![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Oct 4, 2022:
- 7:31 PM Ticket #7730 (Buried Volume: KeyError: 'Ni') created by
- […]
- 7:10 PM Ticket #7461 (Blast Results dialog: add buttons for same actions as in context menu) closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/0088eb25500e7ff50dd56d6f426ae8 …
- 7:08 PM Ticket #7708 (RFE: Normalize the git repository) closed by
- fixed: Added .gitattributes
- 6:17 PM Ticket #7719 ('-o' is not a legal uname option on Mac) closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/3e332740254fe9ace1b007c576bd88 …
- 5:40 PM Ticket #7729 (SyntaxError on startup in core/decorators.py) closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/4ecd4174d311a144d07b0065db59cb …
- 5:31 PM Ticket #7729 (SyntaxError on startup in core/decorators.py) created by
- […]
- 3:54 PM Ticket #7728 (chimerax daily logs many errors in nogui mode) created by
- On plato, running chimerax --nogui, which is encapsulated in a CentOS …
- 12:10 PM Ticket #7727 (AlphaFold database settings should not update at startup) created by
- […]
- 12:03 PM Ticket #7726 (Crash in glDrawElementsInstanced) created by
- […]
- 11:13 AM Ticket #7463 (Additional phenix/douse enhancements) closed by
- fixed
- 10:53 AM Ticket #7724 (Crash in Qt event loop after setting volume contour level) closed by
- can't reproduce: Possibly a graphics driver crash.
- 10:49 AM Ticket #7722 (Maps in sessions with invalid cell angles) closed by
- nonchimerax: Hi Matt, MRC files have a header that says what the angles are …
- 10:32 AM Ticket #7723 (Crash in fork) closed by
- limitation: Hi Lori, The emulation that your Mac uses to run Intel binaries on …
- 10:28 AM Ticket #7725 (Update to AlphaFold database version 4) created by
- Begin forwarded message: From: Sameer Velankar via pdb-l …
- 10:21 AM Ticket #7724 (Crash in Qt event loop after setting volume contour level) created by
- […]
- 9:59 AM 2022-10-6 created by
- 9:58 AM DeveloperMeetings edited by
- (diff)
- 9:56 AM Ticket #7723 (Crash in fork) created by
- […]
- 9:41 AM Ticket #7721 (Session save: Basic Actions: 'QEventLoop' object has no attribute 'exec_') closed by
- duplicate: Hi David, Thanks for reporting this problem. It is fixed in the …
- 9:33 AM Ticket #7720 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 8:58 AM Ticket #7722 (Maps in sessions with invalid cell angles) created by
- […] PCR_average_Movie.cxs
- 6:49 AM Ticket #7721 (Session save: Basic Actions: 'QEventLoop' object has no attribute 'exec_') created by
- […]
- 1:57 AM Ticket #7720 (Crash using File→Open on Windows and/or in return statement) created by
- […]
Oct 3, 2022:
- 7:01 PM Dev2022-10-3 edited by
- (diff)
- 6:30 PM Ticket #5954 (Add Phenix douse tool to add waters) closed by
- fixed
- 6:09 PM Ticket #7689 (Crash closing tool) closed by
- can't reproduce: I changed some code that _may_ fix this problem, though I was never …
- 5:43 PM Ticket #7719 ('-o' is not a legal uname option on Mac) created by
- detectOS.make now has this line: SHORT_OS := $(shell uname -o) '-o' …
- 5:22 PM Ticket #7716 (All residues in MAE file erroneously non-standard) closed by
- fixed: Fixed. Maestro reader was including a trailing space in residue …
- 3:56 PM Ticket #4663 (Make native Apple M1 CPU distribution) closed by
- fixed: Tom was able to get an M1 build and a Universal build up as daily builds.
- 3:55 PM Ticket #6778 (Integrate arm64 macOS into ChimeraX's build/deployment system) closed by
- fixed: Tom was able to hook an M1 build into the build system.
- 3:11 PM Dev2022-10-3 edited by
- (diff)
- 3:03 PM Dev2022-10-3 edited by
- (diff)
- 2:47 PM Ticket #7718 (Document the Linux compiler used for ChimeraX releases and daily builds) created by
- Tristan Croll needs to know the compiler used to compile ChimeraX on …
- 2:25 PM Ticket #7717 (Global hide/show hitting dead tool) closed by
- can't reproduce
- 2:14 PM Dev2022-10-3 edited by
- (diff)
- 1:23 PM Ticket #7717 (Global hide/show hitting dead tool) created by
- […]
- 1:18 PM Ticket #7716 (All residues in MAE file erroneously non-standard) created by
- […] glide-dock_lps_xp_mod4_6.mae
- 12:35 PM Ticket #7715 (DICOM: TypeError: %d format: a number is required, not NoneType) created by
- […]
- 9:40 AM Ticket #7714 (Morph: 'set' object has no attribute 'items') closed by
- duplicate: Hi Feixia, This bug was fixed on Thursday, so get a new daily build …
- 9:33 AM Ticket #7713 ('SaveModelOptionWidget' object has no attribute '_name') closed by
- duplicate
- 9:32 AM Ticket #7712 (Crash in fork) closed by
- limitation
- 9:31 AM Ticket #7711 (Long atom spec crashes ChimeraX) closed by
- duplicate
- 9:30 AM Ticket #7710 (Long atom spec crashes ChimeraX) closed by
- duplicate: Duplicate of #4842
- 9:17 AM Ticket #7714 (Morph: 'set' object has no attribute 'items') created by
- […]
- 6:57 AM Ticket #7713 ('SaveModelOptionWidget' object has no attribute '_name') created by
- […]
Oct 2, 2022:
- 8:56 PM Ticket #7712 (Crash in fork) created by
- […]
- 7:04 PM Ticket #6926 (Problem fetching mmCIF template: URL can't contain control characters) closed by
- duplicate
- 6:56 PM Ticket #7017 (networkx: no libbz2) closed by
- fixed
Oct 1, 2022:
- 9:37 PM Ticket #7711 (Long atom spec crashes ChimeraX) created by
- […]
- 9:36 PM Ticket #7710 (Long atom spec crashes ChimeraX) created by
- […]
- 8:22 AM Ticket #7709 (Simulation stop: 'NoneType' object has no attribute 'atoms') created by
- […]
Sep 30, 2022:
- 4:48 PM Ticket #7708 (RFE: Normalize the git repository) created by
- I mentioned in the group meeting that I was investigating development …
- 3:38 PM Ticket #7705 (Web services not starting) closed by
- fixed: Great. Glad to hear that it works now.
- 3:16 PM 2022-9-29 edited by
- (diff)
- 1:39 PM Ticket #7707 (Make "wait" command with no arguments work with mseries command) created by
- […]
- 1:20 PM Ticket #7706 (Web services not starting) closed by
- duplicate
- 12:49 PM NIAID2022 edited by
- (diff)
- 12:00 PM Ticket #7706 (Web services not starting) created by
- […]
- 12:00 PM Ticket #7705 (Web services not starting) created by
- […]
- 11:37 AM Ticket #7704 (chain.from_seqres not set from PDB file) closed by
- fixed: Bug was side effect of PDB 2-character chain ID support -- the …
Sep 29, 2022:
- 10:59 PM Ticket #7704 (chain.from_seqres not set from PDB file) created by
- After "open 3fx2 format pdb", if you start the shell and do: […] …
- 7:12 PM 2022-9-29 edited by
- (diff)
- 4:07 PM Dev2022-10-3 created by
- 4:06 PM DeveloperMeetings edited by
- (diff)
- 4:05 PM DeveloperMeetings edited by
- (diff)
- 2:56 PM Ticket #7695 (Bug in matchmaker secondary structure code revamp) closed by
- fixed: Fix will be in tomorrow's daily build.
- 2:12 PM NIAID2022 edited by
- (diff)
- 2:09 PM NIAID2022 edited by
- (diff)
- 2:04 PM NIAID2022 edited by
- (diff)
- 1:59 PM NIAID2022 edited by
- (diff)
- 1:57 PM NIAID2022 edited by
- (diff)
- 1:35 PM NIAID2022 edited by
- (diff)
- 10:56 AM Ticket #7701 (glGetFramebufferAttachmentParameteriv: invalid enumerant') closed by
- nonchimerax: The is ChimeraX error is a graphics driver problem. The only way to …
- 10:52 AM Ticket #7703 (Bug in matchmaker secondary structure code revamp) closed by
- duplicate: Duplicate of #7695 -- adding Elaine to recipient list for that ticket.
- 10:49 AM Ticket #7702 (Unknown crash) closed by
- can't reproduce: Run directly from .dmg
- 10:49 AM Ticket #7697 (Crash during window resize in QOpenGLContext.makeCurrent()) closed by
- can't reproduce: Crashed making opengl context current. Could be a Qt bug, could be an …
- 10:45 AM Ticket #7700 (Unknown crash) closed by
- can't reproduce
- 10:44 AM Ticket #7699 (Crash using File→Open dialog on Windows and/or returning from function) closed by
- can't reproduce
- 10:44 AM Ticket #7699 (Crash using File→Open dialog on Windows and/or returning from function) reopened by
- 10:43 AM Ticket #7699 (Crash using File→Open dialog on Windows and/or returning from function) closed by
- can't reproduce: 1.3
- 10:36 AM Ticket #7696 (Bug in matchmaker secondary structure code revamp) closed by
- duplicate
- 10:33 AM Ticket #7694 (Crash making connection callback) closed by
- can't reproduce: 1.1.1, so probably long fixed
- 10:29 AM Ticket #7692 (ChimeraX hangs at startup for minutes when Toolshed not responding) closed by
- duplicate: Duplicate of #7659. Updating recipient list for that ticket to …
- 10:19 AM Ticket #7703 (Bug in matchmaker secondary structure code revamp) created by
- […]
- 10:01 AM Ticket #7702 (Unknown crash) created by
- […]
- 9:44 AM Ticket #7701 (glGetFramebufferAttachmentParameteriv: invalid enumerant') created by
- […]
- 5:15 AM Ticket #7700 (Unknown crash) created by
- […]
- 2:41 AM Ticket #7699 (Crash using File→Open dialog on Windows and/or returning from function) created by
- […]
Sep 28, 2022:
- 11:50 PM Ticket #7698 (More compact VR Toolbar user interface) created by
- The ChimeraX toolbar is the most useful GUI in VR but is cumbersome to …
- 9:26 PM Ticket #7697 (Crash during window resize in QOpenGLContext.makeCurrent()) created by
- […]
- 8:26 PM Ticket #7696 (Bug in matchmaker secondary structure code revamp) created by
- […]
- 7:17 PM Ticket #7695 (Bug in matchmaker secondary structure code revamp) created by
- […] 5o2k.pdb
- 6:21 PM Ticket #7694 (Crash making connection callback) created by
- […]
- 6:16 PM Ticket #7693 (VR flickers with Quest 2 and AirLink or link cable) created by
- The Quest 2 headset exhibits jitter running ChimeraX with connection …
- 5:47 PM Ticket #7690 (Fetching maps from EMDB: ftp connection refused) closed by
- can't reproduce: Today EMDB fetch is working. The EMDB help desk also replied today …
- 5:41 PM Ticket #7692 (ChimeraX hangs at startup for minutes when Toolshed not responding) created by
- When plato was down for maintenance today I started a recent ChimeraX …
- 4:05 PM Ticket #7691 (Clipper closing possible already-closed model during session reset) created by
- […]
Sep 27, 2022:
- 4:35 PM Ticket #7690 (Fetching maps from EMDB: ftp connection refused) created by
- […]
- 3:55 PM Ticket #7683 (Water placement traceback when cannot find Phenix) closed by
- fixed: Made toolshed not rethrow ToolshedError if the originating error is a …
- 3:47 PM Ticket #7689 (Crash closing tool) created by
- […]
- 1:36 PM Ticket #7661 (Crash deleting atoms) closed by
- not a bug: Hi Loc, Thanks for sending the session. If you type "delete atoms" …
- 11:50 AM Ticket #7688 (Crash saving PNG) closed by
- duplicate: Same user has reported this same crash 5 times in past week. It has …
- 11:42 AM Ticket #7688 (Crash saving PNG) created by
- […]
- 11:19 AM Ticket #7687 (Unknown crash) closed by
- can't reproduce: Was running from .dmg
- 10:46 AM Ticket #7687 (Unknown crash) created by
- […]
- 10:21 AM Ticket #7686 (Crash in event loop) closed by
- can't reproduce
- 10:19 AM Ticket #7685 (Crash in atom-spec parser) closed by
- duplicate
- 10:17 AM Ticket #7684 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 10:14 AM Ticket #7681 (Crash getting previous crash info?) closed by
- can't reproduce: Guessing the crash reporter due to the Diagnostics::~Diagnostics() in …
- 10:10 AM Ticket #7680 (Crash in atom-spec parser) closed by
- duplicate: Probable duplicate of #4842
- 9:27 AM Ticket #7686 (Crash in event loop) created by
- […]
- 9:14 AM 2022-9-29 edited by
- (diff)
- 9:14 AM 2022-9-29 created by
- 9:12 AM DeveloperMeetings edited by
- (diff)
- 8:55 AM Ticket #7685 (Crash in atom-spec parser) created by
- […]
- 4:19 AM Ticket #7684 (Crash using File→Open on Windows and/or in return statement) created by
- […]
Sep 26, 2022:
- 6:51 PM Ticket #7683 (Water placement traceback when cannot find Phenix) created by
- […]
- 6:45 PM Ticket #7682 (Update macOS 10.13 build to use 10.14 since PyQt requires it) created by
- Currently we build the Intel Mac ChimeraX distributions targeting …
- 5:55 PM Ticket #7681 (Crash getting previous crash info?) created by
- […]
- 5:15 PM Ticket #7679 (installation issue) closed by
- nonchimerax: So your error of "E: Unable to locate package …
- 4:09 PM ChangeLog edited by
- (diff)
- 4:03 PM ChangeLog edited by
- (diff)
- 3:43 PM Ticket #7680 (Crash in atom-spec parser) created by
- […]
- 2:17 PM Ticket #7679 (installation issue) created by
- […] Untitled 1.pdf
- 1:51 PM Ticket #7593 (FileReader: __init__() got an unexpected keyword argument 'all_geom') closed by
- fixed
- 11:58 AM Ticket #7672 (Delete and add label in same graphics update: could not broadcast ...) closed by
- fixed: Fixed. The error is because the label width exceeds the width of the …
- 11:23 AM Ticket #7676 (Crash saving PNG) closed by
- can't reproduce: Crashed in Pillow trying to save image. Image was already rendered. …
- 11:20 AM Ticket #7677 (Crash saving PNG) closed by
- duplicate
- 11:19 AM Ticket #7673 (issue installing step) closed by
- fixed: The problem reinstalling is that the command should be: sudo …
- 11:19 AM Ticket #7675 (Graphics crash, macOS 11.6.1, Intel Iris Plus Graphics) closed by
- nonchimerax: Intel Mac graphics driver crash.
- 11:10 AM Ticket #7678 (Crashes creating QWebEngineProfile on Windows) created by
- We have about 30 bug reports crashing in creating a QWebEngineProfile …
- 10:57 AM Ticket #7671 (Crash during color drop) closed by
- can't reproduce: *Probably* while trying to color volume.
- 10:51 AM Ticket #7677 (Crash saving PNG) created by
- […]
- 10:46 AM Ticket #7670 (Crash *probably* deleting MatchMaker) closed by
- can't reproduce: Recent changes to not directly connect delete to the OK/Apply signal …
- 10:40 AM Ticket #7669 (Tried to flush backingstore without painting to it first) closed by
- can't reproduce: I *believe* this is a QWebEngine problem (from the "Chrome_IOThread" …
- 10:38 AM Ticket #7664 (Problem opening DICOM data: object of type 'NoneType' has no len()) closed by
- duplicate: This was fixed 8 months ago. Get the current ChimeraX version 1.4 to …
- 9:59 AM Ticket #7676 (Crash saving PNG) created by
- […]
- 9:57 AM Ticket #7668 (Crash disposing of QGridLayout, possibly from XMAS, during garbage ...) closed by
- can't reproduce
- 9:50 AM Ticket #7666 (Crash disposing of Qt widgets during garbage collection) closed by
- can't reproduce
- 9:46 AM Ticket #7665 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 9:41 AM Ticket #7675 (Graphics crash, macOS 11.6.1, Intel Iris Plus Graphics) created by
- […]
- 7:00 AM Ticket #7674 (Report sqm.out; try to make quotes "reusable") created by
- […]
- 4:50 AM Ticket #7673 (issue installing step) created by
- […]
- 2:18 AM Ticket #7672 (Delete and add label in same graphics update: could not broadcast ...) created by
- […]
Sep 25, 2022:
- 11:44 PM Ticket #7671 (Crash during color drop) created by
- […]
- 9:43 PM Ticket #7670 (Crash *probably* deleting MatchMaker) created by
- […]
- 2:00 AM Ticket #7669 (Tried to flush backingstore without painting to it first) created by
- […]
Sep 24, 2022:
- 11:18 AM Ticket #7668 (Crash disposing of QGridLayout, possibly from XMAS, during garbage ...) created by
- […]
- 10:03 AM Ticket #7667 (XMAS distance slider: could not convert string to float: '') created by
- […]
- 9:51 AM Ticket #7666 (Crash disposing of Qt widgets during garbage collection) created by
- […]
- 1:37 AM Ticket #7665 (Crash using File→Open on Windows and/or in return statement) created by
- […]
Sep 23, 2022:
- 7:53 PM Ticket #7664 (Problem opening DICOM data: object of type 'NoneType' has no len()) created by
- […]
- 11:38 AM Ticket #7663 (Crash in Qt event loop running alphafold predict) closed by
- can't reproduce: I guess this is a bug in QtWebEngine.
- 2:18 AM Ticket #7663 (Crash in Qt event loop running alphafold predict) created by
- […]
Sep 22, 2022:
- 6:22 PM 2022-9-22 edited by
- (diff)
- 6:21 PM 2022-9-22 created by
- 6:20 PM DeveloperMeetings edited by
- (diff)
- 5:41 PM Ticket #453 (Undocked panels float above other apps on Mac) closed by
- fixed: I *guess* I'm closing this. It would be nice if the undocked panels …
- 12:38 PM Ticket #7662 (Crash deleting atoms) closed by
- duplicate: followup to #7661
- 12:26 PM Ticket #7660 (Crash in QMainWindow::removeDockWidget while closing tool) closed by
- can't reproduce
- 12:21 PM Ticket #7662 (Crash deleting atoms) created by
- […]
- 12:19 PM Ticket #7661 (Crash deleting atoms) created by
- […]
- 12:17 PM Ticket #7660 (Crash in QMainWindow::removeDockWidget while closing tool) created by
- […]
- 10:49 AM Ticket #7596 (Report simple error if bundle already installed instead of traceback) closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/70febbfc96045a9f41ec8402372f54 …
- 10:23 AM Ticket #7659 (Don't block to check for updates) created by
- […]
- 9:13 AM Ticket #7658 (Model is None after sim stop, and then things go pear-shaped) created by
- […]
- 8:43 AM Ticket #7655 (Crash in event loop) closed by
- can't reproduce
- 7:45 AM Ticket #7657 (glDrawBuffer: invalid operation) created by
- […]
- 3:50 AM Ticket #7656 (Installing ISOLDE into 1.5) created by
- […]
Sep 21, 2022:
- 10:46 PM Ticket #7655 (Crash in event loop) created by
- […]
- 7:46 PM Ticket #7654 (Alpha Fold Google Colab Sign In) created by
- Good evening, I recently started to use ChimeraX for my protein …
- 7:17 PM Ticket #7653 (Add lighting user interface to avoid sooty ambient shadows) created by
- Krishna Reddy notes in this tweet that it is useful to increase the …
- 5:50 PM Ticket #7652 (Unknown crash) closed by
- can't reproduce
- 4:52 PM phenix-9-22-22 edited by
- (diff)
- 4:52 PM phenix-9-22-22 edited by
- (diff)
- 4:50 PM phenix-9-22-22 created by
- 4:25 PM Features edited by
- (diff)
- 4:25 PM Features edited by
- (diff)
- 3:53 PM Ticket #6952 (QMainWindowLayout::tabPosition called with out-of-bounds value) closed by
- can't reproduce: Probably(?) fixed by updating to Qt 6.3.2 -- I can't get the message …
- 3:49 PM Ticket #7343 (Avoid pages of intimidating orange warning text on Toolshed install) closed by
- fixed
- 3:18 PM Ticket #7518 (Modeller web service errors not reported) closed by
- fixed
- 2:39 PM Ticket #7609 (Unintelligible web service error message) closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/ecdecd84db26370cc125be4df64ea3 …
- 2:02 PM Ticket #6425 (Qt6: Mac default button goes blank if dialog loses focus) closed by
- fixed: Seems to have been fixed by Greg's recent PyQt update.
- 12:56 PM Ticket #7652 (Unknown crash) created by
- […]
- 12:01 PM Ticket #7644 (Crash drawing side view) closed by
- can't reproduce
- 11:48 AM Ticket #7651 (Change Chain IDs tool: string index out of range) closed by
- fixed: Hi Dmitry, Thanks for reporting this problem. I have fixed the error …
- 11:22 AM Ticket #7602 (Session reset/restore: 'Tasks' object has no attribute 'remove') closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/ae247498a9053d834c81d1d176456d …
- 11:13 AM Ticket #7641 (wrapped C/C++ object of type QScreen has been deleted) closed by
- duplicate: This was fixed more than a year ago. The error happens when using two …
- 9:23 AM Ticket #7650 (Session reset: 'Tasks' object has no attribute 'remove') closed by
- duplicate
- 9:22 AM Ticket #7651 (Change Chain IDs tool: string index out of range) created by
- […]
- 9:21 AM Ticket #7648 (Unknown crash) closed by
- can't reproduce: Hi David, Thanks for reporting this problem. From the information in …
- 9:08 AM Ticket #7645 (Crash opening PDB) closed by
- can't reproduce
- 9:03 AM Ticket #7642 (Hang in cview) closed by
- can't reproduce
- 7:48 AM Ticket #7650 (Session reset: 'Tasks' object has no attribute 'remove') created by
- […]
- 5:03 AM Ticket #7649 (Second sim stop: 'NoneType' object has no attribute 'atoms') created by
- […]
- 5:02 AM Ticket #7648 (Unknown crash) created by
- […]
- 3:17 AM Ticket #7647 (Second sim stop: 'NoneType' object has no attribute 'atoms') created by
- […]
- 2:16 AM Ticket #7646 (Crash opening PDB file) created by
- […]
- 1:47 AM Ticket #7645 (Crash opening PDB) created by
- […]
- 1:18 AM Ticket #7644 (Crash drawing side view) created by
- […]
Sep 20, 2022:
- 11:11 PM Ticket #7643 (Mac ARM64 build broken: pyproject.toml lz4 compile uses system python) created by
- The Mac ARM64 build is broken for me (goddard) on euclid.cgl.ucsf.edu …
- 8:57 PM Ticket #7642 (Hang in cview) created by
- […]
- 3:47 PM Ticket #7641 (wrapped C/C++ object of type QScreen has been deleted) created by
- […]
- 10:36 AM Ticket #7640 (Crash in color button callback) closed by
- can't reproduce: Code was made more robust on 7/12/22, so may be fixed.
- 10:09 AM Ticket #7640 (Crash in color button callback) created by
- […]
- 9:19 AM Ticket #7639 (Models closed while simulation running) created by
- […]
- 9:07 AM Ticket #7637 (ISOLDE holding ref to deleted structure) closed by
- duplicate
- 9:04 AM Ticket #7635 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 9:02 AM Ticket #7634 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.4, but before going to Python 3..9.11
- 8:09 AM Ticket #7638 (ISOLDE holding ref to deleted structure) created by
- […]
- 8:08 AM Ticket #7637 (ISOLDE holding ref to deleted structure) created by
- […]
- 6:03 AM Ticket #7636 (ISOLDE holding ref to deleted structure) created by
- […]
Sep 19, 2022:
- 9:22 PM Ticket #7635 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 8:36 PM Ticket #7634 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 6:32 PM Dev2022-9-19 edited by
- (diff)
- 6:29 PM Dev2022-9-19 edited by
- (diff)
- 5:57 PM Ticket #7631 (Problem with Shell when incorrect Python executed) closed by
- fixed: As per https://github.com/ipython/ipykernel/pull/942, fixed by …
- 4:39 PM Ticket #7633 (Should we drop macOS 10.14 for the ChimeraX 1.5 release?) created by
- We have one trouble with macOS 10.14 where distribution would be …
- 4:00 PM Ticket #7632 (support beta releases on toolshed) created by
- Would like pre-release bundles to be hidden by default in the toolshed …
- 3:58 PM Dev2022-9-19 edited by
- (diff)
- 3:34 PM Dev2022-9-19 edited by
- (diff)
- 3:30 PM Ticket #7631 (Problem with Shell when incorrect Python executed) created by
- […]
- 3:15 PM Ticket #6508 (Error getting mmCIF templates: URL can't contain control characters) closed by
- fixed: Appears to be in 1.4. See #7618
- 3:11 PM Dev2022-9-19 edited by
- (diff)
- 3:06 PM Ticket #6170 (Fetching mmCIF template: URL can't contain control characters) closed by
- duplicate: duplicate of #6508
- 3:00 PM Dev2022-9-19 edited by
- (diff)
- 2:58 PM Dev2022-9-19 edited by
- (diff)
- 2:56 PM Dev2022-9-19 created by
- 2:55 PM DeveloperMeetings edited by
- (diff)
- 1:50 PM Ticket #7630 (Restore new session in old version) closed by
- duplicate
- 1:49 PM Ticket #7629 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 1:49 PM Ticket #7630 (Restore new session in old version) created by
- […]
- 1:46 PM Ticket #7629 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 1:36 PM Ticket #7627 (ChimeraX/ISOLDE version problems) closed by
- fixed: Glad it's working now. --Eric
- 1:07 PM Ticket #7624 (KeyError in read_json_pae_matrix) closed by
- fixed: Fixed in ChimeraX 1.4. They are using an April 2022 ChimeraX version …
- 12:56 PM Ticket #7623 (Crash saving image) closed by
- can't reproduce: Crashed in Pillow trying to write out the png file for an image that …
- 12:40 PM Ticket #7628 (ChimeraX reports 10 GB virtual memory use on Mac M1, not a bug) closed by
- not a bug
- 12:26 PM Ticket #7628 (ChimeraX reports 10 GB virtual memory use on Mac M1, not a bug) created by
- […]
- 12:16 PM Ticket #7625 (Unknown crash) closed by
- can't reproduce
- 12:01 PM Ticket #7622 (close session set_pbgroup_py_instance: symbol not found) closed by
- duplicate
- 11:46 AM Ticket #7620 (Crash processing mouse event) closed by
- can't reproduce: Was using 8.8GB at the time, though when I performed the same commands …
- 11:46 AM Ticket #7618 (Problems reading mmCIF) closed by
- limitation: Please redownload 6vsj from the PDB. You can do a "open 6vsj …
- 11:33 AM Ticket #7619 (Crash in color button callback) closed by
- can't reproduce: Possibly fixed by commit d7389d14caf539e5563c46b5391cd30eef16a210
- 11:30 AM Ticket #6922 (Update core setup.py to pyproject.toml) closed by
- fixed: Implemented in a series of commits including primarily …
- 11:18 AM Ticket #7627 (ChimeraX/ISOLDE version problems) created by
- […]
- 11:15 AM Ticket #7617 (Crash saving atomic session state) closed by
- can't reproduce
- 11:08 AM Ticket #7616 (Crash saving atomic session state) closed by
- can't reproduce
- 11:01 AM Ticket #7615 (Crash saving atomic session state) closed by
- can't reproduce
- 10:57 AM Ticket #7614 (Crash saving atomic session state) closed by
- can't reproduce
- 10:52 AM Ticket #7613 (Crash saving atomic session state) closed by
- can't reproduce
- 10:45 AM Ticket #7612 (Crash saving atomic session state) closed by
- can't reproduce: Would need the starting session, and even then it would be dicey to …
- 10:38 AM Ticket #7611 (Crash in event loop) closed by
- can't reproduce
- 10:32 AM Ticket #7626 (On windows all of ChimeraX lives under C:\\...\\ChimeraX.app\\bin\\) created by
- I was playing whack-a-mole over the weekend with ChimeraX's app dirs …
- 9:13 AM Ticket #7625 (Unknown crash) created by
- […]
- 7:18 AM Ticket #7624 (KeyError in read_json_pae_matrix) created by
- […]
- 4:37 AM Ticket #7623 (Crash saving image) created by
- […]
Sep 18, 2022:
- 10:48 PM Ticket #7622 (close session set_pbgroup_py_instance: symbol not found) created by
- […]
- 10:43 PM Ticket #7621 (Crash in event loop) created by
- […]
- 4:46 AM Ticket #7620 (Crash processing mouse event) created by
- […]
- 4:16 AM Ticket #7619 (Crash in color button callback) created by
- […]
- 1:51 AM Ticket #6528 (Crash opening mmCIF file) closed by
- can't reproduce
- 1:49 AM Ticket #5083 (Bundle ChimeraX-mmCIF has no module) closed by
- can't reproduce
- 12:39 AM Ticket #7618 (Problems reading mmCIF) created by
- […] 6VSJ.cif
Sep 17, 2022:
- 12:10 PM Ticket #7617 (Crash saving atomic session state) created by
- […]
- 12:06 PM Ticket #7616 (Crash saving atomic session state) created by
- […]
- 12:04 PM Ticket #7615 (Crash saving atomic session state) created by
- […]
- 11:58 AM Ticket #7614 (Crash saving atomic session state) created by
- […]
- 11:56 AM Ticket #7613 (Crash saving atomic session state) created by
- […]
- 11:52 AM Ticket #7612 (Crash saving atomic session state) created by
- […]
- 5:07 AM Ticket #7611 (Crash in event loop) created by
- […]
Sep 16, 2022:
- 9:48 PM Ticket #7610 (Crash loading bundle info) created by
- […]
- 5:41 PM Ticket #7609 (Unintelligible web service error message) created by
- […]
- 5:00 PM Ticket #3636 (mmcif_write fails with temporary/unopened structure) closed by
- fixed: The mmCIF writer uses the model's id hierarchy to group NMR models …
- 4:30 PM Ticket #3539 (Problems with large de novo mmCIF structure) closed by
- limitation
- 4:23 PM Ticket #4162 (Excessive mmCIF warning output) closed by
- fixed: Limited to 10 warnings about hydrogens missing in a residue template. …
- 3:18 PM Ticket #3916 (Saving mmCIF files too slow to work with large structures) closed by
- fixed: Speed up mmCIF code by using Cython. Mostly with "cdef class …
- 1:30 PM Ticket #7548 (Auto-style on 4 chain 120,000 atoms looks bad) closed by
- fixed: The ribbon upper limit that Greg added for performance reasons leaves …
- 10:59 AM Ticket #7608 (Option to 'combine' to retain chain IDs) created by
- ...add an option to combine to retain chain IDs, which would basically …
- 10:42 AM Ticket #7607 (Restore new session in old version) closed by
- duplicate
Sep 15, 2022:
- 7:31 PM Ticket #7607 (Restore new session in old version) created by
- […]
- 4:42 PM Ticket #6877 (support pdbx_struct_mod_residue in mmCIF files) closed by
- wontfix: Using the pdbx_struct_mod_residues to find modified residues is not …
- 4:39 PM Ticket #6554 (VirtualGL: glClear: invalid operation) closed by
- limitation
- 4:38 PM Ticket #6789 (Needed Fedora libraries) closed by
- fixed
- 4:34 PM Ticket #6964 (Fetching version information: certificate verify failed: unable to get ...) closed by
- fixed: The certificate now expires on 21 May 2023.
- 12:58 PM 2022-9-15 edited by
- (diff)
- 12:45 PM Ticket #7605 (Crash saving PNG) closed by
- can't reproduce: ChimeraX crashed in Pillow code trying to save the image file. The …
- 11:00 AM 2022-9-15 edited by
- (diff)
- 10:46 AM Ticket #7606 (Crash saving PNG) closed by
- duplicate: Duplicate of #7605
- 10:43 AM Ticket #7604 (Error in ToolShed error message) closed by
- duplicate: Hi Kartik, This particular problem was fixed awhile ago. You should …
- 10:34 AM Ticket #7601 (Crash in fork()) closed by
- limitation: Hi Lori, Thanks for reporting this problem. The Rosetta emulation …
- 10:30 AM Ticket #7606 (Crash saving PNG) created by
- […]
- 10:25 AM Ticket #7600 (UniProt fetch: HTTP Error 405: Not Allowed) closed by
- duplicate: Hi Marc, Thanks for reporting this problem. UniProt changed the API …
- 10:23 AM Ticket #7605 (Crash saving PNG) created by
- […]
- 10:21 AM Ticket #7599 (Abort during Qt initialization) closed by
- can't reproduce: This happens so early that I'm wondering if we actually expect to get …
- 10:02 AM Ticket #7604 (Error in ToolShed error message) created by
- […]
- 9:59 AM Ticket #7603 (Problems opening MTX file) created by
- […]
- 9:42 AM Ticket #7602 (Session reset/restore: 'Tasks' object has no attribute 'remove') created by
- […]
- 8:03 AM Ticket #7601 (Crash in fork()) created by
- […]
- 12:42 AM Ticket #7600 (UniProt fetch: HTTP Error 405: Not Allowed) created by
- […]
- 12:31 AM Ticket #7599 (Abort during Qt initialization) created by
- […]
Sep 14, 2022:
- 4:15 PM DeveloperMeetings edited by
- (diff)
- 4:15 PM DeveloperMeetings edited by
- (diff)
- 4:02 PM Dev2022-9-14 edited by
- (diff)
- 3:39 PM Dev2022-9-14 created by
- 3:34 PM DeveloperMeetings edited by
- (diff)
- 3:14 PM Ticket #7598 (Toolshed version check produces many errors) created by
- […]
- 3:11 PM Ticket #7597 (Allow map eraser to use cube instead of sphere) created by
- Begin forwarded message: From: "Walton, Travis Steven via …
- 11:16 AM Ticket #7596 (Report simple error if bundle already installed instead of traceback) created by
- Playing around with installing ArtiaX today to see if pip would give …
- 9:42 AM Ticket #7595 (Registration code: ValueError: tuple.index(x): x not in tuple) created by
- This error is reported originally #7594. Made a separate ticket since …
- 6:12 AM Ticket #7594 (Various Clipper problems) created by
- […]
- 5:35 AM Ticket #7593 (FileReader: __init__() got an unexpected keyword argument 'all_geom') created by
- […]
Sep 13, 2022:
- 7:02 PM Ticket #6253 (opening 1plx as trajectory (coordset true) omits inter-residue bonds) closed by
- fixed: Fixed finding the residues to connect.
- 6:19 PM Ticket #1897 (OpenMM ToolShed bundle) closed by
- fixed: We now track the openMM binary distributions on conda-forge, …
- 2:07 PM Ticket #5757 (Make presets useful for 3D printing atomic models) closed by
- fixed: Presets seem to be functional in the NIH3D pipeline.
- 2:00 PM Ticket #7592 (Dead widgets in MatchMaker) closed by
- fixed: fix: …
- 9:59 AM Ticket #7588 (Graphics crash, macOS 10.15.7, Intel Iris Plus Graphics 640) closed by
- nonchimerax: Mac Intel graphics driver crash. No python traceback or log probably …
- 9:54 AM 2022-9-15 created by
- 9:52 AM DeveloperMeetings edited by
- (diff)
- 9:52 AM 2022-9-8 edited by
- (diff)
- 9:08 AM Ticket #7591 (Crash in movie encode (fork ffmpeg)) closed by
- limitation: Hi Titia, Thanks for reporting this problem. We feel the crash …
- 8:57 AM Ticket #7590 (_fix_selected_unparameterised_residue: cannot unpack non-iterable ...) closed by
- duplicate
- 8:57 AM Ticket #7587 (Crash in clipper.symmetry) closed by
- can't reproduce
- 8:39 AM Ticket #7586 (Crash in event loop) closed by
- can't reproduce
- 6:50 AM Ticket #7592 (Dead widgets in MatchMaker) created by
- […]
- 12:31 AM Ticket #7591 (Crash in movie encode (fork ffmpeg)) created by
- […]
- 12:08 AM Ticket #7579 (Allow saving multi-model mmCIF files) closed by
- fixed: Added all_coordsets flag to the mmCIF save function. And that is …
Sep 12, 2022:
- 11:15 PM Ticket #7590 (_fix_selected_unparameterised_residue: cannot unpack non-iterable ...) created by
- […]
- 10:42 PM Ticket #7544 (ChimeraX crashes on start-up) closed by
- fixed: Yuxia reinstalled and deleted preferences and got ChimeraX working. …
- 10:25 PM Ticket #7589 (Saving PDB file 8 times slower than saving mmCIF) created by
- […]
- 10:04 PM Ticket #7588 (Graphics crash, macOS 10.15.7, Intel Iris Plus Graphics 640) created by
- […]
- 5:24 PM Ticket #7587 (Crash in clipper.symmetry) created by
- […]
- 1:58 PM Ticket #7585 (Selection highlighting not continuous) closed by
- fixed: Fixed I think in tonight's daily build. This is a graphics bug in Mac …
- 1:48 PM Ticket #7586 (Crash in event loop) created by
- […]
- 1:33 PM Ticket #7583 (glTexImage3D: out of memory) closed by
- nonchimerax: As the error message says "out of memory". You are trying to display …
- 1:25 PM Ticket #7582 (Crash in QOpenGLContext.create() initializing status bar on Linux) closed by
- nonchimerax: Crashed on QOpenGLContext.create() when first showing a model. Seems …
- 1:13 PM Ticket #7584 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 12:30 PM Ticket #6434 (Support pyproject.toml) closed by
- fixed: As of …
- 11:55 AM Ticket #7581 (Uniprot fetch broken) closed by
- duplicate: Hi, Thanks for reporting this problem. UniProt changed the API for …
- 11:52 AM ChangeLog edited by
- (diff)
- 11:51 AM ChangeLog edited by
- (diff)
- 11:51 AM ChangeLog edited by
- (diff)
- 11:41 AM Ticket #7578 (Crash getting atomic session info) closed by
- can't reproduce: Tested opening PSF "with PDB" (which deletes incomplete structure) and …
- 9:26 AM Ticket #7585 (Selection highlighting not continuous) created by
- […] Screenshot 2022-09-12 at 17.23.15.png
- 4:59 AM Ticket #7584 (Crash using File→Open on Windows and/or in return statement) created by
- […]
Sep 11, 2022:
- 11:00 PM Ticket #7583 (glTexImage3D: out of memory) created by
- […]
- 9:48 AM Ticket #7582 (Crash in QOpenGLContext.create() initializing status bar on Linux) created by
- […]
- 1:42 AM Ticket #7581 (Uniprot fetch broken) created by
- […]
Sep 9, 2022:
- 10:45 PM Ticket #7580 (Unknown crash) created by
- […]
- 7:22 PM Ticket #7579 (Allow saving multi-model mmCIF files) created by
- […]
- 5:46 PM Ticket #7578 (Crash getting atomic session info) created by
- […]
- 1:56 PM Ticket #7564 (Handle 5-character residue names from Protein Databank) closed by
- not a bug: The mmCIF reading code uses fixed width columns for speed, but the …
- 1:36 PM Ticket #7577 (Atomspec /A-B sometimes orders chains B,A breaking commands where ...) created by
- […]
- 11:46 AM Ticket #7565 (Update PDB fetch URLs) closed by
- not a bug: Chimera/ChimeraX don't use those generic URLs -- they use URLs …
- 11:07 AM Ticket #7563 (Improve labels' contrast with background) closed by
- fixed: Fix: …
- 10:04 AM Ticket #7576 (Color Actions: name 'target' is not defined) closed by
- fixed: Hi Maria, Thanks for reporting this problem. It looks like some …
- 8:26 AM Ticket #7576 (Color Actions: name 'target' is not defined) created by
- […]
Sep 8, 2022:
- 4:52 PM Ticket #7572 (Crash in event loop after using silhouettes and high multishadow) closed by
- can't reproduce: Possible graphics driver crash.
- 4:50 PM Ticket #7573 (Crash in event loop after setting volume level) closed by
- can't reproduce: Possibly a graphics driver crash. Had just opened 420 by 420 by 420 …
- 4:45 PM Ticket #7571 (Open .glb file: KeyError: 'byteOffset') closed by
- fixed: Fixed in tonight's ChimeraX builds. The GLTF spec says that …
- 4:31 PM Ticket #7575 (Coordset slider save/restore in session) created by
- The coordset slider should restore from a session if it was present …
- 4:25 PM Ticket #7568 ('type' object is not subscriptable) closed by
- limitation: It seems that type annotations were not supported in the older version …
- 4:12 PM Ticket #7567 (Crash in save dialog) closed by
- can't reproduce: 1.2.5
- 3:55 PM Ticket #7574 (Choose next tool for Phenix ChimeraX user interface) created by
- What will be the next ChimeraX Phenix user interface after the "douse" …
- 10:33 AM Ticket #5157 (PyPi dependency not installed by "devel install") closed by
- limitation: We're going to wait for improvements in Python's pip to handle this case.
- 10:16 AM Ticket #7573 (Crash in event loop after setting volume level) created by
- […]
- 7:20 AM Ticket #7572 (Crash in event loop after using silhouettes and high multishadow) created by
- […]
- 6:44 AM Ticket #7571 (Open .glb file: KeyError: 'byteOffset') created by
- […] human_eukaryotic_cell_and_its_main_components.glb
- 2:45 AM Ticket #7570 (Session save: Unknown class name 'MarkerSetPlus') created by
- […]
- 2:43 AM Ticket #7569 (Session save: Unknown class name 'MarkerSetPlus') created by
- […]
Sep 7, 2022:
- 9:41 PM Ticket #7568 ('type' object is not subscriptable) created by
- […]
- 7:28 PM Ticket #7567 (Crash in save dialog) created by
- […]
- 6:45 PM ChangeLog edited by
- (diff)
- 6:27 PM Ticket #7566 (pseudobonds unexpectedly not displayed) closed by
- fixed: The graphics_changes()->set_gc_adddel() was missing from the …
- 5:18 PM Ticket #7566 (pseudobonds unexpectedly not displayed) created by
- Open 1a0m and use the Sticks preset, then: view /B:5 altlocs change B …
- 1:47 PM Ticket #7565 (Update PDB fetch URLs) created by
- The Protein Databank is deprecating some urls for fetching files. We …
- 12:01 PM Ticket #7564 (Handle 5-character residue names from Protein Databank) created by
- The PDB announced the will switch from 3 character to 5 character …
- 12:00 PM Ticket #7563 (Improve labels' contrast with background) created by
- […] periodic tables.zip
- 11:38 AM Ticket #7562 (Crash in QMessageBox.exec() asking for registration info) created by
- […]
- 10:13 AM Ticket #7561 (Make ChimeraX fetch 8 character PDB identifiers) created by
- The PDB announced they will start using 8 character PDB identifiers. …
Sep 6, 2022:
- 2:23 PM ChangeLog edited by
- (diff)
- 1:16 PM Ticket #7553 (draw selection: glDrawBuffer: invalid operation) closed by
- can't reproduce: Graphics worked for a long time, then failed. Not clear why. May be …
- 1:00 PM Ticket #7559 (Hide cartoon: Cylinder end point, radii or rotation array not contiguous) closed by
- duplicate: This bug was fixed a month ago. Get a new ChimeraX daily build or …
- 12:56 PM 2022-9-8 created by
- 12:55 PM DeveloperMeetings edited by
- (diff)
- 12:54 PM DeveloperMeetings edited by
- (diff)
- 10:27 AM Ticket #7560 (Crash using QFileDialog.getSaveFileName) closed by
- can't reproduce: 1.3
- 9:59 AM Ticket #7558 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce
- 9:58 AM Ticket #7557 (Basic Actions: 'QEventLoop' object has no attribute 'exec_') closed by
- duplicate
- 9:57 AM Ticket #7556 (Mismatch between Cocoa and Carbon for virtual key) closed by
- can't reproduce
- 9:54 AM Ticket #7555 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.4 before Python upgrade
- 9:52 AM Ticket #7554 (Restore new session in old version) closed by
- duplicate
Sep 5, 2022:
- 2:52 PM Ticket #7560 (Crash using QFileDialog.getSaveFileName) created by
- […]
- 12:48 AM Ticket #7559 (Hide cartoon: Cylinder end point, radii or rotation array not contiguous) created by
- […]
Sep 4, 2022:
- 11:32 PM Ticket #7558 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 8:15 PM Ticket #7557 (Basic Actions: 'QEventLoop' object has no attribute 'exec_') created by
- […]
- 7:49 PM Ticket #7556 (Mismatch between Cocoa and Carbon for virtual key) created by
- […]
- 11:36 AM Ticket #7555 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 12:41 AM Ticket #7554 (Restore new session in old version) created by
- […]
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