 6:12 PM Ticket #4985 (Logged AlphaFold command link non-functional) closed by
- fixed: Fixed. Got rid of the "open #1 from alphafold" syntax which was …
- 3:28 PM Ticket #5000 (Test if crash reports include final command -- Yes.) closed by
- not a bug: Yes. Log in a crash report did contain the final command in this test.
- 3:23 PM Ticket #5000 (Test if crash reports include final command -- Yes.) created by
- […]
- 2:34 PM Ticket #4999 (Color key: ZeroDivisionError: float division by zero) created by
- […]
- 12:24 PM Ticket #4998 (Graphics driver error on startup, Windows, Radeon graphics) created by
- […]
- 9:30 AM Ticket #4934 (Crash computing clashes) closed by
- can't reproduce: Hi Maciek, Thanks for the info. Without a reproducible test case, it …
- 9:17 AM Ticket #4996 (Can't write PDB file) closed by
- can't reproduce: Hi Lenye, You should upgrade to the latest ChimeraX production …
- 3:51 AM Ticket #4997 (Graphics slow showing huge structure) created by
- […] 3kz4_CA_only.pdb
- 3:37 AM Ticket #4996 (Can't write PDB file) created by
- […]
Aug 2, 2021:
- 4:27 PM Ticket #4995 (Warn when ambient shadows are slowing down graphics) created by
- When moving an atomic model with the mouse while keeping other models …
- 4:07 PM Ticket #4981 (Bad AlphaFold model trimming) closed by
- fixed: Fixed. PDB 7ck3 chain A has two separate segments with uniprot ids in …
- 3:10 PM Ticket #4994 (AlphaFold fetch in getting attribute structure.chains) created by
- Reported by Tristan in comment 5 of ticket #4981: "open 6w1s; open #1 …
- 1:17 PM Ticket #4993 (Method to identify structure as AlphaFold model) created by
- OK, one more thing. :) It would be nice to have a supported …
- 11:28 AM 2021-8-5 edited by
- (diff)
- 11:27 AM 2021-8-5 created by
- 11:26 AM DeveloperMeetings edited by
- (diff)
- 11:14 AM Ticket #4992 (OpenGL startup errors) closed by
- nonchimerax: These ChimeraX startup errors indicate a problem in your graphics …
- 10:59 AM Ticket #4992 (OpenGL startup errors) created by
- […]
- 10:45 AM Ticket #4982 (UniProt identifier length) closed by
- fixed: This was fixed last Tuesday (July 27). Fix is is current daily builds. …
- 10:45 AM Ticket #4981 (Bad AlphaFold model trimming) reopened by
- Oops! Added the previous comment to the wrong ticket. This problem …
- 10:43 AM Ticket #4981 (Bad AlphaFold model trimming) closed by
- fixed: This was fixed last Tuesday (July 27). Fix is is current daily …
- 9:29 AM Ticket #4990 (Crash in garbage collection during new-object allocation) closed by
- can't reproduce
- 9:25 AM Ticket #4988 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) closed by
- duplicate
- 9:20 AM Ticket #4987 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) closed by
- duplicate
- 9:19 AM Ticket #4986 (Unknown crash) closed by
- can't reproduce: High memory use.
- 8:48 AM Ticket #4980 (Crash with trashed stack) closed by
- can't reproduce
- 8:31 AM Ticket #4991 (CA-only PDB shown as stick-dots) created by
- I couldn't think of a CA-only structure off the top of my head so I …
- 12:52 AM Ticket #4990 (Crash in garbage collection during new-object allocation) created by
- […]
Aug 1, 2021:
- 11:59 PM Ticket #4989 (OpenMM simulation: Graphics kernel error) created by
- […]
- 7:14 PM Ticket #4988 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) created by
- […]
- 7:11 PM Ticket #4987 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) created by
- […]
- 9:54 AM Ticket #4986 (Unknown crash) created by
- […]
- 9:44 AM Ticket #4985 (Logged AlphaFold command link non-functional) created by
- […]
- 6:34 AM Ticket #4984 (Crash in modal dialog) created by
- […]
- 3:06 AM Ticket #4983 (drag and drop has file: prepended) created by
- […]
- 3:04 AM Ticket #4982 (UniProt identifier length) created by
- […]
- 1:58 AM Ticket #4981 (Bad AlphaFold model trimming) created by
- […]
Jul 31, 2021:
Jul 30, 2021:
- 1:50 PM Ticket #4977 (Combine: trying to pass pointer of non-numpy object) closed by
- fixed
- 12:15 PM Ticket #4978 (How to show backbone atoms with ribbon) closed by
- not a bug: Send questions about how to use ChimeraX to chimera-users@… …
- 11:40 AM Ticket #4979 (MatchMaker get percent identity from Python) created by
- I call the matchmaker command (routine cmd_match) from Python in …
- 10:57 AM Ticket #4978 (How to show backbone atoms with ribbon) created by
- […]
- 8:52 AM Ticket #4977 (Combine: trying to pass pointer of non-numpy object) created by
- […]
- 2:44 AM Ticket #4976 (Possibly fetching 'residues' of dead Structure) created by
- […]
Jul 29, 2021:
- 3:16 PM Ticket #4974 (Graphics hardware encountered an error and was reset) closed by
- nonchimerax
- 3:06 PM Ticket #4966 (Alphafold: fetch the predicted aligned error file) closed by
- fixed: Cool. Seems to pick up several fragments (e.g. loops) that also are …
- 2:52 PM Ticket #4973 (Update NetworkX) closed by
- fixed: Done. Networkx updated to 2.6.2.
- 2:39 PM Ticket #2236 (Port Chimera's copy/combine) closed by
- fixed: 'combine' command available in tomorrow's build.
- 1:43 PM ChangeLog edited by
- (diff)
- 1:13 PM Ticket #4975 (Notification of new releases) created by
- It would be desirable for a user to be notified of new ChimeraX …
- 12:27 PM 2021-7-29 edited by
- (diff)
- 10:41 AM Ticket #4971 (Crash checking toolshed) closed by
- can't reproduce: Might be a Windows 7 issue related to its SSL support.
- 10:36 AM Ticket #4970 (Crash opening mmCIF) closed by
- can't reproduce: Need the data file that caused the problem to reproduce.
- 10:15 AM Ticket #4974 (Graphics hardware encountered an error and was reset) created by
- […]
- 9:37 AM Ticket #4972 (ISOLDE: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer') closed by
- fixed: This should be fixed in the latest ISOLDE version. Update your …
- 9:27 AM Ticket #4968 (Atom-spec parser stack overflow) closed by
- duplicate: Duplicate of #4842
- 9:23 AM Ticket #4973 (Update NetworkX) created by
- […]
- 9:14 AM Ticket #4972 (ISOLDE: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer') created by
- […]
- 12:45 AM Ticket #4971 (Crash checking toolshed) created by
- […]
- 12:22 AM Ticket #4970 (Crash opening mmCIF) created by
- […]
Jul 28, 2021:
- 9:03 PM Ticket #4969 (Improvements to fetching AlphaFold models) created by
- Many improvements to fetching AlphaFold models would be nice. 1) …
- 2:18 PM Ticket #4968 (Atom-spec parser stack overflow) created by
- […]
- 10:33 AM Ticket #4948 (volume gaussian bfactor off by factor of 3) closed by
- fixed: Fixed in tonight's build.
- 10:08 AM Ticket #4967 (Unknown crash) closed by
- can't reproduce
- 10:00 AM Ticket #4965 (sip crash on exit) closed by
- can't reproduce: The Qt window toolkit crashed with a floating point exception when …
- 9:48 AM Ticket #4967 (Unknown crash) created by
- […]
- 8:35 AM Ticket #4966 (Alphafold: fetch the predicted aligned error file) created by
- […]
- 4:22 AM Ticket #4965 (sip crash on exit) created by
- […]
- 12:00 AM Ticket #4964 (residue_graph: edges should be a n x 2 array of unsigned ints) created by
- […]
Jul 27, 2021:
- 8:00 PM Ticket #4963 (residue_graph: edges should be a n x 2 array of unsigned ints) created by
- […] combined_70S_model_no_tRNA.pdb
- 3:25 PM Ticket #4948 (volume gaussian bfactor off by factor of 3) reopened by
- I'm confused; in a previous comment comparing REFMAC and ChimeraX, …
- 11:29 AM Ticket #4957 (build start not adjusting for model position matrix) closed by
- fixed: Fix will be in tomorrow's build.
- 11:18 AM Ticket #4960 (Crash opening mmCIF) closed by
- can't reproduce: need the mmCIF file that caused the problem to reproduce
- 11:15 AM Ticket #4959 (Crash opening mmCIF) closed by
- can't reproduce: need the mmCIF file that caused the problem to reproduce
- 10:57 AM Ticket #4962 (Reduce bfactor sharpening noise) created by
- comment:9Changed 9 hours ago by Tristan Croll Comparing against …
- 10:57 AM Ticket #4948 (volume gaussian bfactor off by factor of 3) closed by
- fixed
- 10:35 AM Ticket #4807 (Saved PDB opens with bad record warning) closed by
- fixed: Wasn't recognizing record types with Windows line endings if the …
- 9:09 AM Ticket #4961 (Make resfit command work with nucleic acids) created by
- Begin forwarded message: From: Wen-Jin Winston Wu via ChimeraX-users …
- 9:06 AM Dev2021-8-5 created by
- 9:02 AM 2021-7-29 created by
- 9:01 AM DeveloperMeetings edited by
- (diff)
- 7:36 AM Ticket #4960 (Crash opening mmCIF) created by
- […]
- 7:35 AM Ticket #4959 (Crash opening mmCIF) created by
- […]
- 5:16 AM Ticket #4958 (peptide flip: Simulation must be running!) created by
- […]
Jul 26, 2021:
- 6:41 PM Ticket #4956 (Pseudobonds don't go to atom with ribbon when not hiding backbone atoms) closed by
- duplicate: Hi Jenny, Thanks for reporting this problem. It was fixed about two …
- 6:24 PM Ticket #4957 (build start not adjusting for model position matrix) created by
- I'm running into unexpected behavior when using the build tool. …
- 6:03 PM Ticket #4956 (Pseudobonds don't go to atom with ribbon when not hiding backbone atoms) created by
- […]
- 5:27 PM Ticket #4954 (Long atom spec crashes ChimeraX) closed by
- duplicate: Duplicate of #4842
- 5:22 PM Ticket #4955 (RFE: command to re-show nonstandard residues table) closed by
- not a bug: never mind, now I see that "log metadata" already includes the …
- 5:11 PM Ticket #4952 (Unknown crash) closed by
- can't reproduce: Was using about 8GB
- 5:03 PM Ticket #4955 (RFE: command to re-show nonstandard residues table) created by
- analogous to the nice new "log chains" command :-). Maybe "log …
- 4:38 PM Ticket #4954 (Long atom spec crashes ChimeraX) created by
- […]
- 3:45 PM Ticket #4953 (RFE: make "interfaces" command smarter about glycosylations) created by
- When I open 4n5z and enter "interfaces #1" it makes tiny disconnected …
- 2:53 PM Ticket #4423 (Suport LINKR records) closed by
- fixed: I ginned up a test case to try the change on, but you might want to …
- 2:30 PM Ticket #4952 (Unknown crash) created by
- […]
- 1:43 PM Ticket #4951 (fitmap: AttributeError: 'Volume' object has no attribute 'set_place') closed by
- fixed: Fixed. Placing the fit atomic model and undisplayed simulated map …
- 1:40 PM Ticket #4951 (fitmap: AttributeError: 'Volume' object has no attribute 'set_place') created by
- […]
- 1:23 PM Ticket #4949 (Graphics kernel error) closed by
- nonchimerax: Mac graphics driver crash painting Qt interface.
- 11:01 AM Ticket #4470 (Safeguard against accidental multi-residue swapaa) reopened by
- 10:47 AM Ticket #4950 (KeyError in map menu) closed by
- duplicate: Hi Ibrahim, I'm fairly certain that this is fixed in the latest …
- 10:17 AM Ticket #4950 (KeyError in map menu) created by
- […]
- 9:05 AM Ticket #4947 (Error using saved tool positioning) closed by
- duplicate
- 8:35 AM Ticket #4949 (Graphics kernel error) created by
- […]
- 3:14 AM Ticket #4948 (volume gaussian bfactor off by factor of 3) created by
- […]
Jul 25, 2021:
Jul 23, 2021:
- 11:26 AM Ticket #4945 (Volume mesh: masked_edges(): edge mask array size does not equal ...) closed by
- fixed: Fixed in tonight's daily build. This error was caused by using the …
- 8:41 AM Ticket #4946 (Crash with trashed stack) closed by
- can't reproduce
- 8:38 AM Ticket #4944 (Re: [chimerax-users] How to access ChimeraX remotely from macbook (OS ...) closed by
- not a bug: mistakenly cc'ed to chimera-bugs
- 4:39 AM Ticket #4946 (Crash with trashed stack) created by
- […]
- 4:19 AM Ticket #4945 (Volume mesh: masked_edges(): edge mask array size does not equal ...) created by
- […]
Jul 22, 2021:
- 6:16 PM Ticket #4944 (Re: [chimerax-users] How to access ChimeraX remotely from macbook (OS ...) created by
- […]
- 6:06 PM Ticket #4941 (log chains command: cannot import name 'cmd' from 'chimerax.atomic') closed by
- fixed: Committed cmd.py
- 5:56 PM Ticket #4939 (Session save error after screen disconnected) closed by
- duplicate
- 5:38 PM Ticket #4943 (Re: [chimerax-users] How to access ChimeraX remotely from macbook (OS ...) closed by
- duplicate: Misdirected response to #4943.
- 5:36 PM Ticket #4940 (How to access ChimeraX remotely from macbook (OS mojave)?) closed by
- nonchimerax: ChimeraX cannot make remote display of OpenGL work -- that is an X …
- 5:32 PM Ticket #4943 (Re: [chimerax-users] How to access ChimeraX remotely from macbook (OS ...) created by
- […]
- 4:46 PM Ticket #4942 (phenix connect command traceback when wrong Phenix directory given) created by
- […]
- 4:12 PM Dev2021-7-22 edited by
- (diff)
- 2:26 PM Ticket #4941 (log chains command: cannot import name 'cmd' from 'chimerax.atomic') created by
- […]
- 2:12 PM 2021-7-22 edited by
- (diff)
- 1:41 PM 2021-7-22 edited by
- (diff)
- 1:31 PM Ticket #4940 (How to access ChimeraX remotely from macbook (OS mojave)?) created by
- […]
- 1:17 PM 2021-7-22 edited by
- (diff)
- 1:16 PM 2021-7-22 edited by
- (diff)
- 1:14 PM 2021-7-22 edited by
- (diff)
- 1:02 PM Ticket #4939 (Session save error after screen disconnected) created by
- […]
- 11:16 AM Ticket #4936 (Graphics kernel error / crash in swap_buffers) closed by
- nonchimerax: Apple graphics driver crash. Unfortunately Apple's OpenGL graphics …
- 11:11 AM Ticket #4935 (scalar_width/height session restore not backwards compatible) closed by
- not a bug: In general a session saved in a newer ChimeraX version will not open …
- 9:04 AM Ticket #4937 (Non-standard hydrogen name) closed by
- duplicate
- 8:49 AM Ticket #4933 (FindHBond:: accPhiPsi() takes exactly 8 arguments (9 given)) closed by
- can't reproduce: Don't know why you would be looking for H-bonds _between_ docked …
- 8:37 AM Ticket #4932 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) closed by
- duplicate
- 8:35 AM Ticket #4931 (Non-standard hydrogen name) closed by
- duplicate
- 8:33 AM Ticket #4930 (Unknown crash) closed by
- can't reproduce: That Windows error is suposedly RPC_E_CANTCALLOUT_ININPUTSYNCCALL
- 8:09 AM Ticket #4938 (Crash saving image with surface) created by
- […]
- 7:26 AM Ticket #4937 (Non-standard hydrogen name) created by
- […]
- 6:19 AM Ticket #4936 (Graphics kernel error / crash in swap_buffers) created by
- […]
- 3:53 AM Ticket #4935 (scalar_width/height session restore not backwards compatible) created by
- […] dj-1-22-jul-21.cxs
- 2:21 AM Ticket #4934 (Crash computing clashes) created by
- […]
- 12:43 AM Ticket #4933 (FindHBond:: accPhiPsi() takes exactly 8 arguments (9 given)) created by
- […]
Jul 21, 2021:
- 11:45 PM Ticket #4932 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) created by
- […]
- 9:00 PM Ticket #4931 (Non-standard hydrogen name) created by
- […]
- 8:38 PM Ticket #4923 (macOS build problems on Big Sur caused by wheel file names) closed by
- fixed: Fixed. Builds on macOS 11 now work with "make build-from-scratch" …
- 7:31 PM Ticket #3862 (Tracebacks when exiting on Windows during meeting) closed by
- can't reproduce: Have not seen this again.
- 7:29 PM Ticket #4679 (Crash initially showing Rapid Access) closed by
- can't reproduce: Now there are about 20 reports mostly on Linux, some on Windows, never …
- 6:42 PM Ticket #4726 (Crash initially showing Rapid Access) closed by
- can't reproduce: The fix I tried for this ChimeraX startup crash on Linux of waiting …
- 6:37 PM Ticket #4930 (Unknown crash) created by
- […]
- 6:33 PM Ticket #4904 (Unknown crash) closed by
- can't reproduce: See if we get more crashes using Color Actions. Not enough info in …
- 3:51 PM Ticket #2938 (command to re-show chain table) closed by
- fixed: Implemented as "log chains [model spec]" command. "sequence" commands …
- 10:45 AM Ticket #4929 (Crash in make_current) closed by
- can't reproduce: Crashed on Windows, ChimeraX 1.2.4, when resizing the graphics window. …
- 10:01 AM Ticket #4929 (Crash in make_current) created by
- […]
- 9:29 AM Ticket #4928 (Unknown crash) closed by
- can't reproduce
- 9:14 AM Ticket #4928 (Unknown crash) created by
- […]
- 6:45 AM Ticket #4927 (unknown crash) created by
- […]
Jul 20, 2021:
- 11:08 PM Ticket #4926 (Unknown crash) created by
- […]
- 1:35 PM Ticket #4925 (Image transparency) created by
- […] [[Image(...)]]
- 1:25 PM Ticket #4924 (AlphaFold2 in Google Collab notebook) created by
- […]
- 12:04 PM Ticket #4921 (color byattr: min() arg is an empty sequence) closed by
- fixed: Hi Guillaume, Thanks for supplying the alignment. This problem is …
- 10:58 AM 2021-7-22 edited by
- (diff)
- 10:47 AM Ticket #4906 (Option SpinBox already deleted) closed by
- can't reproduce: Okay, I was able to reproduce it once, but now I can't. This should …
- 10:45 AM Ticket #4923 (macOS build problems on Big Sur caused by wheel file names) created by
- On macOS Big Sur, 11.x, the ChimeraX build fails because bundle wheel …
- 10:13 AM 2021-7-22 created by
- 10:12 AM DeveloperMeetings edited by
- (diff)
- 9:54 AM Ticket #4922 (Permission denied saving .cmap file) closed by
- not a bug: User tried to save a file to a directory where they did not have …
- 9:24 AM Ticket #4919 (Unknown crash) closed by
- can't reproduce
- 9:23 AM Ticket #4918 (Crash showing Open dialog) closed by
- can't reproduce: This supposedly a "wrong thread" error, but I fail to see how that is …
- 8:18 AM Ticket #4922 (Permission denied saving .cmap file) created by
- […]
- 1:50 AM Ticket #4921 (color byattr: min() arg is an empty sequence) created by
- […] macro_for_consurf_pdb_ATOMS_section_With_ConSurf.pdb
- 1:12 AM Ticket #4920 (Crash in matplotlib updating Ramachandran plot) created by
- […]
- 12:50 AM Ticket #4919 (Unknown crash) created by
- […]
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