![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
May 16, 2024:
- 9:36 PM Ticket #15237 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by
- […]
- 6:00 PM Ticket #15225 (AlphaFold3 PAE plot for phospho-protein not working) closed by
- fixed: Fixed in May 16 daily build or 1.8 release candidate. AlphaFold 3 …
- 4:50 PM Ticket #15236 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 4:21 PM Ticket #15217 (Amide nitrogens mistyped as N2) closed by
- fixed: Fixed, committed on the release candidate and daily branches. Fix: …
- 4:18 PM Ticket #15236 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 3:40 PM Ticket #15164 (Segmentations tool lists misleading ID numbers) closed by
- fixed: OK, I've pushed a …
- 2:55 PM Ticket #15209 (simplify "segmentations" command keyword options) closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/a20a72920482207a3b654be82f5e67 …
- 2:30 PM Ticket #15235 (Crash changing Mac display configuration) closed by
- can't reproduce: Crash in displayConfigFinalizedProc(). Not sure why we are seeing …
- 2:05 PM Ticket #15234 (AlphaFold Error Plot: IndexError: list index out of range) closed by
- duplicate
- 2:01 PM Ticket #15233 (Can't save session because NewerVersionQuery not listed) closed by
- duplicate
- 1:58 PM Ticket #15232 (Crash in garbage collection) closed by
- duplicate
- 1:58 PM Ticket #15231 (MD Viewer: self.atomLocation[0]: list index out of range) closed by
- not a bug
- 1:44 PM Ticket #15230 (Crash in garbage collection) closed by
- duplicate
- 1:25 PM Ticket #15228 (Crash in event loop, possibly remote display) closed by
- can't reproduce
- 10:55 AM Ticket #9526 (DICOM Segmentations: include SEG models opened from DICOM in the list ...) closed by
- fixed: Should be …
- 10:54 AM Ticket #15163 (Segmentations tools does not list segmentation models read from file ...) closed by
- fixed: Should be fixed in …
- 10:52 AM 2024-5-16 edited by
- (diff)
- 10:52 AM Ticket #10341 (Segmentations saved in sessions can't be edited) closed by
- fixed: Fixed in …
- 6:14 AM Ticket #15235 (Crash changing Mac display configuration) created by
- […]
- 4:37 AM Ticket #15234 (AlphaFold Error Plot: IndexError: list index out of range) created by
- […]
- 4:37 AM Ticket #15233 (Can't save session because NewerVersionQuery not listed) created by
- […]
- 2:14 AM Ticket #15232 (Crash in garbage collection) created by
- […]
- 1:02 AM Ticket #15231 (MD Viewer: self.atomLocation[0]: list index out of range) created by
- […]
- 12:46 AM Ticket #15230 (Crash in garbage collection) created by
- […]
May 15, 2024:
- 11:21 PM Ticket #15229 (Crash attaching file for bug report) created by
- […]
- 10:03 PM Ticket #15228 (Crash in event loop, possibly remote display) created by
- […]
- 4:21 PM Ticket #15227 (Make alphafold interfaces command work with protein + ligand predictions) created by
- AlphaFold 3 can predict protein + ligand structures. The current …
- 2:12 PM Ticket #15226 (binary wheels generated via pyproject.toml have wrong name on linux) created by
- I just noticed that the AlignmentHdrs and Core wheels use linux_x86_64 …
- 12:11 PM Ticket #15225 (AlphaFold3 PAE plot for phospho-protein not working) created by
- […] fold_pp1_neurabin_4ebp1_70pt_full_data_0.json …
- 11:14 AM Ticket #15191 (ChimeraX cannot find MD/Ensemble Analysis option) closed by
- nonchimerax: "MD/Ensemble Analysis" is a tool category for our older Chimera …
- 11:04 AM Ticket #15218 (Two AlphaFold3 problems) closed by
- duplicate: Fixed in the current ChimeraX daily build. AlphaFold 3 has PAE values …
- 11:03 AM Ticket #15216 (AlphaFold3 with ligands PAE json file: number of structure residues ...) closed by
- duplicate: Fixed in the current ChimeraX daily build. AlphaFold 3 has PAE values …
- 11:02 AM Ticket #15214 (AlphaFold3 with ligands PAE json file: number of structure residues ...) closed by
- duplicate: Yes it is fixed in the current ChimeraX daily build. AlphaFold 3 has …
- 10:53 AM Ticket #15224 (ChimeraX tries to open debugger arguments as if they were files) created by
- When started with a debugger (at least on Mac), ChimeraX somehow gets …
- 10:27 AM Ticket #15222 (Crash in Open→File dialog) closed by
- can't reproduce
- 10:25 AM Ticket #15221 (2D Labels: QColor arguments wrong) closed by
- duplicate: Duplicate of #15112 Looks like a second person used the 'outline' option.
- 10:21 AM Ticket #15220 (OSError in python_instances_of_class) closed by
- duplicate
- 10:20 AM Ticket #15223 (DICOM: Models that track their children in auxiliary data structures ...) created by
- 10:18 AM Ticket #15219 (Crash in garbage collection) closed by
- duplicate
- 10:10 AM Ticket #15215 (Crash in python_instances_of_class) closed by
- duplicate
- 9:12 AM Ticket #15204 (Crash in garbage collection) closed by
- duplicate: Hi Hui-Ting, Thanks for reporting this problem. It is fixed in the …
- 9:04 AM Ticket #15222 (Crash in Open→File dialog) created by
- […]
- 8:42 AM Ticket #15221 (2D Labels: QColor arguments wrong) created by
- […]
- 7:50 AM Ticket #15220 (OSError in python_instances_of_class) created by
- […]
- 7:34 AM Ticket #15219 (Crash in garbage collection) created by
- […]
- 6:37 AM Ticket #15218 (Two AlphaFold3 problems) created by
- […]
- 6:11 AM Ticket #15217 (Amide nitrogens mistyped as N2) created by
- […]
- 5:02 AM Ticket #15216 (AlphaFold3 with ligands PAE json file: number of structure residues ...) created by
- […]
- 4:05 AM Ticket #15215 (Crash in python_instances_of_class) created by
- […]
- 3:23 AM Ticket #15214 (AlphaFold3 with ligands PAE json file: number of structure residues ...) created by
- […]
May 14, 2024:
- 8:14 PM Ticket #15213 (Allow opening AlphaFold PAE json file from Open File dialog) closed by
- fixed: Done. Added these to 1.8 and daily builds. Since the Open File …
- 8:10 PM Ticket #15213 (Allow opening AlphaFold PAE json file from Open File dialog) created by
- Currently AlphaFold PAE data is opened using the special AlphaFold …
- 6:18 PM Ticket #15212 (Followup to #15191: ChimeraX cannot find MD/Ensemble Analysis option) created by
- […]
- 6:03 PM Ticket #15211 (fourup slice view coloring does not track color wells in Volume Viewer) created by
- Tested in UCSF ChimeraX version: 1.9.dev202405140241 (2024-05-14): I …
- 5:44 PM Ticket #15210 (Add script-friendly log output preference setting) created by
- From: Kumpula, Esa-Pekka via ChimeraX-users Sent: Tuesday, May 14, …
- 5:27 PM 2024-5-16 created by
- 5:26 PM Dev2024-5-20 created by
- 5:26 PM DeveloperMeetings edited by
- (diff)
- 4:32 PM Ticket #15209 (simplify "segmentations" command keyword options) created by
- (1) Consolidate resetMouseModes + setMouseModes into one keyword …
- 3:59 PM Ticket #15208 (improve/consolidate Medical Image icons to toggle mouse & ...) created by
- Currently there are 4 icons, or actually 2 icons both appearing twice. …
- 2:14 PM Ticket #15207 (ISOLDE: ResidueStepper holding reference to closed structure) created by
- […]
- 1:28 PM Ticket #14836 (Residue addition problem) closed by
- fixed: Fixed in daily build and 1.8 release branch. I had the …
- 1:26 PM Ticket #15206 (SEQCROW: read_com: KeyError: 'method') created by
- […]
- 1:19 PM Ticket #15205 (Have segmentations interpolate mouse movements) created by
- I was experimenting with 3D slicer and moving my mouse quickly -- much …
- 12:18 PM Ticket #15204 (Crash in garbage collection) created by
- […]
- 12:18 PM Ticket #9526 (DICOM Segmentations: include SEG models opened from DICOM in the list ...) reopened by
- This feature has gone away. Tested in UCSF ChimeraX version: …
- 11:20 AM Ticket #15202 (Crash in garbage collection) closed by
- duplicate
- 11:17 AM Ticket #15201 (Crash in garbage collection) closed by
- duplicate: Hi, Thanks for reporting this problem. It is fixed in the 1.8 release …
- 11:10 AM Ticket #15203 (Crash changing Mac display configuration) created by
- […]
- 11:09 AM Ticket #15098 (Saving a session while a BLAST job is in progress crashes ChimeraX) closed by
- can't reproduce: I'm not able to reproduce this today. I started several blast jobs in …
- 11:05 AM Ticket #15202 (Crash in garbage collection) created by
- […]
- 10:27 AM Ticket #15201 (Crash in garbage collection) created by
- […]
- 9:46 AM Ticket #15198 (AddH adding hydrogen to terminal C?) closed by
- can't reproduce: I can't get AddH to add the bad hydrogen; maybe this file had it initially?
- 9:32 AM Ticket #15200 (Crash changing Mac display configuration) closed by
- can't reproduce
- 9:30 AM Ticket #15199 (UnicodeDecodeError opening PDB file) closed by
- can't reproduce: Would need the file in order to work on this.
- 9:24 AM Ticket #15197 (Matchmaker chain-chooser: 'Sequence' object has no attribute 'structure') closed by
- can't reproduce: I don't think this can happen anymore because in 1.8 Chains are no …
- 9:20 AM Ticket #15196 (Opened PDB file as NBO output file) closed by
- not a bug: File lacked .pdb suffix
- 9:15 AM Ticket #15195 (Crash in garbage collection) closed by
- duplicate
- 9:13 AM Ticket #15194 (Crash in garbage collection) closed by
- duplicate
- 9:13 AM Ticket #15193 (OSError in python_instances_of_class) closed by
- duplicate
- 9:08 AM Ticket #15192 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 8:54 AM Ticket #15190 (Crash in python_instances_of_class) closed by
- duplicate
- 6:07 AM Ticket #15200 (Crash changing Mac display configuration) created by
- […]
- 4:46 AM Ticket #15199 (UnicodeDecodeError opening PDB file) created by
- […]
- 4:10 AM Ticket #15198 (AddH adding hydrogen to terminal C?) created by
- […]
- 2:24 AM Ticket #15197 (Matchmaker chain-chooser: 'Sequence' object has no attribute 'structure') created by
- […]
- 1:16 AM Ticket #15196 (Opened PDB file as NBO output file) created by
- […]
- 1:02 AM Ticket #15195 (Crash in garbage collection) created by
- […]
May 13, 2024:
- 11:45 PM Ticket #15194 (Crash in garbage collection) created by
- […]
- 11:40 PM Ticket #15193 (OSError in python_instances_of_class) created by
- […]
- 9:39 PM Ticket #15192 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 7:16 PM Ticket #15191 (ChimeraX cannot find MD/Ensemble Analysis option) created by
- […]
- 7:08 PM Ticket #15190 (Crash in python_instances_of_class) created by
- […]
- 6:24 PM Ticket #15135 (AlphaFold3 and ChimeraX) closed by
- fixed: Thanks. I saw Pushmeet Kohli's comment that the plan is to release …
- 6:20 PM Ticket #15144 (AlphaFold3 with ligands PAE json file: number of structure residues ...) closed by
- fixed: Fixed in ChimeraX daily build and 1.8 release candidates dated May 14, …
- 5:36 PM Ticket #15188 (KeyError matching selected regions) closed by
- duplicate: Hi Mark, Thanks for reporting this problem. It is fixed in newer …
- 4:38 PM Ticket #15189 (ESMFold fetch: certificate verify failed) closed by
- fixed: Fixed in ChimeraX 1.8 and daily builds.
- 4:38 PM Ticket #15189 (ESMFold fetch: certificate verify failed) created by
- […]
- 4:21 PM Ticket #15188 (KeyError matching selected regions) created by
- […]
- 4:14 PM Ticket #15187 (Multiple Modeller jobs step on each other) created by
- Specifically, since they use the same temp directory, creation/removal …
- 3:58 PM Dev2024-5-13 edited by
- (diff)
- 12:53 PM Ticket #15181 (glDrawBuffer: invalid operation) closed by
- can't reproduce: Probable remote display OpenGL error.
- 12:49 PM Ticket #15176 (Problem in glBufferData) closed by
- can't reproduce: Possibly broken Nvidia graphics driver.
- 12:47 PM Ticket #15186 (Crash changing Mac display configuration) created by
- […]
- 12:41 PM Ticket #15175 (Crash changing Mac display configuration) closed by
- can't reproduce: Probable Qt crash plugging in or unplugging external display. Old …
- 12:38 PM Ticket #15174 (AlphaFold Prediction Requires Newer ChimeraX) closed by
- limitation: To run AlphaFold predictions you need a newer ChimeraX version. This …
- 12:28 PM Ticket #15162 (command "segmentations setHandModes" gives traceback) closed by
- fixed: Should be …
- 12:27 PM Ticket #15169 (Failed to create NSOpenGLContext) closed by
- duplicate: Duplicate of #15170, same reporter, a few minutes apart.
- 12:24 PM Ticket #15168 (Crash changing Mac display configuration) closed by
- can't reproduce: Qt bug with multiple displays on Mac. Maybe the user plugged in or …
- 12:22 PM Ticket #15185 (segmentations set/resetHandModes breaks on non-Windows) closed by
- duplicate: Forgot about #15162
- 12:15 PM Ticket #15184 (segmentations resetMouseModes sets mouse modes to none) closed by
- fixed: As for the other mouse modes, I stepped through the code that saves …
- 12:02 PM Ticket #15177 (label monitoring: 'Changes' object has no attribute ...) closed by
- fixed
- 11:52 AM Ticket #15185 (segmentations set/resetHandModes breaks on non-Windows) created by
- These commands should not work unless we're on a platform that …
- 11:52 AM Ticket #15184 (segmentations resetMouseModes sets mouse modes to none) created by
- 10:57 AM Ticket #15183 (Restoring session: core tasks KeyError) closed by
- fixed: This has been fixed in the daily builds.
- 10:52 AM Ticket #15182 (Crash in garbage collection) closed by
- duplicate: Hi Marc, Thanks for reporting this problem. It is fixed in the 1.8 …
- 10:49 AM Ticket #15180 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 10:40 AM Ticket #15179 (MemoryError opening mmCIF files) closed by
- duplicate
- 10:39 AM Ticket #15178 (MemoryError opening mmCIF files) closed by
- duplicate
- 10:31 AM Ticket #15173 (AlphaFold JSON opened as MOLE JSON) closed by
- duplicate
- 10:29 AM Ticket #15172 (MemoryError opening mmCIF files) closed by
- duplicate
- 10:26 AM Ticket #15170 (Failed to create NSOpenGLContext) closed by
- duplicate
- 10:22 AM Ticket #15167 (Opening binary file as PDB) closed by
- not a bug
- 10:07 AM Ticket #15166 (Bundle ChimeraX-NMRSTAR has no module) closed by
- duplicate: Duplicate of #14882
- 9:55 AM Ticket #15165 (Infinite loop in OpenCommands) closed by
- limitation: User must be opening another file of the same type in their open commands.
- 6:05 AM Ticket #15183 (Restoring session: core tasks KeyError) created by
- […]
- 5:08 AM Ticket #15182 (Crash in garbage collection) created by
- […]
- 4:44 AM Ticket #15181 (glDrawBuffer: invalid operation) created by
- […]
- 2:29 AM Ticket #15180 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 1:25 AM Ticket #15179 (MemoryError opening mmCIF files) created by
- […]
- 1:17 AM Ticket #15178 (MemoryError opening mmCIF files) created by
- […]
May 12, 2024:
- 10:52 PM Ticket #15177 (label monitoring: 'Changes' object has no attribute ...) created by
- […]
- 5:49 PM Ticket #15176 (Problem in glBufferData) created by
- […]
- 4:53 PM Ticket #15175 (Crash changing Mac display configuration) created by
- […]
- 5:39 AM Ticket #15174 (AlphaFold Prediction Requires Newer ChimeraX) created by
- […]
- 1:42 AM Ticket #15173 (AlphaFold JSON opened as MOLE JSON) created by
- […]
May 11, 2024:
- 6:36 PM Ticket #15172 (MemoryError opening mmCIF files) created by
- […]
- 3:29 PM Ticket #15171 (Crash creating QWebEngineProfile) created by
- […]
- 1:28 PM Ticket #15170 (Failed to create NSOpenGLContext) created by
- […]
- 1:25 PM Ticket #15169 (Failed to create NSOpenGLContext) created by
- […]
- 11:36 AM Ticket #15168 (Crash changing Mac display configuration) created by
- […]
- 7:38 AM Ticket #15167 (Opening binary file as PDB) created by
- […]
- 5:49 AM Ticket #15166 (Bundle ChimeraX-NMRSTAR has no module) created by
- […]
- 5:11 AM Ticket #15165 (Infinite loop in OpenCommands) created by
- […]
May 10, 2024:
- 3:45 PM Ticket #15164 (Segmentations tool lists misleading ID numbers) created by
- When I create segmentations in the Segmentations tool it lists them in …
- 3:13 PM Ticket #15163 (Segmentations tools does not list segmentation models read from file ...) created by
- If I used "segmentations create" to create new segmentation models and …
- 2:20 PM Ticket #15162 (command "segmentations setHandModes" gives traceback) created by
- […]
- 1:52 PM Ticket #15161 (ArtiaX: Dynamo: read_file: could not convert string to float) created by
- […]
- 11:45 AM Ticket #14824 (altloc submodel problems) closed by
- fixed: Barring Tristan requesting a subclass instead of checking the parent …
- 11:08 AM Ticket #15160 (Crash in garbage collection) closed by
- can't reproduce
- 11:07 AM Ticket #15159 (Crash in garbage collection) closed by
- can't reproduce
- 10:32 AM Ticket #15160 (Crash in garbage collection) created by
- […]
- 10:27 AM Ticket #15159 (Crash in garbage collection) created by
- […]
- 8:47 AM Ticket #15158 (MemoryError opening mmCIF files) closed by
- duplicate
- 8:46 AM Ticket #15157 (AlphaFold3 with ligands PAE json file: number of structure residues ...) closed by
- duplicate: Duplicate of #15144; adding reporter to recipient list for that ticket.
- 8:41 AM Ticket #15156 (Crash in event loop) closed by
- can't reproduce
- 8:39 AM Ticket #15155 (Unknown crash) closed by
- can't reproduce
- 8:30 AM Ticket #15158 (MemoryError opening mmCIF files) created by
- […]
- 4:10 AM Ticket #15157 (AlphaFold3 with ligands PAE json file: number of structure residues ...) created by
- […]
- 1:43 AM Ticket #15156 (Crash in event loop) created by
- […]
May 9, 2024:
- 8:09 PM Ticket #15138 (Crash painting backing store during popup menu display) closed by
- can't reproduce: The stack trace from earlier to later calls includes […] Looks …
- 4:59 PM Ticket #15155 (Unknown crash) created by
- […]
- 4:00 PM Ticket #15113 (Coordinate set does not match number of atoms) closed by
- can't reproduce
- 3:50 PM Ticket #15106 (Sequence viewer structure association has mismatches for identical ...) closed by
- limitation: Yes, sorry, but it is a basic assumption that the sequence in the …
- 2:42 PM Ticket #15154 (Crash showing Rapid Access at startup) closed by
- can't reproduce
- 2:40 PM Ticket #15153 (AlphaFold3 with ligands PAE json file: number of structure residues ...) closed by
- duplicate: Duplicate of #15144; adding reporter to recipient list for that ticket.
- 2:22 PM Ticket #15150 (AlphaFold Service Broken) closed by
- not a bug: Hi Kayley, Go to the ChimeraX download page …
- 2:18 PM Ticket #15149 (Crash in garbage collection) closed by
- duplicate
- 2:08 PM Ticket #15154 (Crash showing Rapid Access at startup) created by
- […]
- 1:59 PM Ticket #15153 (AlphaFold3 with ligands PAE json file: number of structure residues ...) created by
- […]
- 1:47 PM NIAID2024 edited by
- (diff)
- 11:56 AM Ticket #15148 (Crash in garbage collection) closed by
- duplicate
- 11:55 AM Ticket #15147 (Crash in event loop) closed by
- can't reproduce
- 11:15 AM Ticket #15152 (SEQCROW: IR Spectrum: shapes not aligned) created by
- […]
- 10:58 AM Ticket #15145 (Crash in garbage collection) closed by
- duplicate: Hi Peter, Thanks for reporting this problem. It is fixed in the …
- 10:58 AM Ticket #15151 (In CmdDescs, Or(TupleOf(IntArg, 3), TupleOf(IntArg, 2)) only admits ...) created by
- Even when reversed, this Or will only accept whichever TupleArg comes …
- 10:55 AM Ticket #15140 (QQuickWidget: Failed to make context current) closed by
- can't reproduce
- 10:54 AM Ticket #15139 (Crash in garbage collection) closed by
- duplicate
- 10:48 AM Ticket #15137 (Command history: No space left on device) closed by
- not a bug
- 10:45 AM Ticket #15136 (Crash in garbage collection) closed by
- duplicate
- 10:06 AM Ticket #15150 (AlphaFold Service Broken) created by
- […]
- 5:42 AM Ticket #15149 (Crash in garbage collection) created by
- […]
- 4:45 AM Ticket #15148 (Crash in garbage collection) created by
- […]
- 2:19 AM Ticket #15147 (Crash in event loop) created by
- […]
- 1:30 AM Ticket #15146 (XMAS: update_distances: KeyError: None) created by
- […] XMAS_Y541A_all.xlsx
May 8, 2024:
- 7:50 PM Ticket #15145 (Crash in garbage collection) created by
- […]
- 4:43 PM Ticket #15143 (AlphaFold Error Plot: IndexError: list index out of range) closed by
- fixed: Fixed in 1.9 and 1.8. Code to find the .json or .pkl file with the …
- 3:22 PM Ticket #15144 (AlphaFold3 with ligands PAE json file: number of structure residues ...) created by
- […]
- 3:20 PM Ticket #15143 (AlphaFold Error Plot: IndexError: list index out of range) created by
- […]
- 2:31 PM Ticket #15142 (Segmentations must spawn the volume viewer if it's been closed) created by
- Noticed while creating the tutorial
- 2:15 PM Ticket #15141 ('ui view ___ guidelines ___' should affect the segmentation tool's ...) created by
- Noticed while creating the tutorial
- 2:05 PM Ticket #15140 (QQuickWidget: Failed to make context current) created by
- […]
- 2:04 PM Ticket #15139 (Crash in garbage collection) created by
- […]
- 1:36 PM Ticket #15138 (Crash painting backing store during popup menu display) created by
- […]
- 1:21 PM Ticket #15137 (Command history: No space left on device) created by
- […]
- 12:52 PM Ticket #15136 (Crash in garbage collection) created by
- […]
- 11:57 AM Ticket #15122 (Seq viewer: region not in regions list) closed by
- can't reproduce: If this recurs, may have to catch the exception, print the region, and …
- 11:14 AM Ticket #15123 (2D label clipped) closed by
- fixed: Fix: …
- 11:13 AM ChangeLog edited by
- (diff)
- 11:13 AM ChangeLog edited by
- (diff)
- 10:13 AM Ticket #14980 (False "BLAST job failed" error on session restore) closed by
- fixed: OK, this should actually be fixed now but if you see the error again …
- 8:59 AM Ticket #15134 (Crash in garbage collection) closed by
- duplicate
- 8:58 AM Ticket #15133 (Crash in garbage collection) closed by
- duplicate
- 8:57 AM Ticket #15132 (Crash in QTimer::timerEvent() after opening MRC file) closed by
- can't reproduce
- 8:50 AM Ticket #15130 (Crash in garbage collection) closed by
- can't reproduce
- 8:48 AM Ticket #15128 (AddH: Hydrogen not bonded to exactly one other atom) closed by
- not a bug: Bad structure
- 8:26 AM Ticket #15135 (AlphaFold3 and ChimeraX) created by
- […]
- 7:11 AM Ticket #15134 (Crash in garbage collection) created by
- […]
- 5:33 AM Ticket #15133 (Crash in garbage collection) created by
- […]
- 4:43 AM Ticket #15132 (Crash in QTimer::timerEvent() after opening MRC file) created by
- […]
May 7, 2024:
- 6:00 PM Ticket #15131 (Color "mismatch" due to lighting) closed by
- fixed: From Chris Caffalette <ccaffalett@…>: I solved the …
- 3:28 PM Ticket #15129 (DisplayVersion entry is missing from Windows registry) closed by
- fixed: I have reproduced this bug. And it looks we introduced this bug in …
- 3:12 PM Ticket #14980 (False "BLAST job failed" error on session restore) reopened by
- I discovered to my dismay while looking at something else to do with …
- 11:57 AM Ticket #15131 (Color "mismatch" due to lighting) created by
- […] Render-by-Attribute_test.png
- 11:51 AM Ticket #15130 (Crash in garbage collection) created by
- […]
- 10:57 AM Ticket #15129 (DisplayVersion entry is missing from Windows registry) created by
- Hello, I manage the software distribution at the Frei Universität …
- 10:51 AM Dev2024-5-13 created by
- 10:50 AM 2024-5-9 created by
- 10:49 AM 2024-5-2 edited by
- (diff)
- 10:46 AM DeveloperMeetings edited by
- (diff)
- 9:34 AM Ticket #15127 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 9:10 AM Ticket #15128 (AddH: Hydrogen not bonded to exactly one other atom) created by
- […]
- 9:05 AM Ticket #15121 (UnicodeDecodeError opening PDB file) closed by
- not a bug: Not an actual PDB file
- 6:03 AM Ticket #15127 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 5:30 AM Ticket #15126 (XMAS: CSV file: Unsupported evidence file format: 'Tabular' object has ...) created by
- […] Mappe11.csv
- 2:30 AM Ticket #15125 (ChimeraX does not start) created by
- […] Debug_ChimeraX.txt
May 6, 2024:
- 5:43 PM Ticket #15119 (Alphafold prediction Google sign in error message: "Alphafold ...) closed by
- fixed: Fixed. It appears Google Colab changed how their sign-in page works …
- 4:54 PM Ticket #14818 (ChimeraX 1.8 Ubuntu 22.04 missing dependency) closed by
- fixed: Added libxcb-cursor0 dependency on April 6th.
- 4:36 PM Ticket #15124 (RFE: Mouse modes snapshots or undo stack) created by
- When using the segmentation tool, the user can set a preference to set …
- 4:36 PM Ticket #15123 (2D label clipped) created by
- […]
- 4:29 PM Ticket #15122 (Seq viewer: region not in regions list) created by
- […]
- 4:03 PM Dev2024-5-6 edited by
- (diff)
- 2:39 PM Ticket #15121 (UnicodeDecodeError opening PDB file) created by
- […]
- 1:14 PM Ticket #15120 (Problem when using the 'record movie' button in the slider interface) closed by
- duplicate: This is a problem that happens when using Microsoft OneDrive (a cloud …
- 1:04 PM Ticket #15112 (2D Labels: QColor arguments wrong) closed by
- fixed: Fixed in ChimeraX daily build. I guess no one used that outline width …
- 12:47 PM Ticket #14980 (False "BLAST job failed" error on session restore) closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/763508da7ac7fcc5b204c68828c332 …
- 12:12 PM Ticket #15120 (Problem when using the 'record movie' button in the slider interface) created by
- […] [[Image(...)]]
- 11:18 AM Ticket #15117 (opening session w/ Blast results gives error: BLAST job failed) closed by
- duplicate: See #14980
- 11:12 AM Ticket #15119 (Alphafold prediction Google sign in error message: "Alphafold ...) created by
- […]
- 11:03 AM Ticket #15110 (OpenMM: Context_swiginit: Error compiling kernel: symbol multiply defined) closed by
- wontfix: Unfortunately this is one that can't be fixed other than by running on …
- 10:57 AM Ticket #15118 (Test ticket) reopened by
- 10:57 AM Ticket #15118 (Test ticket) closed by
- fixed
- 10:42 AM Ticket #15116 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 10:40 AM Ticket #15115 (Crash in garbage collection) closed by
- duplicate
- 10:33 AM Ticket #15118 (Test ticket) created by
- comment
- 10:28 AM Ticket #14976 (Make blastprotein command load structures and alignment without GUI) closed by
- fixed: OK. …
- 10:19 AM Ticket #15108 (Crash showing open dialog) closed by
- can't reproduce: Hi Si Hoon, Thanks for reporting this problem. I would recommend …
- 10:15 AM Ticket #15107 (Crash in garbage collection) closed by
- duplicate
- 10:09 AM Ticket #15117 (opening session w/ Blast results gives error: BLAST job failed) created by
- […]
- 10:04 AM Ticket #15022 (Blast protein should align loaded structures even when raw query ...) reopened by
- I still get the same error "Must use different reference and match …
- 6:07 AM Ticket #15116 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 2:35 AM Ticket #15115 (Crash in garbage collection) created by
- […]
- 12:42 AM Ticket #15114 (MemoryError saving session) created by
- […]
May 5, 2024:
- 12:51 PM Ticket #15113 (Coordinate set does not match number of atoms) created by
- […]
- 8:08 AM Ticket #15112 (2D Labels: QColor arguments wrong) created by
- […]
- 12:54 AM Ticket #15111 (MemoryError saving session) created by
- […]
May 4, 2024:
- 11:33 AM Ticket #15110 (OpenMM: Context_swiginit: Error compiling kernel: symbol multiply defined) created by
- […]
- 5:20 AM Ticket #15109 (AssertionError processing command) created by
- […]
- 5:16 AM Ticket #15108 (Crash showing open dialog) created by
- […]
May 3, 2024:
- 11:31 PM Ticket #15107 (Crash in garbage collection) created by
- […]
- 6:48 PM Ticket #15106 (Sequence viewer structure association has mismatches for identical ...) created by
- […] a2g0z0.fasta
- 5:46 PM Ticket #15104 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 12:36 PM Ticket #15064 (Mouse wheel: no Qt.KeyboardModifier.CtrlModifier) closed by
- can't reproduce: I am not able to reproduce this error. It appears that it happened …
- 12:29 PM Ticket #15013 (Dragging docked tool logs "Already setting window visible!") closed by
- fixed: Fixed. Suppressed Qt messages "Already setting window visible!" and …
- 12:17 PM Ticket #15105 (Reading ImageJ Tiff: IndexError: index out of range) closed by
- fixed: Fixed in ChimeraX daily build May 4, 2024 and later. The problem is …
- 12:13 PM Ticket #15105 (Reading ImageJ Tiff: IndexError: index out of range) created by
- From: Christophe Leterrier via ChimeraX-users …
- 11:44 AM Ticket #15104 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 9:28 AM Ticket #15103 (map.volume._update_drawings: KeyError) created by
- […]
- 8:54 AM Ticket #15102 (UnicodeDecodeError reading PDB file on Windows) closed by
- can't reproduce: Probably need to add some Windows-specific codec to the list of codecs …
- 8:43 AM Ticket #15096 (Crash in garbage collection) closed by
- duplicate: Hi Taha, Thanks for reporting this problem. It is fixed in the …
- 5:46 AM Ticket #15102 (UnicodeDecodeError reading PDB file on Windows) created by
- […]
- 12:56 AM Ticket #15101 (ISOLDE: start_sim: Error initializing CUDA) created by
- […]
May 2, 2024:
- 6:43 PM Ticket #15100 (diffplot: Cluster atomic models by projecting atom positions with UMAP) created by
- Klim Verba, Katrina Black and Tom Goddard discussed on April 9, 2024 …
- 5:46 PM Ticket #15022 (Blast protein should align loaded structures even when raw query ...) closed by
- fixed
- 5:02 PM Ticket #15099 (Color a surface using volume data at a range of offsets) closed by
- fixed: Done. In ChimeraX daily builds dated May 2, 2024 or later. I've …
- 5:00 PM Ticket #15099 (Color a surface using volume data at a range of offsets) created by
- Shawn Zheng asked about coloring a membrane surface from a tomogram …
- 4:27 PM Ticket #15097 (Surface created by surface smooth command not saved in sessions) closed by
- fixed: Fixed. Command surface smooth created new surfaces but did not set …
- 4:23 PM Ticket #15098 (Saving a session while a BLAST job is in progress crashes ChimeraX) created by
- 4:13 PM Ticket #15097 (Surface created by surface smooth command not saved in sessions) created by
- […]
- 3:57 PM Ticket #15096 (Crash in garbage collection) created by
- […]
- 3:31 PM Ticket #15088 (Qt path override + missing Medical Image dependency) closed by
- limitation: The path override messages can only be fixed by a newer version of Qt.
- 3:22 PM Ticket #15082 (openmm.OpenMMException: There is no registered Platform called "OpenCL") closed by
- not a bug: Taking out the ChimeraX code that sets OPENMM_PLUGIN_DIR environment …
- 3:19 PM Ticket #15095 (Crash in garbage collection) closed by
- duplicate: Hi Rainer, Thanks for reporting this problem. It is fixed in the …
- 3:16 PM Ticket #15094 (Crash in garbage collection) closed by
- duplicate
- 2:22 PM Ticket #15091 (glDrawBuffer: invalid operation) closed by
- can't reproduce: I think Linux might drop the OpenGL context, maybe when the machine …
- 1:48 PM Ticket #15095 (Crash in garbage collection) created by
- […]
- 11:44 AM Ticket #15094 (Crash in garbage collection) created by
- […]
- 11:11 AM Ticket #15093 (Copick: crash in QCoPickTableModel) created by
- […]
- 10:58 AM Ticket #15085 (AlphaFold Prediction Requires Newer ChimeraX) closed by
- not a bug: Not sure what bug you are reporting. If it is that AlphaFold is not …
- 10:41 AM Ticket #15089 (Crash in garbage collection) closed by
- duplicate
- 10:36 AM Ticket #15087 (pydantic dependency not installed (on upgrade?)) closed by
- duplicate
- 9:37 AM Ticket #15092 (ArtiaX: smbprotocol: TimeoutError) created by
- […]
- 9:33 AM Ticket #15091 (glDrawBuffer: invalid operation) created by
- […]
- 9:28 AM Ticket #15084 (ArtiaX: SurfaceCollectionModel: masked_bounds: arrays used as indices ...) closed by
- duplicate
- 9:17 AM Ticket #15081 (MemoryError opening mmCIF files) closed by
- duplicate
- 8:55 AM Ticket #15090 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by
- […]
- 8:18 AM Ticket #15089 (Crash in garbage collection) created by
- […]
- 6:24 AM Ticket #15088 (Qt path override + missing Medical Image dependency) created by
- […]
- 12:54 AM Ticket #15087 (pydantic dependency not installed (on upgrade?)) created by
- […]
- 12:53 AM Ticket #15086 (pydantic dependency not installed (on upgrade?)) created by
- […]
May 1, 2024:
- 5:05 PM Ticket #15058 (Errors upgrading/installing ChimeraX) closed by
- worksforme: Tt looks like the /usr/bin/chimerax-daily symbolic link was removed by …
- 4:27 PM Ticket #14976 (Make blastprotein command load structures and alignment without GUI) reopened by
- wording (as per comment 27) still not changed as of UCSF ChimeraX …
- 4:23 PM Ticket #15022 (Blast protein should align loaded structures even when raw query ...) reopened by
- Please reopen tickets when there are new concerns.
- 4:05 PM Ticket #15085 (AlphaFold Prediction Requires Newer ChimeraX) created by
- […]
- 2:02 PM Ticket #15084 (ArtiaX: SurfaceCollectionModel: masked_bounds: arrays used as indices ...) created by
- […]
- 2:02 PM Ticket #15083 (ArtiaX: SurfaceCollectionModel: masked_bounds: arrays used as indices ...) created by
- […]
- 1:00 PM Ticket #15082 (openmm.OpenMMException: There is no registered Platform called "OpenCL") created by
- […]
- 12:06 PM Ticket #15081 (MemoryError opening mmCIF files) created by
- […]
- 11:33 AM Ticket #15074 (perframe/coordset: commands executed with old coordset) closed by
- not a bug: We discussed two ways to play through the trajectory showing hydrogen …
- 10:52 AM Ticket #15080 (Better handling of multi-character chain IDs for Modeller) created by
- There is something seriously weird about this structure, and I can …
- 8:38 AM Ticket #15078 (Crash handling text input) closed by
- can't reproduce
- 1:45 AM Ticket #15079 (OpenMM on PyPi) created by
- […]
Apr 30, 2024:
- 8:27 PM Ticket #15078 (Crash handling text input) created by
- […]
- 8:02 PM Training edited by
- (diff)
- 8:02 PM Training edited by
- (diff)
- 1:59 PM Ticket #15077 (ArtiaX: move_children: boolean index did not match indexed array along ...) created by
- […]
- 1:32 PM Ticket #15076 (ArtiaX: delete_selected_particles: arrays used as indices must be of ...) created by
- […]
- 12:20 PM 2024-5-2 edited by
- (diff)
- 11:42 AM Ticket #15075 (Copick: QCoPickTableModel: child item has no parent) created by
- […]
- 11:13 AM Dev2024-5-6 created by
- 11:12 AM Dev2024-4-29 edited by
- (diff)
- 11:12 AM 2024-5-2 created by
- 11:10 AM DeveloperMeetings edited by
- (diff)
- 10:43 AM Ticket #15074 (perframe/coordset: commands executed with old coordset) created by
- I'm trying to visualize the hydrogen bonds of a small molecule in …
- 9:22 AM Ticket #15073 (Crash in QItemSelectionModel::isSelected) closed by
- can't reproduce
- 9:19 AM Ticket #15073 (Crash in QItemSelectionModel::isSelected) created by
- […]
- 9:08 AM Ticket #15071 (Message going to dead viewer's status) closed by
- can't reproduce
- 9:02 AM Ticket #15070 (Crash in garbage collection) closed by
- duplicate: Hi Haaris, Thanks for reporting this problem. It is fixed in the …
- 8:55 AM Ticket #15069 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 7:15 AM Ticket #15072 (Crash setting active window) created by
- […]
- 6:44 AM Ticket #15071 (Message going to dead viewer's status) created by
- […]
- 3:19 AM Ticket #15070 (Crash in garbage collection) created by
- […]
Apr 29, 2024:
- 11:41 PM Ticket #15069 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 5:11 PM Ticket #15054 (Can't save session because NewerVersionQuery not listed) closed by
- fixed: And the ChimeraX that has this problem is a daily build from 27 …
- 12:05 PM Ticket #15041 (Session save failed: Check Water Viewer, Residue already deleted) closed by
- duplicate
- 12:00 PM Ticket #15055 (AlphaFold Prediction Requires Newer ChimeraX) closed by
- fixed: already fixed for daily build
- 11:44 AM Ticket #15067 (QKeyEvent in drag/drop code) closed by
- duplicate: Duplicate of #14793
- 11:40 AM Ticket #15066 (Crash in garbage collection) closed by
- duplicate
- 11:38 AM Ticket #15065 (Crash as menu teardown makes previous window key) closed by
- can't reproduce
- 11:32 AM Ticket #15063 (Crash in event loop) closed by
- can't reproduce
- 11:31 AM Ticket #15062 (Crash in event loop) closed by
- can't reproduce
- 11:28 AM Ticket #15061 (Crash in garbage collection) closed by
- duplicate
- 11:25 AM Ticket #15059 (Crash in garbage collection) closed by
- duplicate
- 11:23 AM Ticket #15068 (ArtiaX: 'MarkerSetPlus' object has no attribute 'session') created by
- […]
- 11:21 AM Ticket #15057 (Crash in garbage collection) closed by
- can't reproduce: We've still got some crashes in garbage collection, just not as many.
- 11:19 AM Ticket #15056 (Crash configuring display) closed by
- can't reproduce
- 11:10 AM Ticket #15052 (Crash in python_instances_of_class) closed by
- duplicate: Hi George, Thanks for reporting this problem. It was fixed in a …
- 11:06 AM Ticket #15051 (Struct Measure: wrapped C/C++ object of type QLabel has been deleted) closed by
- duplicate
- 11:03 AM Ticket #15050 (Add Charge: loop that checks for isolated atoms within residues: list ...) closed by
- fixed: Hi Mitch, Thanks for reporting this problem. I have committed a fix …
- 10:42 AM Ticket #15049 (Crash changing screen/display settings, possibly while in full screen mode) closed by
- can't reproduce
- 10:37 AM Ticket #15047 (Crash in garbage collection) closed by
- duplicate
- 10:35 AM Ticket #15046 (Crash in garbage collection) closed by
- duplicate
- 9:12 AM Ticket #15067 (QKeyEvent in drag/drop code) created by
- […]
- 6:45 AM Ticket #15066 (Crash in garbage collection) created by
- […]
- 5:42 AM Ticket #15065 (Crash as menu teardown makes previous window key) created by
- […]
- 3:15 AM Ticket #15064 (Mouse wheel: no Qt.KeyboardModifier.CtrlModifier) created by
- […]
- 2:59 AM Ticket #15063 (Crash in event loop) created by
- […]
- 2:45 AM Ticket #15062 (Crash in event loop) created by
- […]
- 1:14 AM Ticket #15061 (Crash in garbage collection) created by
- […]
Apr 28, 2024:
- 6:11 PM Ticket #15060 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by
- […]
- 2:26 PM Ticket #15059 (Crash in garbage collection) created by
- […]
- 9:16 AM Ticket #15058 (Errors upgrading/installing ChimeraX) created by
- […] problem_installing_daily_20.04.out
- 8:38 AM Ticket #15057 (Crash in garbage collection) created by
- […]
- 4:33 AM Ticket #15056 (Crash configuring display) created by
- […]
- 3:42 AM Ticket #15055 (AlphaFold Prediction Requires Newer ChimeraX) created by
- […]
Apr 27, 2024:
- 6:43 PM Ticket #15054 (Can't save session because NewerVersionQuery not listed) created by
- […]
- 11:19 AM Ticket #15053 (Segmentation cursors don't open if seg tool opened after view layout ...) created by
- 11:17 AM Ticket #9850 (Issues when Segmentations tool is already open w/o data when new DICOM ...) closed by
- fixed: Was fixed by …
- 8:28 AM Ticket #15052 (Crash in python_instances_of_class) created by
- […]
- 8:17 AM Ticket #15051 (Struct Measure: wrapped C/C++ object of type QLabel has been deleted) created by
- […]
Apr 26, 2024:
- 8:33 PM Ticket #15050 (Add Charge: loop that checks for isolated atoms within residues: list ...) created by
- […] mincell.20nm-2.pdb
- 5:10 PM Ticket #15049 (Crash changing screen/display settings, possibly while in full screen mode) created by
- […]
- 4:04 PM Ticket #15048 (Bundle builder produces incorrect metadata if "category" is not a list) closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/84a01dd48d7e88f93a44bba54e0962 …
- 3:48 PM Ticket #15048 (Bundle builder produces incorrect metadata if "category" is not a list) created by
- [chimerax] category = "General" and [chimerax] categories = …
- 2:59 PM Ticket #9267 (make build-from-scratch fails on Linux) closed by
- fixed: Good point.
- 2:26 PM Ticket #10424 (KeyError in tasks after opening then closing session with BLAST failure) closed by
- fixed: It is …
- 2:25 PM Ticket #14510 (KeyError restoring tasks) closed by
- fixed: It is …
- 2:25 PM Ticket #14404 (Session restore, tasks: KeyError) closed by
- fixed: It is …
- 2:25 PM Ticket #10391 (Session restore: KeyError deleting tasks) closed by
- fixed: It is …
- 1:31 PM Ticket #15022 (Blast protein should align loaded structures even when raw query ...) closed by
- fixed
- 1:27 PM Ticket #15047 (Crash in garbage collection) created by
- […]
- 1:22 PM Ticket #15046 (Crash in garbage collection) created by
- […]
- 12:44 PM Ticket #14733 (Session restore: blast protein: KeyError: '_protein_chain') closed by
- can't reproduce: Most likely. Can't reproduce without the session.
- 12:43 PM Ticket #15029 (value error traceback when checking "List only best chain per hit" ...) closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/973f037a2349527d06167b1cee825b …
- 12:30 PM Ticket #15045 (Crash showing Save File dialog) closed by
- can't reproduce
- 12:25 PM Ticket #15044 (Crash in event loop in NSMenuBarTrackingSession, terminated by SIGKILL) closed by
- can't reproduce
- 12:21 PM Ticket #15043 (Crashed in garbage collection) closed by
- duplicate
- 12:06 PM Ticket #15045 (Crash showing Save File dialog) created by
- […]
- 12:04 PM Ticket #15040 (Crash showing rapid access in QStackedWidget_setCurrentWidget() while ...) closed by
- can't reproduce
- 11:58 AM Ticket #15039 (Crash in garbage collection) closed by
- duplicate
- 11:56 AM Ticket #15038 (Crash in garbage collection) closed by
- duplicate
- 11:55 AM Ticket #15037 (Garbage collection crash) closed by
- duplicate
- 11:53 AM Ticket #15036 (Opening session: RuntimeError: LZ4F_decompress failed) closed by
- limitation
- 8:18 AM Ticket #15044 (Crash in event loop in NSMenuBarTrackingSession, terminated by SIGKILL) created by
- […]
- 8:16 AM Ticket #15043 (Crashed in garbage collection) created by
- […]
- 5:36 AM Ticket #15042 (ArtiaX importing Copick tool: ModuleNotFoundError: No module named ...) created by
- […]
- 3:16 AM Ticket #15041 (Session save failed: Check Water Viewer, Residue already deleted) created by
- […]
- 2:05 AM Ticket #15040 (Crash showing rapid access in QStackedWidget_setCurrentWidget() while ...) created by
- […]
Apr 25, 2024:
- 10:05 PM Ticket #15039 (Crash in garbage collection) created by
- […]
- 9:57 PM Ticket #15038 (Crash in garbage collection) created by
- […]
- 9:40 PM Ticket #15037 (Garbage collection crash) created by
- […]
- 8:02 PM 2024-4-25 edited by
- (diff)
- 7:24 PM Ticket #15036 (Opening session: RuntimeError: LZ4F_decompress failed) created by
- […]
- 6:29 PM Ticket #15035 (Revert Greek/special characters to plain text on output) created by
- I just downloaded a pdb file from AlphaFold DB …
- 6:03 PM Ticket #15033 (Crash in garbage collection) closed by
- duplicate: Hi Mitch, Thanks for reporting this problem. It is fixed in the …
- 6:02 PM Ticket #15031 (Crash in garbage collection) closed by
- duplicate: Hi Daniel, Thanks for reporting this problem. It is fixed in the …
- 5:49 PM Ticket #15001 (Links to example files in Toolshed Building and Distributing bundles ...) closed by
- fixed: Re-enabled zip download while retaining references to GitHub sample code.
- 5:08 PM 2024-4-25 edited by
- (diff)
- 3:37 PM Ticket #15030 (Dock Prep ChargeError) closed by
- duplicate
- 3:27 PM Ticket #15034 (Better user-facing message when sessions require newer internal bundles) created by
- When a session needs a newer version of an internal bundle, like …
- 3:25 PM Ticket #15033 (Crash in garbage collection) created by
- […]
- 3:22 PM Ticket #15027 (Update atomic bundle) closed by
- not a bug: Hi Nishant, The Atomic bundle is shipped as part of the ChimeraX app, …
- 2:25 PM Ticket #15032 (VR user interface suggestions) created by
- From: Scooter Morris Subject: VR comments Date: April 24, 2024 at …
- 2:22 PM Ticket #15026 (Graphics crash, macOS 14.4.1, Intel Iris Plus Graphics) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 2:10 PM NIAID2024 edited by
- (diff)
- 2:08 PM NIAID2024 edited by
- (diff)
- 2:04 PM NIAID2024 edited by
- (diff)
- 2:00 PM Ticket #15031 (Crash in garbage collection) created by
- […]
- 11:45 AM Ticket #15030 (Dock Prep ChargeError) created by
- […]
- 10:44 AM Ticket #15029 (value error traceback when checking "List only best chain per hit" ...) created by
- […]
Apr 24, 2024:
- 6:50 PM Ticket #15028 (Session save failed: Can't convert object of type: <enum 'Matrix'>) closed by
- limitation: Sessions support IntEnum.
- 6:27 PM Ticket #15028 (Session save failed: Can't convert object of type: <enum 'Matrix'>) created by
- […]
- 5:04 PM Ticket #15027 (Update atomic bundle) created by
- […]
- 3:31 PM Ticket #15025 (ChimeraX bug report submission) closed by
- fixed: I've added a check for sequence only results. A summary will be …
- 3:23 PM Ticket #15026 (Graphics crash, macOS 14.4.1, Intel Iris Plus Graphics) created by
- […]
- 2:45 PM Ticket #15025 (ChimeraX bug report submission) created by
- […]
- 2:35 PM Ticket #15023 (Crash in garbage collection) closed by
- duplicate
- 2:33 PM Ticket #15024 (Realsense: Couldn't resolve requests) created by
- […] error1.PNG
- 1:27 PM Ticket #15023 (Crash in garbage collection) created by
- […]
- 11:53 AM Ticket #15022 (Blast protein should align loaded structures even when raw query ...) created by
- […]
- 11:46 AM Ticket #10127 (DICOM session does not restore thresholds or colors) closed by
- fixed: This commit …
- 11:38 AM Ticket #15021 (Spec given to 'hbonds' selects nothing) closed by
- nonchimerax: Well, because it seems that the ligand "residue" is two residues when …
- 11:29 AM Ticket #14917 (Angle tool allows decimal places to go to -1) closed by
- fixed: Fix available in next daily build. (fix: …
- 11:26 AM Ticket #15020 (Level popup persists after PlaneViewer closes) closed by
- fixed: Closed by …
- 11:24 AM Ticket #15018 (Showing molecular surface: Unable to allocate 4.41 MiB for an array) closed by
- limitation: User opened an mmCIF file of a virus with 780 chains then tried to …
- 11:22 AM Ticket #15021 (Spec given to 'hbonds' selects nothing) created by
- […]
- 11:19 AM Ticket #15016 (glDrawBuffer: invalid operation) closed by
- can't reproduce: Possible OpenGL graphics driver bug. But I suspect there is something …
- 10:51 AM Ticket #10389 (wrapped C/C++ object of type DICOMTable has been deleted) closed by
- fixed: Should have been fixed by …
- 10:31 AM Ticket #15020 (Level popup persists after PlaneViewer closes) created by
- While fixing #14618 I discovered that if I timed it just right then …
- 10:27 AM Ticket #14618 (Cancel mouse movement callback if viewers closed) closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/2243441636ccc44cd3454c32544681 …
- 9:10 AM Ticket #15019 (Match structure to itself: list index out of range) closed by
- duplicate
- 8:58 AM Ticket #15015 (Crash in garbage collection) closed by
- can't reproduce: This is after the fix I made, so there still is a less-frequent …
- 8:51 AM Ticket #15014 (Crash in garbage collection) closed by
- duplicate
- 8:50 AM Ticket #15012 (Crash in garbage collection) closed by
- duplicate
- 6:57 AM Ticket #15019 (Match structure to itself: list index out of range) created by
- […]
- 4:44 AM Ticket #15018 (Showing molecular surface: Unable to allocate 4.41 MiB for an array) created by
- […]
- 2:46 AM Ticket #15017 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by
- […]
- 1:12 AM Ticket #15016 (glDrawBuffer: invalid operation) created by
- […]
Apr 23, 2024:
- 11:56 PM Ticket #15015 (Crash in garbage collection) created by
- […]
- 10:21 PM Ticket #14976 (Make blastprotein command load structures and alignment without GUI) closed by
- fixed: I've pushed the changes. YMMV, it was fast for an Alphafold version 2 …
- 8:30 PM Ticket #15014 (Crash in garbage collection) created by
- […]
- 7:47 PM Ticket #15013 (Dragging docked tool logs "Already setting window visible!") created by
- […]
- 4:09 PM Ticket #15012 (Crash in garbage collection) created by
- […]
- 3:57 PM Ticket #15004 (ArtiaX dependency not installed) closed by
- limitation: Any version number change should work. ChimeraX uses pip to install …
- 2:03 PM Ticket #15011 (Alt locs in 7b6w not coalesced) created by
- In 7b6w residue T0B, the alternate locations are separate atoms, …
- 1:38 PM Ticket #14993 (No models) closed by
- fixed: Glad you got it working!
- 11:58 AM Ticket #15009 (MD Viewer: self.atomLocation[0]: list index out of range) closed by
- not a bug: Not a multi-model PDB file
- 11:42 AM Ticket #15006 (Crash in event loop) closed by
- can't reproduce
- 11:39 AM Ticket #15005 (Crash in garbage collection) closed by
- duplicate
- 11:04 AM Ticket #15010 (Better assignment of BLAST results to sequences) created by
- From Tom's ticket, #14976: Besides these 3 new options I also want …
- 11:01 AM Dev2024-4-29 created by
- 10:59 AM 2024-4-25 created by
- 10:58 AM DeveloperMeetings edited by
- (diff)
- 10:53 AM Ticket #15009 (MD Viewer: self.atomLocation[0]: list index out of range) created by
- […]
- 9:51 AM Ticket #15008 (Clipper: 'NoneType' object has no attribute 'dim') created by
- […]
- 9:47 AM Ticket #15007 (Clipper: 'NoneType' object has no attribute 'dim') created by
- […]
Apr 22, 2024:
- 9:53 PM Ticket #15006 (Crash in event loop) created by
- […]
- 5:50 PM Ticket #14982 (combine command: ValueError: Illegal chain ID character: 'Α') closed by
- not a bug: This PDB file has unicode Greek capital letter A (0391) instead of …
- 5:03 PM Ticket #15005 (Crash in garbage collection) created by
- […]
- 4:23 PM Dev2024-4-22 edited by
- (diff)
- 4:15 PM Ticket #15004 (ArtiaX dependency not installed) created by
- […]
- 1:52 PM Ticket #14990 (Surface Color tool: list index out of range) closed by
- duplicate: User had colormap on volume surface with more than 8 colors and then …
- 1:38 PM Ticket #14989 (Crash changing volume level) closed by
- nonchimerax: This ChimeraX crashed happened in Apple's OpenGL graphics driver (in …
- 1:37 PM Ticket #15002 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 1:24 PM Ticket #15003 (PICKLUSTER: handle_scheme: KeyError: 'chain1') created by
- […]
- 12:49 PM Ticket #15002 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 12:29 PM Ticket #15000 (Crash saving atomic session state) closed by
- duplicate: Duplicate of #14998
- 12:28 PM Ticket #14999 (Crash saving atomic session state) closed by
- duplicate: More or less a duplicate of #14998
- 12:27 PM Ticket #15001 (Links to example files in Toolshed Building and Distributing bundles ...) created by
- Roden Luo points out that links to example code files are missing in …
- 12:26 PM Ticket #14998 (Crash saving atomic session state) closed by
- can't reproduce: No good indication of the actual cause of the crash
- 12:14 PM Ticket #14997 (ISOLDE: ResidueStepper references dead Structure) closed by
- duplicate: Duplicate of #14631
- 12:01 PM Ticket #14994 (Crash in check_for_changes) closed by
- can't reproduce
- 11:52 AM Ticket #14991 (ISOLDE: crash in _set_global_k) closed by
- can't reproduce: Yeah - that's almost certainly obsolete.
- 11:03 AM Ticket #14988 (Cannot write into Modeller temporary folder) closed by
- nonchimerax: Hi Robert, If you do not specify a specific folder for Modeller to …
- 10:51 AM Ticket #14987 (Crash in garbage collection) closed by
- duplicate
- 10:49 AM Ticket #14986 (Crash in garbage collection) closed by
- duplicate: Hi Whitney, Thanks for reporting this problem. We believe it is fixed …
- 10:46 AM Ticket #14985 (Infinite loop in OpenCommands) closed by
- fixed: I'm guessing the commands that got run opened another file of the same …
- 9:34 AM Ticket #15000 (Crash saving atomic session state) created by
- […]
- 9:31 AM Ticket #14999 (Crash saving atomic session state) created by
- […]
- 9:30 AM Ticket #14998 (Crash saving atomic session state) created by
- […]
- 9:20 AM Ticket #14997 (ISOLDE: ResidueStepper references dead Structure) created by
- […]
- 9:16 AM Ticket #14996 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by
- […]
- 1:59 AM Ticket #14995 (ArtiaX: cannot load Dynamo table: could not convert string to float) created by
- […]
Apr 21, 2024:
- 10:56 PM Ticket #14994 (Crash in check_for_changes) created by
- […]
- 10:26 PM Ticket #14993 (No models) created by
- […]
- 9:23 PM Ticket #14992 (Crash in QWindowSystemInterface::handleFileOpenEvent) created by
- […]
- 6:31 PM Ticket #14991 (ISOLDE: crash in _set_global_k) created by
- […]
- 3:32 PM Ticket #14990 (Surface Color tool: list index out of range) created by
- […]
- 12:44 AM Ticket #14989 (Crash changing volume level) created by
- […]
Apr 20, 2024:
- 5:32 PM Ticket #14988 (Cannot write into Modeller temporary folder) created by
- […] TAPV-5F1B Chain A MSA.fasta
- 4:09 PM Ticket #14987 (Crash in garbage collection) created by
- […]
- 10:34 AM Ticket #14986 (Crash in garbage collection) created by
- […]
- 8:07 AM Ticket #14985 (Infinite loop in OpenCommands) created by
- […]
Apr 19, 2024:
- 1:20 PM Ticket #14971 (surface dust not working in a multi-line script) closed by
- fixed: Fixed. The "wait 1" is no longer needed to get volume surfaces to be …
- 10:38 AM Ticket #14963 (Alphafold prediction send sequence to Google Colab returned: None) closed by
- can't reproduce: No reply from reporter.
- 10:37 AM Ticket #14984 (Crash in event loop. Linux. No useful details.) closed by
- can't reproduce
- 10:35 AM Ticket #14983 (Garbage collection crash) closed by
- duplicate
- 10:30 AM Ticket #14981 (Coulombic command: UnboundLocalError: local variable 'cmap' referenced ...) closed by
- fixed: Fixed probably long ago. Report is from ancient ChimeraX 1.1!
- 10:27 AM Ticket #14979 (Graphics crash, macOS 11.7.10, NVIDIA GeForce GT 750M) closed by
- nonchimerax
- 4:48 AM Ticket #14984 (Crash in event loop. Linux. No useful details.) created by
- […]
- 2:06 AM Ticket #14983 (Garbage collection crash) created by
- […]
Apr 18, 2024:
- 8:53 PM Ticket #14982 (combine command: ValueError: Illegal chain ID character: 'Α') created by
- […]
- 8:51 PM Ticket #14981 (Coulombic command: UnboundLocalError: local variable 'cmap' referenced ...) created by
- […]
- 7:29 PM Ticket #14980 (False "BLAST job failed" error on session restore) created by
- […] braf_23.cxs
- 5:52 PM 2024-4-18 edited by
- (diff)
- 5:27 PM Ticket #14979 (Graphics crash, macOS 11.7.10, NVIDIA GeForce GT 750M) created by
- […]
- 3:46 PM Ticket #14973 (Crash in event loop after RCSB fetch failed) closed by
- can't reproduce
- 3:43 PM Ticket #14972 (Crash in garbage collection while DockPrep deleting alt-locs) closed by
- duplicate
- 3:41 PM Ticket #14970 (Crash in QTabBar:paintEvent(). QPainter::begin: Paint device returned ...) closed by
- can't reproduce: Probable Qt bug. Crashed in Qt with more than 80 models open, two …
- 1:40 PM Ticket #14975 (Graphics crash, macOS 14.4, Intel Iris Plus Graphics 655) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 1:37 PM Ticket #14974 (Crash splitting molecule) closed by
- can't reproduce
- 1:16 PM Ticket #14978 (ChimeraX bug report submission) closed by
- not a bug
- 12:38 PM Ticket #14978 (ChimeraX bug report submission) created by
- […]
- 12:30 PM Ticket #14977 (Toolshed updates: IndexError: tuple index out of range) created by
- […]
- 12:21 PM Ticket #14976 (Make blastprotein command load structures and alignment without GUI) created by
- I'd like 3 new options to the blastprotein command blastprotein …
- 7:44 AM Ticket #14975 (Graphics crash, macOS 14.4, Intel Iris Plus Graphics 655) created by
- […]
- 7:01 AM Ticket #14974 (Crash splitting molecule) created by
- […] 7jjo.pdb
- 2:49 AM Ticket #14973 (Crash in event loop after RCSB fetch failed) created by
- […]
- 2:45 AM Ticket #14972 (Crash in garbage collection while DockPrep deleting alt-locs) created by
- […]
Apr 17, 2024:
- 11:53 PM Ticket #14971 (surface dust not working in a multi-line script) created by
- […]
- 11:40 PM Ticket #14970 (Crash in QTabBar:paintEvent(). QPainter::begin: Paint device returned ...) created by
- […]
- 3:13 PM Ticket #14968 (Silhouettes artifacts when saving image) closed by
- nonchimerax: Unfortunately only Apple can fix the OpenGL graphics driver and they …
- 1:50 PM Ticket #14969 (Test) closed by
- not a bug
- 1:42 PM Ticket #14969 (Test) created by
- […]
- 1:04 PM Ticket #14967 (Test) closed by
- not a bug
- 11:48 AM Ticket #14968 (Silhouettes artifacts when saving image) created by
- […] [[Image(...)]] smime.p7s
- 11:45 AM Ticket #14967 (Test) created by
- […]
- 10:24 AM Ticket #14962 (Setting background color with RGB sliders not working) closed by
- fixed: Well, "fixed", but because of some systems at UCSF being down the fix …
Apr 16, 2024:
- 11:24 AM Ticket #14966 (Make fitmap search use random placements within the target volume envelope) created by
- Roden Luo the developer of DiffFit points out that choosing the center …
- 11:11 AM Dev2024-4-22 created by
- 11:10 AM 2024-4-11 edited by
- (diff)
- 11:09 AM 2024-4-18 created by
- 11:07 AM DeveloperMeetings edited by
- (diff)
- 8:06 AM Ticket #7936 (ResidueStepper refers to dead Structure) closed by
- fixed: Sorry for the ridiculously long wait, but this will be fixed in the …
- 8:05 AM Ticket #8772 (isolde residue stepper referencing dead structure) closed by
- fixed: See #14894.
- 8:04 AM Ticket #8877 (ResidueStepper referencing dead structure) closed by
- fixed: Sorry it's taken such a long time, but this is now fixed. See #14894 …
- 8:03 AM Ticket #9523 (ISOLDE ResidueStepper holding reference to dead structure) closed by
- fixed: Sorry it's taken such a ridiculously long time, but this will be fixed …
- 8:03 AM Ticket #14538 (ISOLDE: ResidueStepper: self.positions is None) closed by
- fixed: See #14894.
- 8:02 AM Ticket #14599 (ISOLDE session save: ResidueStepper referenced closed AtomicStructure) closed by
- fixed: See #14894.
- 8:01 AM Ticket #14631 (ISOLDE: ResidueStepper references dead Structure) closed by
- fixed: Fixed (finally!). See #14894.
- 8:00 AM Ticket #14828 (ISOLDE: ResidueStepper holding reference to closed structure) closed by
- fixed: See #14894.
- 7:49 AM Ticket #14894 (ISOLDE: ResidueStepper holding reference to closed structure) closed by
- fixed: A neat solution, and works beautifully. After …
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