![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Dec 31, 2020:
- 4:23 PM ChangeLog edited by
- (diff)
- 2:17 PM Ticket #4101 (Problem downloading ChimeraX: "The URL you used has expired") created by
- […]
- 1:25 PM Ticket #4100 (glUniformMatrix4fv: invalid operation) created by
- […]
- 11:57 AM Ticket #4098 (Session file not recognized) closed by
- not a bug: Turns out the extension should have been .cxc
- 4:20 AM Ticket #4099 (No matching residues in matchmaker sequence alignment) created by
- […]
Dec 30, 2020:
- 5:08 PM Ticket #3055 (Add ParmEd to ChimeraX's standard bundles) closed by
- fixed: Installed ParmEd as a prereq. It adds 4.6M to the distribution (on Mac).
- 4:25 PM Ticket #4084 (Wrong numpy parsing in Coulombic C++ module) closed by
- fixed: Thanks, have fixed that up. I found the documentation in the various …
- 9:58 AM Ticket #4098 (Session file not recognized) created by
- […]
- 9:44 AM Ticket #4097 (Error in error message reinstalling bundle) closed by
- duplicate
- 8:22 AM Ticket #4097 (Error in error message reinstalling bundle) created by
- […]
Dec 29, 2020:
Dec 28, 2020:
- 5:34 PM Ticket #4095 (VR initialization failure) created by
- […]
- 4:00 PM Ticket #4091 (Python shell autocomplete: _queue.Empty) closed by
- fixed: ipython implicitly relies on the 'jedi' module for auto-completion, …
- 3:57 PM Ticket #4094 (Python shell autocomplete: _queue.Empty) closed by
- duplicate: Duplicate of #4091; adding Tom to recipient list for that ticket
- 12:58 PM Ticket #4094 (Python shell autocomplete: _queue.Empty) created by
- […]
- 10:24 AM 2020-12-17 edited by
- (diff)
- 9:37 AM Ticket #4092 (Toolshed using internal UI API) closed by
- duplicate
- 9:34 AM Ticket #4090 (Toolshed using internal UI API) closed by
- duplicate
- 9:32 AM Ticket #4089 (Nucleotides: point is None) closed by
- duplicate: I believe this was fixed awhile ago.
- 9:29 AM Ticket #4088 (Crash moving window) closed by
- can't reproduce
- 6:56 AM Ticket #4093 (OpenMM crash uploading OpenCL array) created by
- […]
- 12:06 AM Ticket #4092 (Toolshed using internal UI API) created by
- […]
Dec 27, 2020:
Dec 26, 2020:
- 7:15 PM Ticket #4090 (Toolshed using internal UI API) created by
- […]
- 12:03 PM Ticket #4089 (Nucleotides: point is None) created by
- […]
Dec 23, 2020:
- 8:00 PM Ticket #4088 (Crash moving window) created by
- […]
- 5:45 PM Ticket #4087 (Wide tool can nuke graphics window) created by
- Opening the attached alignment on the right side of the main window …
- 5:20 PM Ticket #4075 (Error saving tool position of stacked tool) closed by
- fixed: Fixed. PyQt returned an int for which side the tool was on, whereas …
- 10:12 AM Ticket #4086 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) closed by
- fixed: Hi Roberto, Thanks for reporting this problem. It has been fixed in …
- 2:53 AM Ticket #4086 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) created by
- […]
Dec 22, 2020:
- 10:03 PM Ticket #4085 (Webcam command broken by pyside2) created by
- […]
- 10:00 PM Ticket #4068 (Programmer documentation missing atomic and map_data classes) closed by
- fixed: Fixed. Took out the LD_LIBRARY_PATH fix that allowed Sphinx to import …
- 9:54 PM Ticket #4073 (Need reliable linking for python C++ modules using libarrays) closed by
- fixed: Fixed. Made all 21 C++ Python modules that depend on libarrays call …
- 6:18 PM Ticket #4084 (Wrong numpy parsing in Coulombic C++ module) created by
- The code in Coulombic esp.cpp in potential_at_points() for parsing …
- 4:16 PM Ticket #4080 (drag-select rectangle invisible on gray background) closed by
- fixed: Fixed. Made the selection drag box always green against any …
- 1:01 PM Ticket #4083 (need some way to see association when model color is white) created by
- If the model color is white and I associate it with a sequence, you …
- 11:55 AM Ticket #4082 (over-selection when clicking feature regions in Sequence Viewer) closed by
- fixed: The code to form a "concise residue spec" from a set of residues was wrong.
- 10:21 AM ChangeLog edited by
- (diff)
- 10:01 AM Ticket #4079 (Crash rendering scene graph) closed by
- can't reproduce
- 9:14 AM Ticket #4082 (over-selection when clicking feature regions in Sequence Viewer) created by
- open uniprot:pdcd1_human open 3bp5 sequence associate /A pdcd1_human …
- 8:38 AM Ticket #4081 (Sequence Viewer assoc dialog incorrectly says not associated) created by
- Opening the attached cxc file fetches uniprot sequences and associates …
- 8:30 AM Ticket #4080 (drag-select rectangle invisible on gray background) created by
- The drag-select rectangle shows as a green line against black …
- 12:15 AM Ticket #4079 (Crash rendering scene graph) created by
- […]
Dec 21, 2020:
- 6:34 PM Ticket #4078 (Testing bug reporter improved error message code) closed by
- fixed: Working.
- 6:31 PM Ticket #4076 (Bug report with bug-reporter failure(!)) closed by
- fixed: Fixed. The bug reporter traceback was from submitting the bug with no …
- 6:27 PM Ticket #4078 (Testing bug reporter improved error message code) created by
- […]
- 4:51 PM Ticket #840 (Make 2d labels a model shown in Model Panel) closed by
- fixed: This was implemented long ago.
- 3:29 PM Ticket #4077 (labels with onTop false have silhouette edge rectangles) created by
- with labels onTop false and graphics silhouette true, all of the 3D …
- 1:59 PM ChangeLog edited by
- (diff)
- 1:48 PM Ticket #4074 (ValueError after closing one session and opening another) closed by
- can't reproduce: Unfortunately the problem (Sequence Viewer showing alignment not …
- 10:17 AM Ticket #4072 (ValueError after closing one session and opening another) closed by
- duplicate: Now in ticket #4074
Dec 20, 2020:
Dec 18, 2020:
- 10:01 PM Ticket #4075 (Error saving tool position of stacked tool) created by
- […]
- 7:30 PM Ticket #4074 (ValueError after closing one session and opening another) created by
- […]
- 6:14 PM Ticket #4073 (Need reliable linking for python C++ modules using libarrays) created by
- About 35 modules of ChimeraX have C++ code that uses the arrays module …
- 3:29 PM Ticket #4072 (ValueError after closing one session and opening another) created by
- […]
- 12:54 PM Ticket #4065 (Opening .nc file: No module named 'Scientific') closed by
- fixed: Fixed netcdf map reader. It was never ported from Chimera 1 and was …
- 11:44 AM Ticket #4071 (Sphinx doesn't like indentation of some code comments) created by
- Make install in docs/devel is issuing warnings from Sphinx that …
- 11:31 AM Ticket #4070 (Error in save error message) closed by
- duplicate
- 11:17 AM Ticket #4070 (Error in save error message) created by
- […]
- 10:22 AM Ticket #4069 (Toolshed using internal UI API) closed by
- duplicate
- 1:55 AM Ticket #4069 (Toolshed using internal UI API) created by
- […]
Dec 17, 2020:
- 9:27 PM Ticket #4066 (Meeting name case sensitive) closed by
- fixed: Fixed. New code that checks a joiners initial message to make sure …
- 7:38 PM 2020-12-17 edited by
- (diff)
- 6:40 PM Ticket #4068 (Programmer documentation missing atomic and map_data classes) created by
- Lots of ChimeraX APIs such as Atoms are Atom are not in the …
- 4:18 PM NeteSOW edited by
- (diff)
- 2:21 PM NeteSOW edited by
- (diff)
- 12:15 PM Ticket #3716 (Error within error message) closed by
- duplicate: Duplicate of #3896.
- 12:14 PM Ticket #3874 (Error in error message reinstalling bundle) closed by
- duplicate: Duplicate of #3896
- 11:18 AM 2020-12-17 edited by
- (diff)
- 11:18 AM 2020-12-17 edited by
- (diff)
- 11:09 AM Ticket #4067 (ChimeraX distribution is too big, over 1 Gbyte uncompressed) created by
- We need to look into trimming ChimeraX bloat. It is absolutely …
- 9:43 AM Ticket #4066 (Meeting name case sensitive) created by
- […]
- 9:26 AM Ticket #4064 (Opening .nc file: No module named 'Scientific') closed by
- duplicate: Duplicate of #4065
- 9:18 AM 2020-12-17 edited by
- (diff)
- 2:29 AM Ticket #4065 (Opening .nc file: No module named 'Scientific') created by
- […]
- 2:24 AM Ticket #4064 (Opening .nc file: No module named 'Scientific') created by
- […]
Dec 16, 2020:
- 11:26 AM Ticket #4060 (VR meeting: LZ4F_decompress failed with code: ERROR_frameSize_wrong) closed by
- can't reproduce: I think we can only wait and see if this error occurs again. Phil, …
- 11:20 AM Ticket #4062 (Toolshed using internal UI API) closed by
- duplicate: Fixed in daily build. Duplicate of #3905.
- 11:18 AM Ticket #4061 (Coulombic: local variable 'cmap' referenced before assignment) closed by
- fixed
- 10:49 AM Ticket #4063 (Selection: Attempt to call an undefined function glBlitFramebuffer) closed by
- can't reproduce: I don't think this error message about not finding the standard OpenGL …
- 10:40 AM Ticket #4059 (Crash popping up menu, two screens, macOS) closed by
- duplicate: Duplicate. Supposedly fixed in Qt 5.15.2 which we updated to two days …
- 9:53 AM Ticket #4063 (Selection: Attempt to call an undefined function glBlitFramebuffer) created by
- […] 5F19_-_WT_-_minimized_-_All.pdb
- 9:38 AM Ticket #4057 (Toolshed using internal UI API) closed by
- duplicate
- 9:00 AM Ticket #4062 (Toolshed using internal UI API) created by
- […]
- 7:04 AM Ticket #4061 (Coulombic: local variable 'cmap' referenced before assignment) created by
- […]
- 6:23 AM Ticket #4060 (VR meeting: LZ4F_decompress failed with code: ERROR_frameSize_wrong) created by
- […]
Dec 15, 2020:
- 10:26 PM Ticket #4059 (Crash popping up menu, two screens, macOS) created by
- […]
- 6:53 PM Ticket #4058 (Volume Viewer: RuntimeWarning: overflow encountered in log) closed by
- fixed: Fixed. I changed the volume viewer code to use float64 for counts …
- 5:41 PM Ticket #4058 (Volume Viewer: RuntimeWarning: overflow encountered in log) created by
- […]
- 4:36 PM Ticket #4057 (Toolshed using internal UI API) created by
- […]
- 3:40 PM Ticket #3974 (Something broke in the PBD look up) closed by
- can't reproduce: Are you certain that there isn't some other output file from Robetta …
- 12:47 PM 2020-12-17 edited by
- (diff)
- 10:15 AM 2020-12-17 created by
- 10:11 AM DeveloperMeetings edited by
- (diff)
- 9:24 AM Ticket #4056 (Toolshed internal UI API) closed by
- duplicate: Already fixed I believe.
- 8:06 AM Ticket #4056 (Toolshed internal UI API) created by
- […]
Dec 14, 2020:
- 4:32 PM Ticket #3853 (Bug in chimeraX 1.1 version) closed by
- can't reproduce: No response from request for more information.
- 3:06 PM Ticket #4055 (Problem with open-command providers after bundle reinstall) created by
- […]
- 3:00 PM Ticket #4010 (Adding second residue to Chain makes new Chain) closed by
- fixed: Apparently already fixed in the daily build. However, the daily build …
- 1:47 PM Ticket #4054 (Cannot make a tool undockable) closed by
- fixed: Fixed. Bug introduced when converting PyQt5 to PySide2. Dockable and …
- 1:26 PM Ticket #4052 (Crash destroying/disconnecting screen) closed by
- duplicate: Crash when second screen disconnected. I guess ChimeraX was on an …
- 1:22 PM Ticket #4050 (Crash changing screens) closed by
- duplicate: Duplicate of #3682. Fixed in daily builds.
- 12:46 PM Ticket #4054 (Cannot make a tool undockable) created by
- […]
- 12:02 PM Ticket #3383 (Redirect Python logging to the ChimeraX log) closed by
- fixed: Removed the explicit (and less flexible) support for Python logging …
- 11:36 AM Ticket #4049 (Crash posting popup menu on dual monitor) closed by
- can't reproduce
Dec 13, 2020:
Dec 12, 2020:
- 4:38 PM Ticket #4052 (Crash destroying/disconnecting screen) created by
- […]
- 2:22 PM WikiStart edited by
- (diff)
- 2:19 PM WikiStart edited by
- (diff)
- 2:18 PM WikiStart edited by
- (diff)
- 2:18 PM Funding created by
- 10:47 AM Ticket #4051 (Open imod contours: TypeError: int expected instead of float) closed by
- fixed: Fixed. Code tried to set contour link color using float rgba instead …
- 10:44 AM Ticket #4051 (Open imod contours: TypeError: int expected instead of float) created by
- […]
- 2:38 AM Ticket #4050 (Crash changing screens) created by
- […]
Dec 11, 2020:
- 9:20 PM Ticket #4049 (Crash posting popup menu on dual monitor) created by
- […]
- 6:47 PM Ticket #4048 (Replace PyOpenGL with Qt OpenGL API) created by
- Might want to drop PyOpenGL and call OpenGL functions through PySide2. …
- 5:18 PM Ticket #4027 (AddH wheel on Toolshed won't install: wheel filename has py38 instead ...) closed by
- fixed: The AddH wheel is now just "py3".
- 5:14 PM Ticket #4047 (Crash while garbage collecting during object allocation) closed by
- duplicate: Duplicate of #3949
- 5:00 PM Ticket #3986 (Volume Viewer step/style menus only accept press in middle macOS, Qt 5.15) closed by
- fixed: Fixed. Removed setting style sheet on volume view step and style menu …
- 2:16 PM Ticket #3946 (Make OpenFileNameArg check that file exists) closed by
- fixed: The various open/save arg types now have a 'check_existence' class …
- 12:57 PM Ticket #4047 (Crash while garbage collecting during object allocation) created by
- […]
- 12:02 PM Ticket #4046 (Toolshed error in "already installed" error message) closed by
- duplicate: Hi Brian, Thanks for reporting this problem. The Toolshed is trying …
- 11:56 AM Ticket #4046 (Toolshed error in "already installed" error message) created by
- […]
- 10:11 AM Ticket #4044 (MemoryError restoring map from session) closed by
- nonchimerax: Out of memory. Not sure if you are showing a huge structure or if you …
- 10:06 AM Ticket #4043 (Graphics hardware encountered an error and was reset) closed by
- nonchimerax: Buggy Apple graphics driver: "Graphics hardware encountered an error …
- 9:49 AM Ticket #4045 (Toolshed error in "already installed" error message) closed by
- duplicate
- 9:40 AM Ticket #4042 (Crash while garbage collecting during object allocation) closed by
- duplicate: Duplicate of #3949
- 5:26 AM Ticket #4045 (Toolshed error in "already installed" error message) created by
- […]
- 2:06 AM Ticket #4044 (MemoryError restoring map from session) created by
- […]
- 1:53 AM Ticket #4043 (Graphics hardware encountered an error and was reset) created by
- […]
Dec 10, 2020:
- 8:38 PM Ticket #4042 (Crash while garbage collecting during object allocation) created by
- […]
- 8:33 PM Ticket #1635 (Replace PyQt5 with PySide2) closed by
- fixed: Done. The switch to PySide2 was done a weeks ago in daily builds and …
- 8:10 PM Ticket #3760 (Startup warning: Unable to load numpy_formathandler accelerator from ...) reopened by
- On Windows binary wheel for PyOpenGL-accelerate for Python 3.8 is …
- 7:40 PM 2020-12-10 edited by
- (diff)
- 7:38 PM 2020-12-10 edited by
- (diff)
- 12:06 PM Ticket #4041 ("sel" specifier vs. "select" keyword) created by
- […]
- 11:43 AM Ticket #4040 (Crash in QtWebEngineCore) created by
- […]
- 11:18 AM Ticket #4033 (AddH not installable into ChimeraX 1.1 due to "py38" in wheel name) closed by
- fixed
- 11:15 AM Ticket #4037 (Could not find a version that satisfies the requirement ...) closed by
- fixed: Hi Michael, Thanks for reporting this problem. We believe it is …
- 10:56 AM Ticket #4039 (Splash screen crash report that was not a crash) closed by
- can't reproduce: The Python traceback is when calling sess.ui.splash_info("Starting …
- 10:41 AM Ticket #4039 (Splash screen crash report that was not a crash) created by
- […]
- 10:28 AM 2020-12-10 edited by
- (diff)
- 10:25 AM 2020-12-10 created by
- 10:19 AM DeveloperMeetings edited by
- (diff)
- 9:52 AM Ticket #4038 (ISOLDE: OpenMM: residue_graph: edges should be a n x 2 array of ...) closed by
- duplicate: Duplicate of #4016
- 5:26 AM Ticket #4038 (ISOLDE: OpenMM: residue_graph: edges should be a n x 2 array of ...) created by
- […]
- 3:45 AM Ticket #4037 (Could not find a version that satisfies the requirement ...) created by
- […]
Dec 9, 2020:
- 6:14 PM Ticket #3383 (Redirect Python logging to the ChimeraX log) reopened by
- From an email by Tom Goddard: ChimeraX startup is currently showing …
- 5:40 PM Ticket #3760 (Startup warning: Unable to load numpy_formathandler accelerator from ...) closed by
- fixed: Fixed. PyOpenGL-accelerate only compiles the numpy_formathandler …
- 1:37 PM Ticket #4036 (crash in set_alt_loc) closed by
- fixed: One of the set_alt_loc() routines hadn't been marked up as capable of …
- 12:29 PM Ticket #4036 (crash in set_alt_loc) created by
- […]
Dec 8, 2020:
- 7:42 PM Ticket #4035 (Problem installing ISOLDE) created by
- […]
- 7:34 PM Ticket #3898 (Toolshed Python 3.8 bundle won't install in Python 3.7) closed by
- fixed
- 6:55 PM Ticket #4034 (Error adding tool in favorites menu, PySide2 issue) closed by
- fixed: Fixed. Some code to handle PySide2 QAction signal argument …
- 6:48 PM Ticket #4034 (Error adding tool in favorites menu, PySide2 issue) created by
- […]
- 5:20 PM Ticket #4032 ("toolshed install" not allowing upgrade) closed by
- fixed: The fix is the same as #3996. "toolshed install" used to need the …
- 2:53 PM Ticket #4029 (glClear: invalid enumerant) closed by
- nonchimerax: This error is likely a bad graphics driver. Possibly your machine …
- 2:28 PM Ticket #4030 (Crash in graphics driver) closed by
- nonchimerax: Apple graphics driver bug. "Graphics hardware encountered an error …
- 2:27 PM Ticket #4028 (Crash in shader / graphics driver) closed by
- nonchimerax: Apple Intel graphics driver crash. "Graphics hardware encountered an …
- 1:15 PM Ticket #4033 (AddH not installable into ChimeraX 1.1 due to "py38" in wheel name) created by
- […]
- 1:13 PM Ticket #4031 (self.main_window is None) closed by
- can't reproduce: Probably the "topLevelChanged" signal fired after the tool was …
- 11:45 AM Ticket #4032 ("toolshed install" not allowing upgrade) created by
- […]
- 9:58 AM Ticket #4013 (macOS daily build, "developer can't be verified", even though ...) closed by
- fixed: Fixed. New PySide2 releases may add or remove external non-system …
- 8:44 AM Ticket #4031 (self.main_window is None) created by
- […]
- 8:12 AM Ticket #4030 (Crash in graphics driver) created by
- […]
- 5:55 AM Ticket #4029 (glClear: invalid enumerant) created by
- […]
Dec 7, 2020:
- 5:57 PM Ticket #4028 (Crash in shader / graphics driver) created by
- […]
- 5:51 PM Ticket #4026 (Contour level mouse mode: UnboundLocalError: local variable 'levels') closed by
- fixed: Fixed. Volume was shown but surface and image models were …
- 5:36 PM Ticket #4025 (macOS: Graphics hardware encountered an error) closed by
- nonchimerax: Apple graphics driver bug.
- 5:35 PM Ticket #4024 (macOS: Graphics hardware encountered an error) closed by
- nonchimerax: Apple graphics driver bug.
- 6:22 AM Ticket #4027 (AddH wheel on Toolshed won't install: wheel filename has py38 instead ...) created by
- […]
Dec 6, 2020:
Dec 5, 2020:
- 6:26 PM Ticket #4025 (macOS: Graphics hardware encountered an error) created by
- […]
- 6:20 PM Ticket #4024 (macOS: Graphics hardware encountered an error) created by
- […]
- 7:05 AM Ticket #4023 (Better error handling on web service failure) created by
- […]
Dec 4, 2020:
- 8:00 PM Ticket #4022 (Testing crash reporting on Linux) closed by
- fixed: Working.
- 7:57 PM Ticket #4022 (Testing crash reporting on Linux) created by
- […]
- 7:49 PM Ticket #4021 (Testing crash reporting on Windows) closed by
- fixed: Works. Will be interesting to see how many crashes get reported on …
- 7:46 PM Ticket #4021 (Testing crash reporting on Windows) created by
- […]
- 7:33 PM Ticket #4020 (Testing adding python tracebacks to crash reports) closed by
- fixed: Python tracebacks in crash report working on Mac.
- 7:30 PM Ticket #4020 (Testing adding python tracebacks to crash reports) created by
- […]
- 11:06 AM Ticket #4019 (Allow surface and mesh levels in Volume Viewer) created by
- On 4 Dec 2020, at 15:08, Daniel Larsson wrote: Hi Elaine, Thank you …
- 9:03 AM Ticket #4017 (Crash showing tooltip) closed by
- can't reproduce
- 8:57 AM Ticket #4014 (ISOLDE installed but not Clipper dependency) closed by
- duplicate: Duplicate of #4015
- 6:10 AM Ticket #4018 (ISOLDE: OpenMM: find_glycan_template_name_and_link: multiple bonds ...) created by
- […]
- 6:09 AM Ticket #4017 (Crash showing tooltip) created by
- […]
- 4:12 AM Ticket #4016 (ISOLDE: OpenMM: residue_graph: edges should be a n x 2 array of ...) created by
- […]
- 3:53 AM Ticket #4015 (ISOLDE installed but not Clipper dependency) created by
- […]
- 3:52 AM Ticket #4014 (ISOLDE installed but not Clipper dependency) created by
- […]
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