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Timeline
Jan 18, 2023:
- 4:59 PM Ticket #8318 (Looking Glass: libHoloPlayCore.dylib is an incompatible architecture) closed by
- limitation: I'm not going to fix this unless some user tests the ARM library and …
- 4:56 PM Ticket #8313 (AlphaFold: A UTF-8 locale is required. Got ANSI_X3.4-1968) closed by
- fixed: Fixed. I monkeypatched Python _locale.nl_langinfo(CODESET) to force …
- 1:00 PM Ticket #8275 (Provide user agent information) closed by
- fixed: [https://github.com/RBVI/cxwebservices/commit/ec56094df96fd3e647e7b4d50 …
- 11:55 AM Ticket #8327 (Crash saving image) created by
- […]
- 11:15 AM phenix-1-12-23 edited by
- (diff)
- 9:29 AM Ticket #8326 (Crash showing Rapid Access at startup) closed by
- can't reproduce
- 8:07 AM Ticket #8326 (Crash showing Rapid Access at startup) created by
- […]
- 6:52 AM Ticket #7996 (Rebuild residue to template: template problem) closed by
- fixed
- 6:51 AM Ticket #8083 (ISOLDE session restore: 'AtomicStructure' object has no attribute 'session') closed by
- fixed: Loading the new session deleted the existing model while a simulation …
- 6:41 AM Ticket #7766 (OpenMMException: Error initializing context: clCreateCommandQueue) closed by
- limitation: Error is CL_OUT_OF_HOST_MEMORY.
- 6:39 AM Ticket #7594 (Various Clipper problems) closed by
- fixed: Handling of map_to_structure_factors MTZ files should be greatly …
- 6:37 AM Ticket #7470 (Start simulation: openmm.OpenMMException: Error compiling kernel: ...) closed by
- duplicate: Sorry about not responding to this at the time... there was a spate of …
- 6:33 AM Ticket #6626 (Backrub requires N- and C-terminal flanking residues to be present) closed by
- limitation: I've removed the auto-fit rotamer option (which used this code) from …
- 6:32 AM Ticket #6540 (OpenMM crash) closed by
- can't reproduce
- 6:31 AM Ticket #6445 (ISOLDE/OpenMM: Error initializing context: clCreateContext) closed by
- limitation
- 6:28 AM Ticket #6083 (CUDA/OpenCL errors: CUDA_ERROR_OUT_OF_MEMORY) closed by
- limitation: Sorry I never responded at the time - seems there's a handful of …
- 6:24 AM Ticket #6081 (Symmetry handler using dead structure) closed by
- fixed
- 6:21 AM Ticket #6017 (openmm.OpenMMException: Error initializing context: clCreateContext) closed by
- can't reproduce
- 6:20 AM Ticket #5631 (ISOLDE: fix unparameterized residues: Residue already deleted) closed by
- fixed: Fixed in the new GUI.
- 6:20 AM Ticket #4989 (OpenMM simulation: Graphics kernel error) closed by
- can't reproduce: Not sure why I never responded to this at the time - sorry about that. …
- 6:17 AM Ticket #4942 (phenix connect command traceback when wrong Phenix directory given) closed by
- wontfix: Obsolete now, due to the R24 ChimeraX-Phenix interface.
- 6:16 AM Ticket #4896 (OpenMMException: No compatible OpenCL platform is available) closed by
- can't reproduce
- 6:15 AM Ticket #4888 (OpenMMException: invalid value for --gpu-architecture) closed by
- fixed
- 6:14 AM Ticket #4805 (ISOLDE: crash in find_clashing_atoms) closed by
- fixed
- 6:14 AM Ticket #4800 (ISOLDE: item.data is a method/function, not tuple) closed by
- fixed: Zombie ticket, long since fixed.
- 6:13 AM Ticket #4774 (Crash hitting "play" button) closed by
- can't reproduce: Never was able to reproduce this - and given that I've since redone …
- 6:11 AM Ticket #4740 (ISOLDE: wrapped C/C++ object of type QTableWidget has been deleted) closed by
- fixed: Fixed by new GUI.
- 6:10 AM Ticket #4738 (OpenMMException: /usr/local/cuda/bin/nvcc: not found) closed by
- fixed: These days, if the CUDA platform exists but encounters an error on …
- 6:09 AM Ticket #4721 (tilted slab: 'numpy.ndarray' object is not callable) closed by
- fixed: Closing this, since the headline errors are fixed. I'd still like to …
- 6:05 AM Ticket #4706 (Peptide flip: Simulation must be running!) closed by
- fixed: This was effectively fixed by ISOLDE's new GUI, which replaces …
- 6:03 AM Ticket #4702 (OpenMMException: Error compiling kernel: Compile Server Error) closed by
- can't reproduce: Just doing some spring cleaning and closing out old tickets. Hopefully …
- 6:01 AM Ticket #4658 (OpenMMException: Error compiling kernel: Compile Server Error) closed by
- can't reproduce
- 6:00 AM Ticket #4654 (ISOLDE: volumecommand.volume being passed session of None) closed by
- fixed
- 5:59 AM Ticket #4623 (ISOLDE: wrapped C/C++ object of type QLabel has been deleted) closed by
- fixed: Long since fixed, but I forgot to close this ticket. Sorry!
- 5:57 AM Ticket #4507 (ISOLDE: wrapped C/C++ object of type QTableWidget has been deleted) closed by
- fixed: Fixed by new GUI.
- 5:47 AM Ticket #4305 (ISOLDE residue validation: cannot unpack non-iterable ...) closed by
- fixed: Long since fixed, but forgot to close the ticket. Sorry!
- 5:47 AM Ticket #4267 (Problem docking ISOLDE widget) closed by
- fixed: This should be mostly fixed by the new ISOLDE GUI - its minimum height …
- 5:44 AM Ticket #4166 (ISOLDE/ParmEd: UnboundLocalError: local variable 'compiler_package' ...) closed by
- fixed
- 5:43 AM Ticket #4122 (End of simulation: 'PositionRestraintMgr' object has no attribute ...) closed by
- fixed: Finally got around to making sure ISOLDE (as of the next release) can …
- 5:41 AM Ticket #4093 (OpenMM crash uploading OpenCL array) closed by
- can't reproduce
- 5:40 AM Ticket #4018 (ISOLDE: OpenMM: find_glycan_template_name_and_link: multiple bonds ...) closed by
- fixed
- 5:39 AM Ticket #4003 (OpenMM OpenCL crash on Mac in Intel graphics driver) closed by
- can't reproduce
- 5:38 AM Ticket #3966 (Clipper: Failure to read BUSTER MTZ file) closed by
- fixed: Seems I never closed this. Doing so now.
- 5:37 AM Ticket #3917 (ISOLDE: get_symmetry_handler: structure is None) closed by
- fixed: Clearing out the backlog of fixed-but-unclosed tickets.
- 5:36 AM Ticket #3807 (OpenMM crash with 0.91 run directly from .dmg) closed by
- can't reproduce
- 5:36 AM Ticket #3805 (Flip peptide bond: Simulation must be running) closed by
- fixed
- 5:35 AM Ticket #3774 ('ProperDihedral' object has no attribute '_c_pointer_ref') closed by
- fixed: Most likely a GUI table failing to refresh itself when the selected …
- 5:34 AM Ticket #3768 (OpenMM/OpenCL crash) closed by
- can't reproduce
- 5:33 AM Ticket #3752 (ISOLDE validation: not enough values to unpack) closed by
- fixed
- 5:32 AM Ticket #3747 (Register shift: m > k must hold) closed by
- fixed: Sorry... forgot to close this ticket at the time.
- 5:31 AM Ticket #3743 (ISOLDE crash on startup (divide by zero; structure-prediction program ...) closed by
- fixed: Sorry... found and fixed the bug back then, but failed to close the …
- 5:29 AM Ticket #3712 (Clipper map roaming overflow in computing bounds) closed by
- can't reproduce
- 5:27 AM Ticket #3699 (Starting simulation: clEnqueueNDRangeKernel (-4)) closed by
- can't reproduce
- 5:27 AM Ticket #3696 (ISOLDE color-picker problem) closed by
- fixed: Turns out I have a really bad habit of not closing out old tickets... …
- 5:25 AM Ticket #3616 (cartoon() 'atoms' parameter type changed) closed by
- fixed
- 5:24 AM Ticket #3613 (ISOLDE: cannot import name 'save' from 'chimerax.core.commands') closed by
- fixed
- 5:23 AM Ticket #3601 (_show_selected_unparameterised_residue: not enough values to unpack) closed by
- fixed: Sorry for not closing this back then... better late than never!
- 5:21 AM Ticket #3593 (stepper.step_forward: index is out of bounds) closed by
- fixed: The offending code was retired some time ago. :)
- 5:20 AM Ticket #3569 (Problem reading MTZ data: list index out of range) closed by
- fixed: Clearing out old tickets - this was fixed quite some time ago.
- 5:18 AM Ticket #3566 (OpenMM: No template found for residue) closed by
- fixed: Clearing out the backlog of old tickets which (for various reasons) I …
- 5:16 AM Ticket #3538 (Problem matching GLYCAM templates) closed by
- can't reproduce
- 5:16 AM Ticket #3535 (Nucleotides: asking for distance from None) closed by
- fixed: Sorry for the necropost - just closing out old tickets. :)
- 5:14 AM Ticket #3508 (ISOLDE's self.selected_model is dead) closed by
- fixed: Well, I've *finally* gotten around to making ISOLDE gracefully recover …
- 5:12 AM Ticket #3407 (Maximum common substructure) closed by
- worksforme: I still need to revisit this at some time in the future to make it …
- 5:10 AM Ticket #3377 (Template mismatch errors) closed by
- fixed: Closing out old tickets - ISOLDE's had functionality to help with …
- 5:09 AM Ticket #3298 (Crash getting global interpreter lock) closed by
- fixed
- 5:08 AM Ticket #3221 (Chain mix up using ISOLDE) closed by
- can't reproduce
- 5:07 AM Ticket #3156 (Error initializing context: clGetPlatformIDs) closed by
- can't reproduce: Hmm... looks like I forgot to close out this ticket. I trust …
- 5:02 AM Ticket #3143 (Starting simulation: Error initializing context: clGetDeviceIDs) closed by
- fixed
- 5:01 AM Ticket #3068 (Crash starting ISOLDE) closed by
- can't reproduce
- 5:01 AM Ticket #3049 (OpenMM coordinate update: RuntimeError: Release Object) closed by
- can't reproduce
- 5:00 AM Ticket #3034 (Infrequent ISOLDE crash) closed by
- fixed: Fixed, I guess... (problem hasn't cropped up in a long long time).
- 3:56 AM Ticket #3021 (ISOLDE: various errors) closed by
- can't reproduce
- 3:55 AM Ticket #2992 (ISOLDE referencing a Structure that's been deleted) closed by
- fixed: All the scenarios I know of that could potentially lead to this error …
- 3:54 AM Ticket #2905 (OpenMM: Multiple matching templates found for residue) closed by
- fixed: While I do occasionally see cases where a tightly-constrained …
- 3:50 AM Ticket #2798 (Arcane version-conflict reporting) closed by
- fixed
- 3:50 AM Ticket #2796 (Crash opening structure in conjunction with ISOLDE) closed by
- can't reproduce
- 3:48 AM Ticket #2773 (Crash installing ISOLDE(?)) closed by
- can't reproduce: Just going through and closing out old tickets.
- 3:47 AM Ticket #2764 (ISOLDE not longer compatible with 0.9) closed by
- fixed: Doing some spring cleaning, closing out obsolete old tickets.
- 3:46 AM Ticket #2735 (OpenMM crash running simulation) closed by
- can't reproduce
- 3:44 AM Ticket #2652 (ISOLDE: using deleted 'session' attribute of dead Structure) closed by
- fixed: From the next ISOLDE release onwards, closing the working model with a …
- 3:42 AM Ticket #2531 ("spotlight moved" trigger handler using dead Structure) closed by
- fixed
- 3:42 AM Ticket #2424 (Array of coordinates is None) closed by
- fixed
- 3:41 AM Ticket #2374 (ISOLDE: multiple different errors) closed by
- fixed
- 3:39 AM Ticket #2336 (ChimeraX bug report submission) closed by
- fixed: Clearing out old tickets (this was fixed long ago, but I forgot to …
- 3:38 AM Ticket #2204 (ISOLDE: ramaplot: wrapped C/C++ object of type QVBoxLayout has been deleted) closed by
- fixed
- 3:37 AM Ticket #1856 (OpenGL error, glClear: invalid framebuffer operation) closed by
- can't reproduce: Doing some spring-cleaning, clearing away old tickets. Haven't seen …
- 2:46 AM Ticket #5746 (OpenMMException: Error compiling program: nvrtc: error: failed to open ...) closed by
- can't reproduce
- 2:45 AM Ticket #5745 (OpenMM: Error compiling program: nvrtc: error: failed to open ...) closed by
- fixed: Long since fixed - ISOLDE now automatically falls back to using OpenCL …
- 2:43 AM Ticket #5670 (OpenMM: Error uploading array TabulatedFunction) closed by
- can't reproduce
- 2:42 AM Ticket #3269 (Custom multitouch trackpad bindings) closed by
- fixed: Sorry for not closing this at the time…
- 2:41 AM Ticket #2906 (Building OpenMM installer in devtoolset-7) closed by
- wontfix: Closing out this ancient ticket, since things have well and truly moved on.
Jan 17, 2023:
- 7:32 PM Ticket #8320 (volume multiply: local variable 'v0' referenced before assignment) closed by
- fixed: Fixed "volume multiply" with one map and inPlace true. Made a new …
- 7:32 PM Ticket #8325 (Add an inPlace option to the "volume scale" command) created by
- In ticket #8320 Tristan was trying to invert an map in place using the …
- 5:25 PM 2023-1-19 edited by
- (diff)
- 5:25 PM 2023-1-19 edited by
- (diff)
- 5:24 PM 2023-1-19 created by
- 5:22 PM DeveloperMeetings edited by
- (diff)
- 5:08 PM Training edited by
- (diff)
- 2:49 PM Ticket #8324 (Crash in removeDockWidget from clicking on a half-docked panel) created by
- […]
- 1:37 PM Ticket #8323 (Coot-like "replace fragment") created by
- As per this thread: …
- 12:54 PM Ticket #8319 (Looking Glass: libHoloPlayCore.dylib is an incompatible architecture) closed by
- duplicate: Duplicate of #8318.
- 11:48 AM Ticket #8306 (Crash in Qt event loop after showing Volume Viewer, lots of clipper use) closed by
- can't reproduce
- 11:43 AM Ticket #8305 (AlphaFold prediction failure) closed by
- not a bug: From the files you attached, your prediction sequence is DNA …
- 10:10 AM Ticket #8322 (Unsupported scale factor (0.000000) detected on Display0) closed by
- limitation: Looks the same as #8226
- 10:04 AM Ticket #8321 (Crash QGridLayout destructor) closed by
- can't reproduce: My best guess is that it's XMAS gui code from the session.
- 9:43 AM Ticket #8317 (Crash in event loop) closed by
- can't reproduce
- 9:40 AM Ticket #8316 (Crash in Qt event loop after showing cartoons) closed by
- can't reproduce
- 9:36 AM Ticket #8315 (Crash in event loop) closed by
- can't reproduce
- 9:32 AM Ticket #8314 (AlphaFold: NotImplementedError: A UTF-8 locale is required) closed by
- duplicate: duplicate of #8313
- 9:18 AM Ticket #8311 (MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted) closed by
- duplicate
- 9:14 AM Ticket #8310 (MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted) closed by
- duplicate: long ago fixed
- 9:10 AM Ticket #8309 (Crash in event loop) closed by
- can't reproduce
- 9:00 AM Ticket #8307 (Dead Structure Measurement tool trying to show status) closed by
- duplicate: duplicate of #8148
- 8:57 AM Ticket #4917 (Keyboard interrupt while finding possible templates) closed by
- fixed: Took your advice on that... but forgot to actually close the ticket at …
- 8:56 AM Ticket #4920 (Crash in matplotlib updating Ramachandran plot) closed by
- can't reproduce
- 8:55 AM Ticket #4958 (peptide flip: Simulation must be running!) closed by
- fixed
- 8:54 AM Ticket #5576 (Update coordinates: OpenMM: RuntimeError: Release Object) closed by
- can't reproduce
- 8:53 AM Ticket #5783 (Problem swapping pseudo symmetric side chains) closed by
- can't reproduce
- 8:51 AM Ticket #5799 (ISOLDE crash in get_shell_of_residues: extremely deep recursion in ...) closed by
- fixed: Resolving this as "effectively" fixed, since the new soft-core …
- 8:49 AM Ticket #5813 (Version conflict during ISOLDE initialization?!?) closed by
- can't reproduce
- 8:48 AM Ticket #5822 (ISOLDE: .cif does not appear to contain any valid residue templates) closed by
- fixed: Never did hear back about those templates, I'm afraid. Anyway, as of …
- 8:45 AM Ticket #5899 (ISOLDE: swap equivalent atoms: Values array length 3 does not match ...) closed by
- fixed
- 8:44 AM Ticket #5900 (ISOLDE: add real-space map: structure is None) closed by
- fixed: Very sorry about the super-slow response, but this is now fixed.
- 8:42 AM Ticket #5957 (Ramachandran plot accessing deleted widgets) closed by
- fixed: Ramachandran plot was completely reworked in the ISOLDE 1.4 release.
- 8:41 AM Ticket #5961 (Crash in OpenMM getState) closed by
- fixed
- 8:41 AM Ticket #6050 (ISOLDE vs. submodels) closed by
- can't reproduce
- 8:38 AM Ticket #8322 (Unsupported scale factor (0.000000) detected on Display0) created by
- […]
- 8:35 AM Ticket #6087 (ISOLDE: swap equivalent atoms: Values array length 3 does not match ...) closed by
- fixed
- 8:35 AM Ticket #6088 (ISOLDE: add real-space map: structure is None) closed by
- fixed: This should all be fixed now.
- 8:34 AM Ticket #6095 ((ISOLDE?) segmentation fault) closed by
- can't reproduce
- 8:33 AM Ticket #6128 (Failure opening .mtz file: Spgr_cacheobj: symops fail) closed by
- can't reproduce
- 8:28 AM Ticket #6142 (ISOLDE: various errors) closed by
- fixed: Going to tentatively close this as fixed - haven't seen another …
- 8:25 AM Ticket #6245 (ISOLDE _show_selected_clash: 'residues' is empty) closed by
- fixed: If I recall correctly, the clashes table wasn't clearing itself when …
- 8:23 AM Ticket #6283 (phi-psi in isolde does not show current selection.) closed by
- not a bug: Sorry about the ridiculously slow response - seems this one fell off …
- 8:19 AM Ticket #6304 (Various errors) closed by
- fixed: Everything now seems to be working OK for both ortho and mono camera modes.
- 8:16 AM Ticket #6306 (Crash finding clashing atoms) closed by
- fixed: This was able to happen if the user hit the sim stop button while the …
- 8:15 AM Ticket #6455 (ISOLDE: crash in find_clashing_atoms) closed by
- fixed: This was able to happen if the user hit the sim stop button while the …
- 8:11 AM Ticket #6510 (Zoom/recenter with mouse) closed by
- fixed: This is now all working quite nicely - with Clipper active, …
- 8:06 AM Ticket #6783 (ISOLDE not listing clashes) closed by
- fixed: Abandoned the use of forces as a proxy for clashes - the Clashes table …
- 8:04 AM Ticket #7691 (Clipper closing possible already-closed model during session reset) closed by
- fixed: Going to close this as *probably* fixed - will revisit if it crops up …
- 8:03 AM Ticket #7709 (Simulation stop: 'NoneType' object has no attribute 'atoms') closed by
- fixed: Another instance of the rotamer preview bug.
- 8:01 AM Ticket #6844 (Flip peptide bond: wrapped C/C++ object of type QTableWidget has been ...) closed by
- fixed: Totally rebuilt GUI as of 1.4, taking care of this bug amongst others.
- 8:00 AM Ticket #8321 (Crash QGridLayout destructor) created by
- […]
- 7:59 AM Ticket #7168 (ISOLDE/OpenMM: fitting Ramachandran outliers: Particle coordinate is nan) closed by
- fixed: This should become *almost* impossible in ISOLDE 1.6 (when it comes …
- 7:51 AM Ticket #7270 (ISOLDE: sim_manager is None) closed by
- fixed: This should be fixed in the latest versions. Please let me know if it …
- 7:49 AM Ticket #7394 (Stop simulation: model is None) closed by
- fixed: This was happening if the simulation was stopped with the rotamer …
- 7:42 AM Ticket #7504 (ISOLDE Deleting symmetry model: 'AtomicStructure' object has no ...) closed by
- fixed: As of the next release, ISOLDE will now recover gracefully when the …
- 7:39 AM Ticket #7636 (ISOLDE holding ref to deleted structure) closed by
- fixed
- 7:39 AM Ticket #7638 (ISOLDE holding ref to deleted structure) closed by
- fixed
- 7:38 AM Ticket #7639 (Models closed while simulation running) closed by
- fixed
- 7:37 AM Ticket #7647 (Second sim stop: 'NoneType' object has no attribute 'atoms') closed by
- fixed
- 7:37 AM Ticket #7649 (Second sim stop: 'NoneType' object has no attribute 'atoms') closed by
- fixed
- 7:36 AM Ticket #7658 (Model is None after sim stop, and then things go pear-shaped) closed by
- fixed
- 7:35 AM Ticket #7756 (Stopping simulation: 'NoneType' object has no attribute 'atoms') closed by
- fixed: This was happening if a simulation was stopped with the rotamer …
- 7:34 AM Ticket #7873 (ISOLDE: wrapped C/C++ object of type WinAutoResizeQComboBox has been ...) closed by
- fixed
- 7:32 AM Ticket #8089 (Clipper: AttributeError: 'NoneType' object has no attribute ...) closed by
- fixed
- 7:31 AM Ticket #8098 (ISOLDE: 'AtomicStructure' object has no attribute 'session') closed by
- fixed
- 7:30 AM Ticket #8099 (ISOLDE: close session: 'AtomicStructure' object has no attribute ...) closed by
- fixed: As of the next release, ISOLDE will now recover gracefully if the …
- 7:12 AM Ticket #8320 (volume multiply: local variable 'v0' referenced before assignment) created by
- […]
- 7:01 AM Ticket #8204 ('close' after paused simulation: 'AtomicStructure' object has no ...) closed by
- fixed
- 7:00 AM Ticket #8269 (ISOLDE: closing structure after paused sim: 'AtomicStructure' object ...) closed by
- fixed
- 7:00 AM Ticket #8319 (Looking Glass: libHoloPlayCore.dylib is an incompatible architecture) created by
- […] env&log.txt
- 6:56 AM Ticket #8318 (Looking Glass: libHoloPlayCore.dylib is an incompatible architecture) created by
- […]
- 4:08 AM Ticket #8317 (Crash in event loop) created by
- […]
- 3:52 AM Ticket #8316 (Crash in Qt event loop after showing cartoons) created by
- […]
- 3:48 AM Ticket #8315 (Crash in event loop) created by
- […]
Jan 16, 2023:
- 5:42 AM Ticket #8314 (AlphaFold: NotImplementedError: A UTF-8 locale is required) created by
- […]
- 5:39 AM Ticket #8313 (AlphaFold: A UTF-8 locale is required. Got ANSI_X3.4-1968) created by
- […]
- 2:40 AM Ticket #8312 (ISOLDE: "start sim": No compatible OpenCL platform is available) created by
- […]
Jan 15, 2023:
- 5:29 PM Ticket #8311 (MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted) created by
- […]
- 5:19 PM Ticket #8310 (MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted) created by
- […]
- 2:56 PM Ticket #8309 (Crash in event loop) created by
- […]
- 1:33 PM Ticket #8308 (Crash opening mmCIF) created by
- […]
Jan 14, 2023:
- 2:22 PM Ticket #8307 (Dead Structure Measurement tool trying to show status) created by
- […]
- 1:10 PM Ticket #8306 (Crash in Qt event loop after showing Volume Viewer, lots of clipper use) created by
- […]
- 7:58 AM Ticket #8305 (AlphaFold prediction failure) created by
- […] results.zip
Jan 13, 2023:
- 2:18 PM Ticket #8304 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: Hi Andrew, Thanks for reporting this problem. We believe it is fixed …
- 2:15 PM Ticket #8303 (Crash saving image) closed by
- can't reproduce
- 2:12 PM Ticket #8304 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 2:08 PM Ticket #8303 (Crash saving image) created by
- […]
- 1:55 PM phenix-1-12-23 edited by
- (diff)
- 1:54 PM Features edited by
- (diff)
- 1:54 PM Features edited by
- (diff)
- 12:02 PM Ticket #8299 (Graphics crash, macOS 13.1, M1 Pro graphics) closed by
- nonchimerax: Apple M1 graphics driver crash. This is the first one I have ever …
- 11:51 AM Ticket #8301 (New AlphaFold errors) closed by
- nonchimerax: I worked on this error 8 months ago, ticket #6961 …
- 11:38 AM Ticket #8302 (Log panel is blank, Windows) closed by
- nonchimerax: […]
- 11:37 AM Ticket #8302 (Log panel is blank, Windows) created by
- Log panel is blank. Also Help Viewer shows nothing. Apparently Qt …
- 11:10 AM Ticket #8301 (New AlphaFold errors) created by
- […]
- 10:46 AM Ticket #8300 (Didn't find section 'Peptide bond' in tab 'ISOLDE') closed by
- limitation: Currently you need to restart ChimeraX after installing ISOLDE for the …
- 9:48 AM Ticket #8298 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce
- 9:46 AM Ticket #8297 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce
- 6:31 AM Ticket #8300 (Didn't find section 'Peptide bond' in tab 'ISOLDE') created by
- […]
- 1:34 AM Ticket #8299 (Graphics crash, macOS 13.1, M1 Pro graphics) created by
- […]
Jan 12, 2023:
- 6:30 PM Ticket #8298 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 4:39 PM Ticket #8297 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 4:06 PM 2023-1-12 edited by
- (diff)
- 4:05 PM 2023-1-12 edited by
- (diff)
- 4:05 PM 2023-1-12 edited by
- (diff)
- 2:59 PM Ticket #8295 (Allow different case for fetch database name) closed by
- fixed
- 1:14 PM Ticket #8294 (Code signature problem?) closed by
- nonchimerax: The code signature for ChimeraX 1.5 is of course fine, since it works …
- 1:08 PM Ticket #8293 (Graphics crash, macOS 10.15.4, Intel Iris Plus Graphics) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 12:59 PM Ticket #8296 (Add movieFramerate option to "coordset slider" command) closed by
- fixed: Done. The default recorded movie playback speed is 25 frames per …
- 12:54 PM Ticket #8296 (Add movieFramerate option to "coordset slider" command) created by
- […]
- 9:00 AM Ticket #8295 (Allow different case for fetch database name) created by
- […]
- 8:48 AM Ticket #8280 (ISOLDE: 'close' after 'sim pause': 'AtomicStructure' object has no ...) closed by
- fixed: OK, ISOLDE now recovers gracefully if the working model is deleted …
- 8:06 AM Ticket #8294 (Code signature problem?) created by
- […]
Jan 11, 2023:
- 11:04 PM Ticket #8293 (Graphics crash, macOS 10.15.4, Intel Iris Plus Graphics) created by
- […]
- 6:12 PM Ticket #8292 (Adding DisplayVersion to registry for WIndows installation) closed by
- fixed: ChimeraX uses innosetup to build the installer. I've added the …
- 3:49 PM Training edited by
- (diff)
- 3:44 PM Training edited by
- (diff)
- 1:23 PM Ticket #8288 (List index out of range for UniProt DGAL_ECOLI) closed by
- fixed: If the accession code (P02927) maps to a different entry (P0AEE6), the …
- 11:20 AM Ticket #8291 (Crash in event loop after using XMAS) closed by
- can't reproduce
- 11:09 AM Ticket #8289 (Long atom spec crashes ChimeraX) closed by
- duplicate
- 5:07 AM Ticket #8292 (Adding DisplayVersion to registry for WIndows installation) created by
- […]
- 5:05 AM Ticket #8291 (Crash in event loop after using XMAS) created by
- […]
- 12:03 AM Ticket #8290 (Mol2 not creating metal-coordination pseudobonds) created by
- […]
Jan 10, 2023:
- 5:06 PM Ticket #8289 (Long atom spec crashes ChimeraX) created by
- […]
- 4:59 PM phenix-1-12-23 edited by
- (diff)
- 4:49 PM Ticket #8288 (List index out of range for UniProt DGAL_ECOLI) created by
- […]
- 4:45 PM Ticket #8287 (ChimeraX 1.4 says at startup 1.5 update available even though 1.5 is ...) created by
- […]
- 4:41 PM Ticket #8286 (ChimeraX Update Available does not show install instructions) created by
- […]
- 4:32 PM Ticket #8285 (Add option to uniprot open command to associate sequence with a ...) created by
- I'd like to be able to associate a uniprot sequence opened with the …
- 4:23 PM Ticket #8284 (Show fusion protein regions in sequence viewer) created by
- From ticket #8283: Actually, what I would REALLY like even better (or …
- 4:20 PM Ticket #8283 (RFE: improve chain info for fusion proteins (list multiple UniProt IDs)) closed by
- fixed: Ok, the Log chain table now shows all the uniprot identifiers for a …
- 2:29 PM Ticket #8283 (RFE: improve chain info for fusion proteins (list multiple UniProt IDs)) created by
- It would really help to understand fusion/insertion proteins if the …
- 2:21 PM phenix-1-12-23 created by
- 2:20 PM Features edited by
- (diff)
- 1:46 PM Ticket #8282 (Clipper: Cannot determine the correct value for the free reflections) created by
- […]
- 1:10 PM Ticket #8281 (Host name resolution failed getting toolshed info) closed by
- nonchimerax
- 12:29 PM 2023-1-12 edited by
- (diff)
- 12:29 PM Dev2022-1-16 created by
- 12:28 PM Dev2022-1-9 edited by
- (diff)
- 12:27 PM 2023-1-12 created by
- 12:26 PM DeveloperMeetings edited by
- (diff)
- 12:22 PM Ticket #8281 (Host name resolution failed getting toolshed info) created by
- […]
- 11:31 AM Ticket #8256 (Documentation links missing) reopened by
- The daily build continues to have bold text instead of links, likely …
- 10:52 AM Ticket #8279 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce
- 10:50 AM Ticket #8278 (Crash after opening session file) closed by
- can't reproduce
- 10:39 AM Ticket #8277 (Crash using registration dialog) closed by
- can't reproduce: Hi Sampathkumar, Thanks for reporting this problem. I recommend …
- 10:32 AM Ticket #8276 (Crash handling text input) closed by
- can't reproduce
- 6:59 AM Ticket #8280 (ISOLDE: 'close' after 'sim pause': 'AtomicStructure' object has no ...) created by
- […]
- 6:26 AM Ticket #8279 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 1:43 AM Ticket #8278 (Crash after opening session file) created by
- […]
Jan 9, 2023:
- 10:25 PM Ticket #8277 (Crash using registration dialog) created by
- […]
- 5:40 PM Ticket #8276 (Crash handling text input) created by
- […]
- 4:57 PM Dev2022-1-9 edited by
- (diff)
- 4:57 PM Dev2022-1-9 edited by
- (diff)
- 4:48 PM Ticket #8275 (Provide user agent information) created by
- Have web service requests from ChimeraX identify the requester via …
- 4:22 PM Dev2022-1-9 edited by
- (diff)
- 1:45 PM Ticket #8272 (Open command with a directory when a file was expected) closed by
- fixed: Not sure how this produced a traceback. For me (using "open …
- 11:36 AM Ticket #8256 (Documentation links missing) closed by
- fixed: I made the default bash for the chimera account /usr/local/bin/bash, …
- 10:03 AM Ticket #8153 (Atoms lost reading pdbe_bio file, atoms not grouped by model in mmCIF file) closed by
- fixed: "fixed" this by extending previous found PDB (NMR) model. You will …
- 7:20 AM Ticket #8274 (ArtiaX session save: Unknown class name 'MarkerSetPlus') created by
- […]
- 2:51 AM Ticket #8273 (Crash showing Rapid Access at startup) created by
- […]
Jan 6, 2023:
- 1:00 PM Ticket #8271 (Restore new session in old ChimeraX) closed by
- limitation
- 12:58 PM Ticket #8272 (Open command with a directory when a file was expected) created by
- […]
- 11:32 AM Dev2022-1-9 edited by
- (diff)
- 11:21 AM Ticket #8270 (Specific graphic bug) closed by
- not a bug: Yes. We made "close session" reset the graphical settings like …
- 11:15 AM Ticket #8268 (AlphaFold: sequence argument not recognized) closed by
- not a bug: Sequences of amino acids must be upper case letters. Yours are all …
- 11:15 AM Ticket #8271 (Restore new session in old ChimeraX) created by
- […]
- 11:13 AM Ticket #8267 (Segger: "import tables" failure) closed by
- fixed: Your old daily build of ChimeraX (September 2021) has a broken version …
- 10:14 AM Ticket #8270 (Specific graphic bug) created by
- […]
- 4:24 AM Ticket #8269 (ISOLDE: closing structure after paused sim: 'AtomicStructure' object ...) created by
- […]
Jan 5, 2023:
- 4:27 PM Ticket #8268 (AlphaFold: sequence argument not recognized) created by
- […]
- 2:18 PM NIAID2022 edited by
- (diff)
- 2:15 PM NIAID2022 edited by
- (diff)
- 2:07 PM NIAID2022 edited by
- (diff)
- 1:37 PM NIAID2022 edited by
- (diff)
- 1:06 PM Ticket #8267 (Segger: "import tables" failure) created by
- […]
- 12:55 PM Ticket #8264 (Can't run MacOS initially from command line) closed by
- nonchimerax: This is an Apple gatekeeper issue. I didn't see anyone trying to …
- 12:04 PM 2023-1-5 edited by
- (diff)
- 11:33 AM 2023-1-5 edited by
- (diff)
- 11:30 AM 2023-1-5 edited by
- (diff)
- 10:20 AM Ticket #8265 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce
- 10:00 AM Ticket #8262 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce
- 7:11 AM Ticket #8266 (Mac compiler error) created by
- […]
- 6:52 AM Ticket #8265 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 6:51 AM Ticket #8264 (Can't run MacOS initially from command line) created by
- […]
- 6:07 AM Ticket #8263 (Problems with combine command) created by
- […] combined_models_in_clipper_then_trimmed.jpg
Jan 4, 2023:
- 7:40 PM Ticket #8262 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 4:00 PM Ticket #8261 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: Hi Joseph, Thanks for reporting this problem. We believe it is fixed …
- 3:55 PM Ticket #8261 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 3:04 PM Ticket #8255 (Wrong orientation for defined axis) closed by
- fixed: fix: …
- 10:48 AM Ticket #8118 (Crash with segidChains true) closed by
- fixed: Some segment IDs were blank, resulting in null chain IDs. These …
- 9:56 AM Ticket #8259 (Crash fetching available Toolshed packages) closed by
- duplicate
- 9:55 AM Ticket #8258 (Crash fetching available Toolshed packages) closed by
- can't reproduce: Hi Uma, Please upgrade to the ChimeraX 1.5 release. If you then …
- 9:50 AM Ticket #8257 (MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted) closed by
- duplicate
- 8:34 AM Ticket #8260 (Font sizes in daily build) created by
- […] Screenshot_20230104_163126.png
- 2:06 AM Ticket #8259 (Crash fetching available Toolshed packages) created by
- […]
- 2:01 AM Ticket #8258 (Crash fetching available Toolshed packages) created by
- […]
Jan 3, 2023:
- 10:32 PM Ticket #8257 (MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted) created by
- […]
- 7:05 PM Ticket #8254 (Add record and speed buttons to volume series slider) closed by
- fixed: Done. Made volume series slider use same controls as other sliders …
- 3:31 PM Ticket #8256 (Documentation links missing) created by
- In the 1.5 release, clicking on Help→Programming Manual, then "API …
- 3:23 PM Ticket #8255 (Wrong orientation for defined axis) created by
- […] 6idf.pdb
- 2:38 PM Ticket #8254 (Add record and speed buttons to volume series slider) created by
- The volume series slider gui uses custom Qt code to put a 1/2 …
- 2:18 PM Ticket #8210 (Crash running two AlphaFold predictions in two ChimeraX instances) closed by
- nonchimerax
- 2:16 PM Ticket #8252 (glUniformMatrix4fv: invalid operation) closed by
- nonchimerax: OpenGL driver problem. Failed using OpenGL drawing status message.
- 2:13 PM Ticket #8250 (Crash in _adjust_surface_geometry) closed by
- limitation: Memory allocation failed when trying to subdivide volume surface …
- 2:01 PM Dev2022-1-9 created by
- 2:00 PM Dev2022-12-19 edited by
- (diff)
- 1:56 PM 2023-1-5 created by
- 1:55 PM DeveloperMeetings edited by
- (diff)
- 1:54 PM DeveloperMeetings2022 created by
- 1:52 PM GroupMeetings2022 created by
- 1:47 PM Ticket #6719 (Block trigger handlers) closed by
- fixed: Okay, incorporated this but named the context manager "blocked" and …
- 1:03 PM Ticket #8239 (Graphics crash, macOS 10.14.6, NVIDIA GeForce GTX 775M) closed by
- nonchimerax: Apple Nvidia graphics driver crash.
- 12:49 PM Ticket #8235 (Crash saving image in Pillow, ChimeraX 1.3, Linux 3.10) closed by
- nonchimerax: Crash reported several times before in Pillow saving image file, …
- 12:41 PM Ticket #8231 (Crash in bug reporter) closed by
- nonchimerax: ChimeraX was trying to show the Bug Reporter panel because the …
- 12:29 PM Ticket #8222 (Graphics crash, macOS 10.15.7, Intel HD Graphics 4000) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 11:33 AM Ticket #8253 (Slider no longer working smoothly) closed by
- not a bug: Ugh. My bad. Had just added a new GUI widget to adjust the controlling …
- 10:39 AM Ticket #8251 (No space left on device saving command history) closed by
- nonchimerax
- 10:33 AM Ticket #8249 (Crash in QMainWindow::removeDockWidget) closed by
- can't reproduce
- 10:29 AM Ticket #8248 (Crash in color chooser) closed by
- duplicate: duplicate of #7995
- 10:03 AM Ticket #8247 (Session open: function 'set_pbgroup_py_instance' not found) closed by
- duplicate: Hi Lingyi, Thanks for reporting this problem. It has been fixed in …
- 9:56 AM Ticket #8246 (Crash showing bug reporter) closed by
- can't reproduce: 1.2.4
- 9:54 AM Ticket #8245 (H-bonds: acc_phi_psi() takes 8 positional arguments but 9 were given) closed by
- not a bug: Hi Garima, I don't know how you generated this PDB file, but it has a …
- 9:32 AM Ticket #8253 (Slider no longer working smoothly) created by
- […]
- 6:54 AM Ticket #8252 (glUniformMatrix4fv: invalid operation) created by
- […]
- 12:22 AM Ticket #8251 (No space left on device saving command history) created by
- […]
Jan 2, 2023:
- 2:09 PM Ticket #8250 (Crash in _adjust_surface_geometry) created by
- […]
- 1:25 PM Ticket #8249 (Crash in QMainWindow::removeDockWidget) created by
- […]
- 6:40 AM Ticket #8248 (Crash in color chooser) created by
- […]
Jan 1, 2023:
- 5:26 PM Ticket #8247 (Session open: function 'set_pbgroup_py_instance' not found) created by
- […]
- 2:05 PM Ticket #8246 (Crash showing bug reporter) created by
- […]
Dec 31, 2022:
- 1:51 AM Ticket #8245 (H-bonds: acc_phi_psi() takes 8 positional arguments but 9 were given) created by
- […] stableL28.pdb
Dec 30, 2022:
- 1:42 PM ChangeLog edited by
- (diff)
- 9:13 AM Ticket #8244 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: Hi Laura, Thanks for reporting this problem. We believe it is fixed …
- 8:40 AM Ticket #8244 (Crash using File→Open on Windows and/or in return statement) created by
- […]
Dec 29, 2022:
- 5:36 PM Ticket #8170 (Files should use symmetry information if available) closed by
- fixed: Okay, I have added a commit to the still-outstanding pull request to …
- 4:52 PM Ticket #8243 (Re: [EXTERNAL] Re: Issue with installation of ISOLDE on macOS 11.7.2) closed by
- duplicate: Followup to #8240
- 4:51 PM Ticket #8241 (Re: [EXTERNAL] Re: Issue with installation of ISOLDE on macOS 11.7.2) closed by
- duplicate: Followup to #8240
- 3:10 PM Ticket #8237 (Restore new session in old ChimeraX) closed by
- limitation
- 2:24 PM Ticket #8243 (Re: [EXTERNAL] Re: Issue with installation of ISOLDE on macOS 11.7.2) created by
- […] [[Image(...)]]
- 1:51 PM Ticket #8242 (Re: [EXTERNAL] Re: Issue with installation of ISOLDE on macOS 11.7.2) created by
- […] [[Image(...)]]
- 12:16 PM Ticket #8241 (Re: [EXTERNAL] Re: Issue with installation of ISOLDE on macOS 11.7.2) created by
- […] [[Image(...)]]
- 9:31 AM Ticket #8240 (Re: [EXTERNAL] Re: Issue with installation of ISOLDE on macOS 11.7.2) created by
- […] [[Image(...)]]
Dec 28, 2022:
- 7:14 PM Ticket #8239 (Graphics crash, macOS 10.14.6, NVIDIA GeForce GTX 775M) created by
- […]
- 8:49 AM Ticket #8238 (User-installed bundles interfering with build) created by
- When doing "make install" from top ChimeraX directory: …
Dec 27, 2022:
- 11:25 PM Ticket #8237 (Restore new session in old ChimeraX) created by
- […]
- 8:25 PM Ticket #8230 (Wiggle tool not found after installation) closed by
- limitation: We had several bugs that prevented the Wiggle wheel (.whl file) from …
- 12:42 PM Ticket #8236 (Graphics hardware encountered an error and was reset) created by
- […]
- 11:41 AM Ticket #8226 (Unsupported scale factor (0.000000) detected on Display0) closed by
- limitation: Hi Kelvin, Thanks for that info. This isn't a problem with the …
- 9:50 AM Ticket #8234 (Crash using File→Open on Windows and/or in return statement) closed by
- duplicate: Same problem: upgrade to 1.5!
- 9:45 AM Ticket #8232 (Crash in event loop) closed by
- can't reproduce
- 9:41 AM Ticket #8225 (Wiggle tool not known after installation) closed by
- duplicate: Duplicate of #8230
- 9:39 AM Ticket #8229 (Wiggle tool not found after installation) closed by
- duplicate
- 9:37 AM Ticket #8228 (Wiggle tool not found after installation) closed by
- duplicate
- 9:35 AM Ticket #8227 (Wiggle tool not found after installation) closed by
- duplicate
Dec 26, 2022:
Dec 25, 2022:
- 1:24 AM Ticket #8234 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 1:20 AM Ticket #8233 (Crash using File→Open on Windows and/or in return statement) created by
- […]
Dec 24, 2022:
- 5:09 AM Ticket #8232 (Crash in event loop) created by
- […]
- 1:23 AM Ticket #8231 (Crash in bug reporter) created by
- […]
Dec 23, 2022:
- 7:57 PM Ticket #8230 (Wiggle tool not found after installation) created by
- […]
- 7:56 PM Ticket #8229 (Wiggle tool not found after installation) created by
- […]
- 7:41 PM Ticket #8228 (Wiggle tool not found after installation) created by
- […]
- 10:48 AM Ticket #8227 (Wiggle tool not found after installation) created by
- […]
- 8:16 AM Ticket #8226 (Unsupported scale factor (0.000000) detected on Display0) created by
- […]
- 8:00 AM Ticket #8225 (Wiggle tool not known after installation) created by
- […]
Dec 22, 2022:
- 1:28 PM Ticket #6617 (RFE: speed control on playback sliders) closed by
- fixed: Playback speed control available in next daily build.
- 1:15 PM ChangeLog edited by
- (diff)
- 9:40 AM Ticket #8224 (Crash in event loop) closed by
- can't reproduce
- 9:32 AM ChangeLog edited by
- (diff)
- 2:03 AM Ticket #8224 (Crash in event loop) created by
- […]
Dec 21, 2022:
- 6:33 PM Ticket #5887 (swapna) closed by
- fixed: swapna command available in next daily build
- 4:07 PM Ticket #7462 (Sequence Viewer context menu "blast" should provide more options) closed by
- fixed: Okay, it fills in the actual sequence instead of the alignment index …
- 2:27 PM Ticket #8208 (Session restore: rotamer model not child of parent) closed by
- fixed: The per-residue manager that tracks the active rotamers was creating …
- 10:34 AM Ticket #8223 (mmCIF: 'SaveOptionsWidget' object has no attribute 'compute_sheets') closed by
- duplicate: Hi Hong, Thanks for reporting this problem. It was fixed about 6 …
- 9:58 AM Ticket #8223 (mmCIF: 'SaveOptionsWidget' object has no attribute 'compute_sheets') created by
- […]
Dec 20, 2022:
- 5:32 PM Ticket #8219 (Failed to create NSOpenGLContext) closed by
- can't reproduce: The Qt window toolkit used by ChimeraX could not create an OpenGL …
- 5:21 PM DeveloperMeetings edited by
- (diff)
- 11:34 AM Ticket #8222 (Graphics crash, macOS 10.15.7, Intel HD Graphics 4000) created by
- […]
- 9:42 AM Ticket #8221 (Restore new session in old ChimeraX) closed by
- limitation
- 9:41 AM Ticket #8220 (Crash in event loop) closed by
- can't reproduce
Dec 19, 2022:
- 7:49 PM Ticket #8221 (Restore new session in old ChimeraX) created by
- […]
- 7:01 PM Ticket #8220 (Crash in event loop) created by
- […]
- 6:44 PM Ticket #8219 (Failed to create NSOpenGLContext) created by
- […]
- 3:00 PM Dev2022-12-19 created by
- 2:59 PM DeveloperMeetings edited by
- (diff)
- 2:42 PM Ticket #8196 (Volume disappears) closed by
- not a bug: I would imagine it would be best if specifying the contour level were …
- 1:34 PM Ticket #8218 (Bio assembly of 2JTN missing many atoms) created by
- Fetching pdbe_bio:2jtn yields a _file_ with 182 protein residues and …
- 1:24 PM Ticket #8198 (Index Error: list index out of range) closed by
- fixed: Changed cx_unified.py so that if rebonding produces a mess (atoms with …
- 12:02 PM Ticket #8207 (Fake Atom Error) closed by
- fixed: I have submitted a pull request on cx_unified.py that fixes this. …
- 11:03 AM Ticket #8217 (Open MRC file: Device not configured) closed by
- nonchimerax: Appears to be a operating file system read error. Here's what the C …
- 10:51 AM Ticket #8216 (Graphics crash, macOS 10.15.7, Intel HD Graphics 4000) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 10:48 AM Ticket #8217 (Open MRC file: Device not configured) created by
- […]
- 10:47 AM Ticket #8209 (Graphics crash, macOS 12.5.1, Intel Iris Graphics 6100) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 10:35 AM Ticket #8213 (Linux: QAccessibleTable::indexOfChild invalid child) closed by
- can't reproduce: Wait for a report on Qt6
- 7:36 AM Ticket #8216 (Graphics crash, macOS 10.15.7, Intel HD Graphics 4000) created by
- […]
Note:
See TracTimeline
for information about the timeline view.
