![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Apr 24, 2021:
Apr 23, 2021:
- 7:01 PM Ticket #4556 (Open and save commands ignore log option: run("open 1a0m", log=False)) created by
- […]
- 4:13 PM Ticket #4554 (Error when no surfaces) closed by
- fixed: Fixed. Added error message when no surfaces specified when coloring …
- 12:55 PM Ticket #4555 (ISOLDE/Clipper: Spgr_descr: No such HM symbol) created by
- […]
- 6:50 AM Ticket #4553 (Windows fatal exception: access violation) closed by
- can't reproduce
- 5:55 AM Ticket #4554 (Error when no surfaces) created by
- […]
Apr 22, 2021:
- 7:21 PM Ticket #4553 (Windows fatal exception: access violation) created by
- […]
- 5:21 PM 2021-4-22 edited by
- (diff)
- 3:20 PM NTTData edited by
- (diff)
- 3:18 PM NeteSOW edited by
- (diff)
- 3:18 PM NeteSOW edited by
- (diff)
- 3:14 PM NTTData edited by
- (diff)
- 3:13 PM NTTData edited by
- (diff)
- 3:08 PM NTTData created by
- 3:04 PM Funding edited by
- (diff)
- 2:56 PM NeteSOW edited by
- (diff)
- 2:44 PM Funding edited by
- (diff)
- 10:40 AM Ticket #4550 (Crash showing rapid access) closed by
- can't reproduce: Well, "Windows fatal exception: access violation" could be almost …
- 10:19 AM Ticket #4546 (Coulombic keyword typo) closed by
- fixed: Changed declaration to dist_dep
- 10:13 AM Ticket #4545 (No addcharge command) closed by
- fixed: There is no addcharge command yet, so commented it out of bundle_info.xml
- 9:47 AM 2021-4-22 edited by
- (diff)
- 9:44 AM 2021-4-22 edited by
- (diff)
- 1:11 AM Ticket #4552 (Help viewer: self.tabs.currentWidget() is None) created by
- […]
- 12:06 AM Ticket #4551 (Weird shadows during 'fly') created by
- […] weird_lighting_during_fly.mp4
Apr 21, 2021:
- 10:13 PM Ticket #4550 (Crash showing rapid access) created by
- […]
- 10:56 AM Ticket #4549 (Updates tool launched before main window ready?) created by
- […]
- 8:02 AM Ticket #4548 (ISOLDE: Unparameterised residue detected) created by
- […]
- 12:36 AM Ticket #4509 (Toolshed reporting obsolete command) closed by
- fixed: Changed message to show which versions of a bundle to install, This …
Apr 20, 2021:
- 10:39 PM Ticket #4547 (Duplicate manager initialization) created by
- […]
- 8:29 PM Ticket #4546 (Coulombic keyword typo) created by
- […]
- 7:59 PM Ticket #4545 (No addcharge command) created by
- […]
- 7:03 PM 2021-4-22 edited by
- (diff)
- 7:02 PM 2021-4-22 edited by
- (diff)
- 7:01 PM 2021-4-22 edited by
- (diff)
- 6:54 PM 2021-4-22 edited by
- (diff)
- 4:44 PM Ticket #4544 (Can't open PDB file with exotic characters for output on Windows) created by
- […]
- 4:37 PM 2021-4-22 edited by
- (diff)
- 4:35 PM Ticket #4436 (VR: socket error: Unable to write) closed by
- fixed: I added the ssh option for joining to the Meeting panel under options …
- 12:18 PM Ticket #1927 (coil not same as protein nonhelix nonstrand?) closed by
- not a bug: the thin segments separate individual strands and helices; if the …
- 11:55 AM Ticket #2290 (Basic Actions: showing ribbons unintuitive) closed by
- not a bug
- 11:25 AM 2021-4-22 created by
- 11:22 AM DeveloperMeetings edited by
- (diff)
- 11:16 AM Ticket #3586 (Automatic log compacting) closed by
- fixed: Some simple-minded compaction will be in tomorrow's daily build (i.e. …
- 9:25 AM Ticket #2115 (Erratic shell tab completion) closed by
- fixed: Seemingly fixed in current daily build
- 9:01 AM Ticket #4543 (GaudiViewX not compatible with latest ChimeraX) closed by
- nonchimerax: Will try to notify GaudiViewX developers about how to update.
- 8:50 AM Ticket #4542 (Permission denied saving command history) closed by
- can't reproduce: Would want to see the error occur again with the post-1.0 changes made …
- 8:44 AM Ticket #4540 (Atom name > 4 characters) closed by
- fixed: This limitation has been lifted in 1.2 and the daily build, though …
- 6:00 AM Ticket #4543 (GaudiViewX not compatible with latest ChimeraX) created by
- […]
- 4:27 AM Ticket #4542 (Permission denied saving command history) created by
- […]
- 12:01 AM Ticket #4541 (Silhouettes look wrong) created by
- […] volumesilh.tif
Apr 19, 2021:
- 10:57 PM Ticket #4540 (Atom name > 4 characters) created by
- […]
- 10:52 PM Ticket #4539 (Permission denied setting timestamp) created by
- […]
- 7:19 PM Ticket #4538 (traceback trying to change tether opacity) closed by
- fixed: Fixed in 1.2 includes 1.3, ie it is fixed in 1.2 onward.
- 7:17 PM Ticket #2893 (conference does not send models to participants) closed by
- duplicate: Duplicate of #2892.
- 7:15 PM Ticket #4538 (traceback trying to change tether opacity) reopened by
- 7:10 PM Ticket #2291 (Tile command: 'Volume' object has no attribute 'atomspec') closed by
- fixed: duplicate of other tickets (e.g. #2202) and has been fixed
- 7:03 PM Ticket #2892 (conference does not send models to participant) closed by
- wontfix: Use the meeting command. Conference didn't work and Conrad retired so …
- 6:53 PM Ticket #2658 (Ribbon 'guides' is None after session restore) closed by
- can't reproduce
- 6:19 PM Ticket #4538 (traceback trying to change tether opacity) closed by
- fixed: Fixed in 1.2. cartoon tether with no structure specifier did not work …
- 5:56 PM Ticket #4537 (VR meeting head hands not syncing) closed by
- fixed: Fixed Code change that delayed initiating vr meeting tracking until …
- 5:40 PM Ticket #963 (lots of DNA/RNA tethers with cartoon suppress false) closed by
- wontfix: wontfix is OK with me assuming tether-opacity bug #4538 is fixed
- 5:37 PM Ticket #4538 (traceback trying to change tether opacity) created by
- […]
- 5:15 PM Ticket #4537 (VR meeting head hands not syncing) created by
- […]
- 5:09 PM Ticket #226 (Identify hinged groups of atoms found by morph calculation) closed by
- fixed: I believe this is implemented as the colorSegments and colorCore …
- 5:06 PM Ticket #4534 (VR: unsupported operand type(s) for *: 'NoneType' and 'Place') closed by
- duplicate: Duplicate of #4438. FIxed.
- 5:02 PM Ticket #4533 (Can't select pseudobonds between models when they have non-identity ...) closed by
- fixed: Fixed. Code simply didn't handle this case correctly. Usually global …
- 4:57 PM Ticket #1027 ("like" operator in atomspec) closed by
- duplicate: duplicate of #480
- 4:51 PM Ticket #1968 (use ajax to update ChimeraX download page) reopened by
- 4:50 PM Ticket #1968 (use ajax to update ChimeraX download page) closed by
- fixed: Partially implemented using symbolic links for daily and candidate …
- 4:49 PM Ticket #2359 (Optimize ribbon drawing) closed by
- fixed: Ribbon code was optimized about a year ago before the 1.0 release. …
- 4:48 PM Ticket #1758 (Ribbon color change slow because it recomputes ribbon) closed by
- fixed: Fixed, probably when I cleaned up and optimized ribbon code before 1.0 …
- 4:46 PM Ticket #2207 (tile command ignores volume models) closed by
- fixed: fixed, at least in my relatively simple test cases
- 4:19 PM Ticket #1753 (cartoon style command interprets spec with atoms but without ...) closed by
- fixed: apparently fixed, including the 2gbp example
- 3:54 PM Ticket #4536 (consistent model color scheme) created by
- Discussion from email thread: Yes, we need to come up with something …
- 3:41 PM Ticket #4535 (Actions / Atoms & Bonds / Hide does not work on selected pseudobonds) created by
- […]
- 3:25 PM Ticket #4534 (VR: unsupported operand type(s) for *: 'NoneType' and 'Place') created by
- […]
- 2:31 PM Ticket #2466 (pseudobonds to ribbons difficult to select and get balloon help for) closed by
- duplicate: Same as #4526
- 2:30 PM Ticket #4526 (cannot select pseudobonds to cartoon) closed by
- fixed: Fixed in 1.2. Pseudobond picking was not using ribbon coordinates …
- 12:40 PM Ticket #1226 (RFE: some way to get back initial default cartoon style) closed by
- fixed: we added a Ribbons/Slabs preset to do this ages ago
- 12:33 PM Ticket #3167 (Add crystalcontacts command) closed by
- fixed: command and GUI added to daily build approximately March 8, 2021 …
- 12:00 PM Ticket #4533 (Can't select pseudobonds between models when they have non-identity ...) created by
- […]
- 11:35 AM Ticket #4531 (Crash in QOpenGLFunctions::initializeOpenGLFunctions() closed by
- can't reproduce: Crash in Qt initializing OpenGL 6 QtGui …
- 11:27 AM Ticket #4530 (access violation trying to create Atoms collection) closed by
- can't reproduce: I am baffled. The crash is during "open 2mfr", autostyling is making …
- 9:53 AM Ticket #4532 (ISOLDE: wrapped C/C++ object of type QTableWidget has been deleted) closed by
- duplicate
- 9:37 AM Ticket #4532 (ISOLDE: wrapped C/C++ object of type QTableWidget has been deleted) created by
- […]
- 9:09 AM Ticket #4529 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) closed by
- duplicate
- 9:09 AM Ticket #4528 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) closed by
- duplicate: Hi Stefan, Thanks for reporting this problem. I _believe_ it is …
- 9:05 AM Ticket #4527 (Crash in Qt reacting to window move) closed by
- can't reproduce
- 8:56 AM Ticket #4525 (Toolshed using internal UI API) closed by
- duplicate
- 5:46 AM Ticket #4531 (Crash in QOpenGLFunctions::initializeOpenGLFunctions() created by
- […]
- 1:04 AM Ticket #4530 (access violation trying to create Atoms collection) created by
- […]
Apr 18, 2021:
- 3:26 AM Ticket #4529 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) created by
- […]
- 3:22 AM Ticket #4528 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) created by
- […]
Apr 17, 2021:
- 9:46 PM Ticket #4527 (Crash in Qt reacting to window move) created by
- […]
- 8:28 AM Ticket #4526 (cannot select pseudobonds to cartoon) created by
- Usually cannot get a pseudobond between cartoon segments to be …
Apr 16, 2021:
- 1:35 PM Ticket #4525 (Toolshed using internal UI API) created by
- […]
- 11:07 AM Ticket #4523 (Drawing many pseudobonds: glTexImage2D: invalid value) closed by
- duplicate: This ChimeraX error was from showing contacts with distance labels and …
- 11:00 AM Ticket #4522 (Status bar: glClear: invalid framebuffer operation) closed by
- can't reproduce: Looks like OpenGL error occurred on first use (calling glClear()) …
- 10:51 AM Ticket #4521 (Looking Glass: Could not make graphics context current) closed by
- can't reproduce: The LookingGlass rendering works by creating a fullscreen QWindow on …
- 10:02 AM Ticket #4524 (Case sensitive chain IDs not working in wildcards) created by
- […]
- 5:07 AM Ticket #4523 (Drawing many pseudobonds: glTexImage2D: invalid value) created by
- […]
- 2:03 AM Ticket #4522 (Status bar: glClear: invalid framebuffer operation) created by
- […]
Apr 15, 2021:
- 10:56 PM Ticket #4521 (Looking Glass: Could not make graphics context current) created by
- […]
- 10:22 PM Ticket #4520 (Join meeting failed, first message does not have "join" key) closed by
- fixed: Fixed. There was another part of code that create the VR tracker in …
- 7:26 PM Ticket #4520 (Join meeting failed, first message does not have "join" key) created by
- […]
- 6:03 PM Dev2021-4-15 edited by
- (diff)
- 5:12 PM Dev2021-4-15 edited by
- (diff)
- 4:15 PM Ticket #4517 (Bug report not formatted) closed by
- can't reproduce: Could only find one mention of JSON crash logs for macOS "JSON crash …
- 3:46 PM Ticket #4518 ('Model' object has no attribute 'is_clip_cap') closed by
- fixed: Fixed in 1.2. Error was from a volume surface having a non-clip cap …
- 2:23 PM 2021-4-15 edited by
- (diff)
- 12:50 PM 2021-4-15 edited by
- (diff)
- 12:47 PM 2021-4-15 edited by
- (diff)
- 12:15 PM Ticket #4519 (Report hex color components) created by
- […]
- 11:20 AM ChangeLog edited by
- (diff)
- 11:00 AM Ticket #4511 (Ring fill doesn't update on coordinate changes) closed by
- fixed: Confirmed that adding the set_gc_ring()s fixes the problem.
- 8:52 AM Ticket #4514 (Toolshed using internal UI API) closed by
- duplicate
- 8:49 AM Ticket #4512 (Crash with trashed stack) closed by
- can't reproduce
- 6:41 AM Ticket #4518 ('Model' object has no attribute 'is_clip_cap') created by
- […]
- 3:55 AM Ticket #4517 (Bug report not formatted) created by
- […]
- 1:11 AM Ticket #4516 (optionally generate separate X3D objects for each nucleotide) created by
- From chimerax-users: > [T]he 3D models exported by ChimeraX aren’t …
Apr 14, 2021:
- 8:38 PM Ticket #4515 (Creating meeting timed out making tunnel to server) created by
- Ssh command to make tunnel to server when starting meeting timed out …
- 8:31 PM Ticket #4514 (Toolshed using internal UI API) created by
- […]
- 8:09 PM Ticket #4513 (Registration check failure) created by
- […] Screenshot (626).png
- 7:15 PM ChangeLog edited by
- (diff)
- 7:13 PM ChangeLog edited by
- (diff)
- 7:10 PM ChangeLog edited by
- (diff)
- 6:16 PM Ticket #4512 (Crash with trashed stack) created by
- […]
- 6:01 PM ChangeLog edited by
- (diff)
- 5:54 PM Ticket #4511 (Ring fill doesn't update on coordinate changes) created by
- If you open 1mtx as a trajectory (open 1mtx coords t) and fill the …
- 5:39 PM Ticket #4406 (Restoring new session in older ChimeraX: _pickle.UnpicklingError: ...) closed by
- fixed: The bug is probably that the session file was written using the …
- 5:38 PM Ticket #4227 (Better session-restore error message) closed by
- fixed: The bug is probably that the session file was written using the …
- 4:34 PM Ticket #4510 (Surface color tool does not update volume data menu value) closed by
- fixed: Fixed in 1.2.
- 4:19 PM Ticket #4510 (Surface color tool does not update volume data menu value) created by
- […]
- 4:15 PM Ticket #4506 (Surface color session save remembering wrong coloring) closed by
- fixed: Fixed in 1.2 and 1.3. Session save of surface autorecolor handlers …
- 3:48 PM ChangeLog edited by
- (diff)
- 2:52 PM Ticket #4509 (Toolshed reporting obsolete command) created by
- […]
- 12:10 PM Ticket #4508 (Adjust color brightness/contrast) created by
- […]
- 11:27 AM Ticket #4507 (ISOLDE: wrapped C/C++ object of type QTableWidget has been deleted) created by
- […]
- 10:48 AM Ticket #4506 (Surface color session save remembering wrong coloring) created by
- […]
- 10:26 AM Ticket #4431 (More user-friendly session error handling) closed by
- fixed: The bug is probably that the session file was written using the …
Apr 13, 2021:
- 3:46 PM 2021-4-15 edited by
- (diff)
- 3:33 PM Ticket #2452 (protons not properly stripped in 3qm8 heme) closed by
- fixed: It was indeed the alt locs -- the non-altloc metal and parent atom …
- 1:21 PM Ticket #4492 (wrapped C/C++ object of type ChainMenuButton has been deleted) closed by
- can't reproduce: It looks like somehow the MatchMaker UI stayed up after the Qt side …
- 12:00 PM Ticket #4505 (Read PSF+DCD combo directly) created by
- Given the difficulty of creating a PDB for a large system in some …
- 10:46 AM Ticket #4504 (case-sensitive residue names) created by
- […]
- 10:31 AM Dev2021-4-15 created by
- 10:29 AM 2021-4-8 edited by
- (diff)
- 10:29 AM 2021-4-15 created by
- 10:26 AM DeveloperMeetings edited by
- (diff)
- 9:15 AM Ticket #4503 (Crash while garbage collecting during object allocation) closed by
- can't reproduce: Clearly happening during a session restore in this particular case …
Apr 12, 2021:
- 10:57 PM Ticket #4503 (Crash while garbage collecting during object allocation) created by
- […]
- 7:19 PM Ticket #4502 (Clip cap coloring script does not color cap unless "wait 1" command used) created by
- […]
- 6:30 PM Ticket #4453 (Overlapping labels) closed by
- fixed: Hi Jack, The fix will be in tomorrow's daily build. If you restore …
- 6:28 PM Ticket #4485 (a reply to UCSF Computer Graphics Lab) closed by
- duplicate: basically duplicate of #4453
- 5:59 PM Ticket #4500 (glUniformMatrix4fv: invalid operation) closed by
- can't reproduce: Not enough info to debug. Invalid Operation opengl error in …
- 4:16 PM Ticket #4501 (Easier import for MD) created by
- If when you tried to load a trajectory file (dcd etc) it asked you …
- 3:37 PM Ticket #4487 (ChimeraX writes multimodel PDB with multiple END records) closed by
- fixed
- 2:31 PM Ticket #4497 (Crash with trashed stack) closed by
- can't reproduce
- 2:30 PM Ticket #4500 (glUniformMatrix4fv: invalid operation) created by
- […]
- 2:19 PM Ticket #4499 (RFE: coulombic coloring of surface caps to automatically update) created by
- This might require having a map "under the hood," however, even if …
- 2:14 PM Ticket #4498 (RFE: make Shift modifier switch "clip rotate" mousemode to "clip translate") created by
- Make Shift modifier switch the "clip rotate" mousemode to translating …
- 1:54 PM Ticket #4488 (coordination pbonds thinner on last frame of trajectory) closed by
- fixed: Setting metal-coordination groups to their default radius/color was …
- 1:08 PM Ticket #4497 (Crash with trashed stack) created by
- […]
- 12:52 PM Ticket #4493 (Graphics crash, macOS 10.15.7, Intel Iris Pro) closed by
- nonchimerax: Apple Intel graphics driver crash, 2.3 GB memory in use.
- 12:48 PM Ticket #4490 (Graphics crash, macOS 11.2.3, Intel Iris Plus 645) closed by
- nonchimerax: ChimeraX crashed in the macOS Intel graphics driver. This is a known …
- 10:28 AM Ticket #4496 (Error in toolshed error message) closed by
- duplicate
- 10:27 AM Ticket #4495 (Toolshed using internal UI API) closed by
- duplicate
- 10:25 AM Ticket #4494 (Cannot save settings because it is being used by another process) closed by
- duplicate: *possibly* fixed on 9/17/20
- 10:13 AM Ticket #4491 (Crash during garbage collection) closed by
- can't reproduce
- 9:25 AM Ticket #4496 (Error in toolshed error message) created by
- […]
- 8:08 AM Ticket #4495 (Toolshed using internal UI API) created by
- […]
- 5:01 AM Ticket #4494 (Cannot save settings because it is being used by another process) created by
- […]
- 1:39 AM Ticket #4493 (Graphics crash, macOS 10.15.7, Intel Iris Pro) created by
- […]
Apr 11, 2021:
- 7:36 PM Ticket #4492 (wrapped C/C++ object of type ChainMenuButton has been deleted) created by
- […]
- 4:50 AM Ticket #4491 (Crash during garbage collection) created by
- […]
Apr 10, 2021:
Apr 9, 2021:
- 11:23 PM Ticket #4489 (SEQCROW: No such file or directory: ...) created by
- […]
- 6:50 PM Ticket #4488 (coordination pbonds thinner on last frame of trajectory) created by
- example data sent in e-mail in case it's private, originally from …
- 5:27 PM Ticket #4487 (ChimeraX writes multimodel PDB with multiple END records) created by
- The extra END records prevent opening the resulting file as a …
- 12:56 PM Ticket #4482 (Compute clip caps immediately in scripts so they can be colored) closed by
- fixed: Fixed. Made clip and view commands update the clip cap surfaces …
- 8:54 AM Ticket #4486 (Save session: No space left on device) closed by
- nonchimerax
Apr 8, 2021:
- 11:39 PM Ticket #4486 (Save session: No space left on device) created by
- […]
- 9:55 PM Ticket #4485 (a reply to UCSF Computer Graphics Lab) created by
- […] A session that exhibits the bug.cxs
- 8:59 PM Ticket #4469 (Crash OpenGL makeCurrent() in wrong thread) closed by
- fixed: Partial fix. I have put in code that prevents calling …
- 7:17 PM 2021-4-8 edited by
- (diff)
- 7:16 PM 2021-4-8 edited by
- (diff)
- 7:00 PM Ticket #3760 (Startup warning: Unable to load numpy_formathandler accelerator from ...) closed by
- fixed: Fixed. Made sure ChimeraX build compiles PyOpenGL-accelerate from …
- 6:10 PM NeteSOW edited by
- (diff)
- 4:14 PM Ticket #4484 (side by side camera: background color wrong) closed by
- fixed: Fixed. Background color for right view was wrong when a green …
- 3:42 PM Ticket #4483 (side by side camera: zoom misaligns) closed by
- fixed: Hi Randy, Ok, zooming in side-by-side camera mode will be fixed in …
- 2:17 PM NeteSOW edited by
- (diff)
- 1:47 PM NeteSOW edited by
- (diff)
- 1:44 PM NeteSOW edited by
- (diff)
- 1:11 PM NeteSOW edited by
- (diff)
- 8:49 AM Ticket #4481 (Crash during garbage collection) closed by
- can't reproduce
- 8:48 AM Ticket #4480 (Dual display crash) closed by
- duplicate
- 5:07 AM Ticket #4390 (ISOLDE: update selected residue info: wrapped C/C++ object of type ...) closed by
- fixed
- 5:07 AM Ticket #4096 (ISOLDE: setting text of deleted QLabel) closed by
- fixed: Will be fixed in the next ISOLDE release (in a few weeks).
- 4:08 AM Ticket #4484 (side by side camera: background color wrong) created by
- […]
- 4:03 AM Ticket #4483 (side by side camera: zoom misaligns) created by
- […]
- 3:59 AM Ticket #2007 (Can't zoom after opening structure factors, scroll is changed to ...) closed by
- fixed: Old ticket, long fixed.
Apr 7, 2021:
- 7:46 PM Ticket #4482 (Compute clip caps immediately in scripts so they can be colored) created by
- Command scripts that create a clip cap then try to color it don't work …
- 6:06 PM 2021-4-8 edited by
- (diff)
- 12:39 PM Ticket #4481 (Crash during garbage collection) created by
- […]
- 11:40 AM Ticket #4480 (Dual display crash) created by
- […]
- 11:37 AM Ticket #4478 (Corrupted file history) closed by
- can't reproduce: This error is because the previous time you ran ChimeraX it saved your …
- 11:15 AM Ticket #4479 (Read small-molecule CIF files) created by
- ChimeraX currently cannot read small molecule CIF file. For the …
- 10:20 AM Ticket #4477 (Problem handling command failure on command line) closed by
- fixed
- 6:37 AM Ticket #4478 (Corrupted file history) created by
- […]
- 5:41 AM Ticket #4477 (Problem handling command failure on command line) created by
- […]
Apr 6, 2021:
- 6:20 PM 2021-4-8 created by
- 6:19 PM DeveloperMeetings edited by
- (diff)
- 5:28 PM Ticket #4466 ("color single" command is not undoable) closed by
- fixed: Fixed. I removed the color option to color single because it was …
- 4:17 PM Ticket #4461 (MemoryError despite seemingly moderate memory usage) closed by
- nonchimerax: Rebooting the computer fixed the problem as reported in #4473.
- 4:16 PM Ticket #4462 (MemoryError despite seemingly moderate memory usage) closed by
- nonchimerax: Rebooting the computer fixed the problem as reported in #4473.
- 4:13 PM Ticket #4476 (Out of memory opening large session) closed by
- duplicate: Same as #4475.
- 4:12 PM Ticket #4475 (Out of memory opening large session) closed by
- duplicate: Same memory error opening this session in this report in ChimeraX 1.0 …
- 4:09 PM Ticket #4474 (Out of memory opening large session) closed by
- duplicate: Same as #4473
- 4:02 PM Ticket #4473 (Out of memory opening session) closed by
- duplicate: By "Got up to 7.3 GB of files..." do you mean Task Manager reported …
- 3:57 PM Ticket #4460 (Python script on startup command-line, QTimer errors) closed by
- fixed: Added code to report these errors. Has the side effect of reporting …
- 3:46 PM Ticket #4476 (Out of memory opening large session) created by
- […]
- 3:46 PM Ticket #4475 (Out of memory opening large session) created by
- […]
- 3:14 PM Ticket #4460 (Python script on startup command-line, QTimer errors) reopened by
- The fix seems to have suppressed error reporting when opening files …
- 3:11 PM Ticket #4474 (Out of memory opening large session) created by
- […]
- 3:05 PM Ticket #4473 (Out of memory opening session) created by
- […]
- 2:42 PM Ticket #4469 (Crash OpenGL makeCurrent() in wrong thread) reopened by
- There have been 5 previous reports of this same crash in …
- 1:55 PM Ticket #4470 (Safeguard against accidental multi-residue swapaa) closed by
- fixed: swapaa now asks for confirmation before swapping multiple residues
- 1:36 PM Ticket #4472 (coulombic: KeyError: 'OXT') closed by
- duplicate: Hi Rayeed, The 'coulombic' command has made significantly more robust …
- 1:02 PM Ticket #4472 (coulombic: KeyError: 'OXT') created by
- […] BioI.cxs
- 11:57 AM Ticket #4468 (Startup files opened twice on macOS) closed by
- fixed: On MacOS 10.12+, the UI is informed about specific file-drop events to …
- 9:46 AM Ticket #4471 (builtin attrs as list; should be dict) closed by
- fixed: This was fixed in the next build
- 9:37 AM Ticket #4469 (Crash OpenGL makeCurrent() in wrong thread) closed by
- can't reproduce: Here it would be helpful to have the Python stack trace. The various …
- 8:20 AM Ticket #4471 (builtin attrs as list; should be dict) created by
- […]
- 7:08 AM Ticket #4470 (Safeguard against accidental multi-residue swapaa) created by
- […]
Apr 5, 2021:
- 9:37 PM Ticket #4469 (Crash OpenGL makeCurrent() in wrong thread) created by
- […]
- 6:46 PM Ticket #4468 (Startup files opened twice on macOS) created by
- […]
- 6:02 PM Ticket #4467 (Python scripts don't have __file__ attribute) closed by
- fixed: Fixed. ChimeraX runs Python scripts in a sandbox module it creates. …
- 5:59 PM Ticket #4460 (Python script on startup command-line, QTimer errors) closed by
- fixed: Now script errors only exit Chimera in nogui mode. It was the …
- 5:59 PM Ticket #4467 (Python scripts don't have __file__ attribute) created by
- […]
- 5:10 PM Ticket #4465 ("color image" command "file none" is not recognized) closed by
- fixed: Fixed. Argument parsing was only handling file names of existing …
- 5:02 PM Ticket #4466 ("color single" command is not undoable) created by
- The command "color #1 purple" is undoable but "color single #1 purple" …
- 4:55 PM Ticket #4465 ("color image" command "file none" is not recognized) created by
- The "file none" option is documented to turn off coloring by image …
- 4:50 PM Ticket #4464 (No error message given for bad files on start-up command line) closed by
- fixed: Fixed. Starting ChimeraX in GUI mode it opens the command-line files …
- 4:45 PM Ticket #4464 (No error message given for bad files on start-up command line) created by
- If I start ChimeraX listing a non-existent file on the command-line it …
- 4:44 PM Ticket #4463 (Errors in Python scripts should show traceback just for the script) closed by
- fixed: Fixed. The code that runs the script is using Python exec(). When it …
- 4:27 PM Ticket #4463 (Errors in Python scripts should show traceback just for the script) created by
- […]
- 2:30 PM Ticket #4462 (MemoryError despite seemingly moderate memory usage) created by
- […]
- 2:21 PM Ticket #4461 (MemoryError despite seemingly moderate memory usage) created by
- […]
- 2:05 PM Ticket #3261 (Make model-panel coloring issue command) closed by
- fixed: Model Panel now issues "color single" commands for the color buttons. …
- 1:32 PM Ticket #4447 (Wrong distance between atoms when models have different positions) closed by
- fixed: When the initial position of a Structure (which is what a centroid is) …
- 11:22 AM Ticket #4458 (Windows crash in threading wait) closed by
- can't reproduce: The Python traceback for this ChimeraX crash didn't give any …
- 11:17 AM Ticket #4457 (Crash in initializeOpenGLFunctions) closed by
- nonchimerax: Crash caused by Qt window toolkit with multiple screens. ChimeraX 1.1 …
- 11:14 AM Ticket #4456 (Thread-restore crash) closed by
- can't reproduce: Looks like a Qt problem in very old ChimeraX 0.93
- 10:57 AM Ticket #4460 (Python script on startup command-line, QTimer errors) created by
- If I start ChimeraX from a shell with a Python script argument and the …
- 10:34 AM Ticket #4459 (Super useful stack trace) closed by
- duplicate
- 10:03 AM Ticket #4455 (BLAST failure) closed by
- can't reproduce: Hi Kaitlyn, This failure may have been a temporary problem with our …
- 9:47 AM Ticket #4459 (Super useful stack trace) created by
- […]
- 9:34 AM Ticket #4452 (Crash during garbage collection) closed by
- can't reproduce
- 9:31 AM Ticket #4458 (Windows crash in threading wait) created by
- […]
- 8:50 AM Ticket #4457 (Crash in initializeOpenGLFunctions) created by
- […]
Apr 4, 2021:
- 9:01 PM Ticket #4456 (Thread-restore crash) created by
- […]
- 10:57 AM Ticket #4455 (BLAST failure) created by
- […]
Apr 3, 2021:
Apr 2, 2021:
- 7:05 PM Ticket #4453 (Overlapping labels) created by
- […] movie-hydrogen bonds.mp4
- 6:30 PM Ticket #4452 (Crash during garbage collection) created by
- […]
- 5:42 PM Ticket #4451 (Crash in garbage collection during session restore) closed by
- can't reproduce
- 5:39 PM Ticket #2784 (Volume morph slider) closed by
- fixed: Done. Duplicate of #4445.
- 5:39 PM Ticket #4445 (Morph volume slider option) closed by
- fixed: Fixed. Added a morph map slider that appears automatically when …
- 2:23 PM Ticket #4451 (Crash in garbage collection during session restore) created by
- […]
- 12:22 PM Ticket #4449 (Out of memory mousing over large map) closed by
- duplicate: Duplicate of #4448
- 12:20 PM Ticket #4448 (Out of memory mousing over large map) closed by
- not a bug
- 12:20 PM Ticket #4448 (Out of memory mousing over large map) reopened by
- 12:18 PM Ticket #4448 (Out of memory mousing over large map) closed by
- not a bug: User error. Out of memory, as the error message says MemoryError: …
- 12:00 PM Ticket #4450 (Make volume morph interpolate maps if grids not aligned) created by
- Currently the volume morph command just interpolates matching grid …
- 11:56 AM Ticket #4446 (volume morph reverts orientation) closed by
- not a bug: I think this is a misunderstanding, not a bug. The volume morph …
- 11:51 AM Ticket #4449 (Out of memory mousing over large map) created by
- […]
- 11:08 AM Ticket #4448 (Out of memory mousing over large map) created by
- […]
- 10:06 AM Ticket #4447 (Wrong distance between atoms when models have different positions) created by
- […]
- 9:17 AM Ticket #4446 (volume morph reverts orientation) created by
- […]
- 7:45 AM Ticket #4445 (Morph volume slider option) created by
- […]
Apr 1, 2021:
- 8:47 PM 2021-4-1 edited by
- (diff)
- 7:59 PM Ticket #4444 (Marker delete mouse mode does not log command) closed by
- fixed: Fixed. It only failed to log the command when the last marker was deleted.
- 7:38 PM Ticket #4438 (meeting: self.room_to_scene is None) closed by
- fixed: Fixed. The problem is that when the joiner connects they do not send …
- 6:13 PM Dev2021-4-1 edited by
- (diff)
- 6:12 PM Dev2021-4-1 edited by
- (diff)
- 6:10 PM Dev2021-4-1 edited by
- (diff)
- 5:19 PM Ticket #4444 (Marker delete mouse mode does not log command) created by
- […]
- 5:15 PM Ticket #4439 (Large meeting session: msgpack.exceptions.BufferFull) closed by
- fixed: Fixed. I set the message pack object size limit in the meeting code …
- 5:05 PM Ticket #4441 (volume step 4: invalid file offset) closed by
- fixed: Fixed. Volume step_aligned_region(clamp = True) was producing region …
- 4:41 PM Ticket #2708 (AddH: 5ky0: list index out of range while finding roomiest) closed by
- fixed: Fix available in next daily build.
- 4:18 PM Ticket #4443 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) closed by
- duplicate: Hi Shon, Thanks for reporting this problem. This bug is fixed in the …
- 4:11 PM Ticket #4442 (volume step 4: invalid file offset) closed by
- duplicate
- 4:02 PM Ticket #2720 (RFE: selector or attribute for standard residues with missing atoms) closed by
- fixed: Though I like the fact that the original name indicates that only …
- 3:17 PM Ticket #4443 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) created by
- […] bugged session.cxs
- 2:26 PM Dev2021-4-1 edited by
- (diff)
- 2:25 PM Dev2021-4-1 edited by
- (diff)
- 2:24 PM Dev2021-4-1 edited by
- (diff)
- 2:07 PM Dev2021-4-1 edited by
- (diff)
- 12:52 PM Ticket #4442 (volume step 4: invalid file offset) created by
- […]
- 12:51 PM Ticket #4441 (volume step 4: invalid file offset) created by
- […]
Mar 31, 2021:
- 7:21 PM Ticket #4437 (VR: Socket error: Unable to write) closed by
- duplicate: Same as #4436.
- 7:04 PM Dev2021-4-1 created by
- 7:00 PM DeveloperMeetings edited by
- (diff)
- 6:59 PM 2021-4-1 created by
- 6:58 PM DeveloperMeetings edited by
- (diff)
- 3:01 PM Ticket #4440 (Error starting Space Navigator) closed by
- not a bug: This says you don't have the Space Navigator device driver installed …
- 1:24 PM Ticket #4440 (Error starting Space Navigator) created by
- […]
- 12:21 PM Ticket #4433 (linux xdg-install: cannot import name 'localized_app_name' from '__main__') closed by
- fixed: Turns out bug was a side effect of using the Shell tool. The linux …
- 9:59 AM Ticket #4439 (Large meeting session: msgpack.exceptions.BufferFull) created by
- […]
- 9:52 AM Ticket #4438 (meeting: self.room_to_scene is None) created by
- […]
- 9:22 AM Ticket #4437 (VR: Socket error: Unable to write) created by
- […]
- 9:18 AM Ticket #4436 (VR: socket error: Unable to write) created by
- […]
- 8:53 AM Ticket #4435 (Error in toolshed error message) closed by
- duplicate: Hi Manoj, Thanks for reporting this problem. The issue is that you …
- 8:47 AM Ticket #4434 (Setting temp file missing) closed by
- duplicate
Mar 30, 2021:
- 9:46 PM Ticket #4435 (Error in toolshed error message) created by
- […]
- 5:09 PM Ticket #4434 (Setting temp file missing) created by
- […]
- 2:18 PM Ticket #4433 (linux xdg-install: cannot import name 'localized_app_name' from '__main__') created by
- […]
- 10:02 AM Ticket #4432 (Dual display crash) closed by
- can't reproduce: A lot of window resizing going on in response to a mouse event. I …
- 7:02 AM Ticket #4432 (Dual display crash) created by
- […]
Mar 29, 2021:
- 5:10 PM Ticket #4431 (More user-friendly session error handling) created by
- […] test.cxs
- 12:01 PM Ticket #4425 (Segger: 'MainWindow' object has no attribute 'save_dialog') closed by
- duplicate: This Segger bug was fixed long ago. You are using ChimeraX 0.93 which …
- 12:01 PM Ticket #4149 (Binary installation of AmberTools) closed by
- fixed
- 11:57 AM Ticket #4428 ("mark connected" with no surfaces: ValueError: shapes not aligned) closed by
- fixed: Fixed. The mark connected command did not properly handle the case …
- 11:48 AM Ticket #4426 (Dual display crash) closed by
- nonchimerax: ChimeraX crashed on macOS with two displays while showing a popup …
- 11:45 AM Ticket #4430 (Hybrid-36 LINK records) created by
- […] model_2b_working_noh_real_space_refined.pdb
- 11:38 AM Ticket #4418 (Shell sluggish) closed by
- can't reproduce: ...since no one seems to be reproducing this problem.
- 11:30 AM Ticket #4421 (Dual display crash) closed by
- can't reproduce: It looks like ChimeraX crashed possibly when a second screen was added …
- 11:21 AM Dev2021-3-18 edited by
- (diff)
- 10:52 AM Ticket #4429 (Toolshed using internal UI API) closed by
- duplicate
- 10:50 AM Ticket #4427 (keyPressEvent received by dead widget) closed by
- can't reproduce
Mar 28, 2021:
- 1:02 PM Ticket #4429 (Toolshed using internal UI API) created by
- […]
- 12:24 PM Ticket #4428 ("mark connected" with no surfaces: ValueError: shapes not aligned) created by
- […]
- 6:56 AM Ticket #4427 (keyPressEvent received by dead widget) created by
- […]
Mar 27, 2021:
- 10:27 AM Ticket #4426 (Dual display crash) created by
- […]
- 9:45 AM Ticket #4425 (Segger: 'MainWindow' object has no attribute 'save_dialog') created by
- […]
Mar 26, 2021:
- 10:24 PM Ticket #4424 (Missing bonds) created by
- […] chimera-bug.pdf
- 6:15 AM Ticket #4423 (Suport LINKR records) created by
- […]
- 5:54 AM Ticket #4422 (Version misreported) created by
- […] chimerax_wrong_version_display.png
- 12:34 AM Ticket #4421 (Dual display crash) created by
- […]
Mar 25, 2021:
- 10:29 PM 2021-3-25 edited by
- (diff)
- 8:47 PM Ticket #4412 (segmentation color command: 'numpy.float64' object cannot be ...) closed by
- fixed: Fixed. User gave a floating-point value map as the segmentation …
- 8:22 PM Ticket #4420 (Want per-model silhouette edges) created by
- On Mar 25, 2021, at 10:09 PM, Andre LB Ambrosio wrote: Dear all, I …
- 7:02 PM Ticket #4419 (Add a command to make user defined color palettes) created by
- Begin forwarded message: From: Abhilash Padvannil Subject: …
- 6:18 PM Ticket #4408 (Color key: unsupported locale setting) closed by
- fixed
- 5:58 PM Ticket #4409 (Session restore clearing log impairs debugging) closed by
- fixed: Now the log is not cleared if the session restore is unsuccessful. …
- 5:29 PM Ticket #4410 (Color key: 'FontOption' object has no attribute '_callback') closed by
- fixed: Needed to prevent the initial creation of the option's menu from also …
- 5:17 PM Ticket #4411 (Build Structure tool issuing command with incorrect keyword) closed by
- fixed: Hi Tony, thanks for letting me know! Fixed now. --Eric
- 4:49 PM Ticket #3909 (Large structure 5y6p opens unexpectedly slowly, 27 seconds) closed by
- fixed: I have to say, this was a nightmare to track down. I thought …
- 3:23 PM NeteSOW edited by
- (diff)
- 2:08 PM NeteSOW edited by
- (diff)
- 2:07 PM NeteSOW edited by
- (diff)
- 1:38 PM NeteSOW edited by
- (diff)
- 1:19 PM NeteSOW edited by
- (diff)
- 1:05 PM NeteSOW edited by
- (diff)
- 9:29 AM Ticket #4418 (Shell sluggish) created by
- […]
- 9:06 AM Ticket #4417 (Bundle Builder findable OpenMM headers) created by
- […]
- 9:04 AM Ticket #4416 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) closed by
- duplicate: Hi Yuhang, Thanks for reporting this problem. We believe this issue …
- 9:02 AM Ticket #4415 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) closed by
- duplicate: Hi Saw, Thanks for reporting this problem. We believe this issue has …
- 9:00 AM Ticket #4414 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) closed by
- duplicate
- 8:53 AM Ticket #4416 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) created by
- […]
- 8:51 AM Ticket #4415 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) created by
- […]
- 8:50 AM Ticket #4414 (MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ...) created by
- […]
- 8:36 AM Dev2021-3-18 edited by
- (diff)
- 5:32 AM Ticket #4413 (Make --force-reinstall the default when building from source) created by
- […]
- 3:22 AM Ticket #4412 (segmentation color command: 'numpy.float64' object cannot be ...) created by
- […]
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