![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Aug 22, 2022:
- 10:02 PM Ticket #7419 (Drag select blacks out graphics) closed by
- fixed: Fixed. It is not clear if this is an OpenGL driver bug. When the …
- 6:57 PM Ticket #7486 (Crash computing ribbons) closed by
- can't reproduce: Appears it was in the C++ ribbon_extrusions() code called by …
- 6:22 PM Ticket #7482 (Operation not permitted opening file from HTML link) closed by
- not a bug: Yep, looks like the user clicked a recent file thumbnail image and did …
- 6:08 PM Ticket #7488 (make BILD transparency work) closed by
- limitation: Ticket #3838 explains that we do not have the resources (funding / …
- 5:54 PM Ticket #7492 (Can ChimeraX with Qt 6 run on Debian 9?) closed by
- not a bug: Just noting the GitHub discussion in Trac so we can easily find it.
- 5:53 PM Ticket #7492 (Can ChimeraX with Qt 6 run on Debian 9?) created by
- Looks like Debian 9 Linux distro based on glibc 2.24 is too old to run …
- 5:51 PM Ticket #7342 (Axes/Planes/Centroids tool) closed by
- fixed
- 4:41 PM Dev2022-8-22 edited by
- (diff)
- 4:37 PM Dev2022-8-22 created by
- 4:28 PM DeveloperMeetings edited by
- (diff)
- 12:10 PM Ticket #7490 (read CASTp) closed by
- duplicate: Hi Andrea, Chimera and ChimeraX are different programs. Chimera has …
- 12:06 PM Ticket #7491 (Make --cmd startup option behave like executing a script in its ...) closed by
- fixed: Fixed. Made the commands given with the --cmd option run as if they …
- 12:04 PM Ticket #7491 (Make --cmd startup option behave like executing a script in its ...) created by
- Christian noted that the shell --cmd option in ChimeraX where several …
- 11:38 AM Ticket #7485 (Surface.vertices is None) closed by
- duplicate: Duplicate of #7466
- 11:34 AM Ticket #7490 (read CASTp) created by
- […]
- 11:30 AM Ticket #7487 (H-bonds: cannot import name 'report_exception' from 'chimerax.core.logger') closed by
- fixed: Fix: …
- 11:26 AM Ticket #7466 (Coloring surface: self.vertices is None) closed by
- fixed: Fixed. This error in color command was caused by the previous failed …
- 11:15 AM Ticket #7484 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 11:14 AM Ticket #7483 (Crash using File→Open on Windows) closed by
- can't reproduce: 1.2.5
- 10:57 AM Ticket #7489 (Test if ticket assigned to tic20 uses Tristan's old or new email address) closed by
- not a bug
- 10:53 AM Ticket #7489 (Test if ticket assigned to tic20 uses Tristan's old or new email address) created by
- 10:42 AM Ticket #7480 (Opening new session in old ChimeraX) closed by
- duplicate
- 10:41 AM Ticket #7479 (Crash draining NSAutoreleasePool during dialog exec) closed by
- can't reproduce: Supposedly happens when an object is released more times that it's …
- 10:20 AM Ticket #7430 (why does this script show DICOM as surface style?) closed by
- fixed: Forgot to commit the fix to the git code repository. I guess I was in …
- 10:19 AM Ticket #7431 ("close session" does not reset volume model color rotation) closed by
- fixed
- 9:24 AM Ticket #7488 (make BILD transparency work) created by
- From Francois Berenger: In the old Chimera (not X), if I put two …
- 7:52 AM Ticket #7487 (H-bonds: cannot import name 'report_exception' from 'chimerax.core.logger') created by
- […]
- 3:04 AM Ticket #7486 (Crash computing ribbons) created by
- […]
- 1:48 AM Ticket #7485 (Surface.vertices is None) created by
- […]
- 1:13 AM Ticket #7484 (Crash using File→Open on Windows and/or in return statement) created by
- […]
Aug 21, 2022:
- 11:49 PM Ticket #7483 (Crash using File→Open on Windows) created by
- […]
- 1:27 PM Ticket #7482 (Operation not permitted opening file from HTML link) created by
- […]
- 5:30 AM Ticket #7481 (QMainWindowLayout::tabPosition called with out-of-bounds value '0') created by
- […]
Aug 20, 2022:
Aug 19, 2022:
- 11:07 AM Ticket #7479 (Crash draining NSAutoreleasePool during dialog exec) created by
- […]
- 9:21 AM Ticket #7478 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 9:20 AM Ticket #7477 (Crash during SMILES translation) closed by
- can't reproduce
- 9:17 AM Ticket #7476 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 9:12 AM Ticket #7475 (No symmetries for 2bbv) closed by
- duplicate: Asked and answered on the chimerax-users list.
- 6:18 AM Ticket #7478 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 1:26 AM Ticket #7477 (Crash during SMILES translation) created by
- […]
- 12:36 AM Ticket #7476 (Crash using File→Open on Windows and/or in return statement) created by
- […]
Aug 18, 2022:
- 6:20 PM Ticket #7475 (No symmetries for 2bbv) created by
- […] 2bbv practice.cxs
- 4:30 PM Ticket #7473 (name 'notImplemented' is not defined) closed by
- fixed
- 3:40 PM Ticket #7471 (Incomplete secondary structure) closed by
- duplicate: Asked and answered on the chimerax-users list.
- 3:20 PM Ticket #7474 (allow user to specify job name (folder name) for alphafold predict) created by
- Elaine: paraphrase of conversation with Phil during NIAID zoom …
- 1:42 PM NIAID2022 edited by
- (diff)
- 12:13 PM Ticket #7473 (name 'notImplemented' is not defined) created by
- […]
- 8:35 AM Ticket #7472 (Crash or hang at startup) created by
- […]
Aug 17, 2022:
- 4:02 PM Ticket #7471 (Incomplete secondary structure) created by
- […] Screen Shot 2022-08-15 at 10.54.07 PM.png
- 1:38 PM Ticket #7470 (Start simulation: openmm.OpenMMException: Error compiling kernel: ...) created by
- […]
- 10:43 AM Ticket #7469 (libGLU.so.1: cannot open shared object file: No such file or directory) closed by
- limitation: The Ubuntu and RHEL packages have dependencies that pull this in. So …
- 10:31 AM Ticket #7468 (Hang/crash at startup) closed by
- can't reproduce
Aug 16, 2022:
- 4:56 PM Ticket #7469 (libGLU.so.1: cannot open shared object file: No such file or directory) created by
- […]
- 3:01 PM Ticket #7468 (Hang/crash at startup) created by
- […]
- 11:34 AM Ticket #7440 (Emulate Chimera per-helix coloring) closed by
- fixed: Available in next daily build
- 10:53 AM Ticket #7452 (Problem reading ORCA output file) closed by
- fixed
- 10:29 AM Ticket #7467 (Coloring surface: self.vertices is None) closed by
- duplicate: Duplicate of #7466
- 9:38 AM Ticket #7464 (Session save: seg fault appending to unprocessed list) closed by
- can't reproduce: Hi Shayan, Thanks for reporting this problem. I would recommend that …
- 9:32 AM Ticket #7460 (FindHBond: accPhiPsi() takes exactly 8 arguments (9 given)) closed by
- can't reproduce: Probably something hinky about the structure
- 7:57 AM Ticket #7467 (Coloring surface: self.vertices is None) created by
- […]
- 7:57 AM Ticket #7466 (Coloring surface: self.vertices is None) created by
- […]
- 4:40 AM Ticket #7465 (Crash showing Rapid Access at startup) created by
- […]
Aug 15, 2022:
- 8:58 PM Ticket #7464 (Session save: seg fault appending to unprocessed list) created by
- […]
- 3:40 PM Ticket #7463 (Additional phenix/douse enhancements) created by
- limit density values to 3 significant digits (Rotamers too) reveal map …
- 3:32 PM Ticket #7462 (Sequence Viewer context menu "blast" should provide more options) created by
- ... instead of always just using defaults, which prevents blasting …
- 3:10 PM Ticket #7461 (Blast Results dialog: add buttons for same actions as in context menu) created by
- The context menu actions are not very discoverable by people who don't …
- 2:55 PM Ticket #7460 (FindHBond: accPhiPsi() takes exactly 8 arguments (9 given)) created by
- […]
- 2:44 PM Ticket #7431 ("close session" does not reset volume model color rotation) reopened by
- Also the following does not reset volume coloring, so I'm pretty sure …
- 2:35 PM Ticket #7430 (why does this script show DICOM as surface style?) reopened by
- This is not fixed... tested in UCSF ChimeraX version: …
- 2:16 PM Ticket #7459 (Cannot fetch mmCIF: Network is down) closed by
- fixed: Great! --Eric
- 1:40 PM Ticket #7459 (Cannot fetch mmCIF: Network is down) created by
- […]
- 11:56 AM Ticket #7457 ("move label" mouse mode broken) closed by
- fixed: Squirrel away PickedTriangle as attribute of PickedModel for code …
- 11:32 AM Ticket #7458 (update uniref databases for blast protein) created by
- I am told that we are using versions from 2012 (yikes) and that there …
- 11:01 AM Ticket #7457 ("move label" mouse mode broken) created by
- […]
- 9:46 AM Ticket #7447 (Newer-version check failure) closed by
- limitation: Then this was a bug during the web services upgrade process that …
- 9:20 AM Ticket #7456 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 9:19 AM Ticket #7455 (Crash in fork) closed by
- nonchimerax: Was using 9.0GB at the time
- 9:17 AM Ticket #7454 (Graphics crash, macOS 12.5, Intel Iris Plus Graphics) closed by
- can't reproduce: Possible graphics driver bug
- 9:16 AM Ticket #7453 (Calling [C++: N10atomstruct5ChainE] _cpp_demotion failed) closed by
- can't reproduce: Hi Naeyma, Thanks for reporting this problem. I recommend you …
- 9:04 AM Ticket #7450 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 8:55 AM Ticket #7449 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 8:53 AM Ticket #7448 (Crash using File→Open on Windows) closed by
- can't reproduce: 1.3
- 8:45 AM Ticket #7445 (Mismatch between Cocoa and Carbon for virtual key) closed by
- can't reproduce: Crash in text-input handling, possibly while trying to input an …
- 8:35 AM Ticket #7444 (Graphics crash, macOS 11.6.8, Intel Iris Plus Graphics 645) closed by
- can't reproduce: Graphics driver bug?
- 8:22 AM Ticket #7456 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 6:18 AM Ticket #7455 (Crash in fork) created by
- […]
- 6:01 AM Ticket #7454 (Graphics crash, macOS 12.5, Intel Iris Plus Graphics) created by
- […]
- 12:31 AM Ticket #7453 (Calling [C++: N10atomstruct5ChainE] _cpp_demotion failed) created by
- […]
Aug 14, 2022:
- 7:37 AM Ticket #7452 (Problem reading ORCA output file) created by
- […] c3po-opt-freq-casscf-tz.out
- 7:30 AM Ticket #7451 (Problem reading ORCA output file) created by
- […]
Aug 13, 2022:
- 6:21 PM Ticket #7450 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 5:56 PM Ticket #7449 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 5:39 PM Ticket #7448 (Crash using File→Open on Windows) created by
- […]
- 12:52 AM Ticket #7447 (Newer-version check failure) created by
- […]
- 12:03 AM Ticket #7446 (Crash recording movie) created by
- […]
Aug 12, 2022:
- 10:08 PM Ticket #7445 (Mismatch between Cocoa and Carbon for virtual key) created by
- […]
- 6:52 PM Ticket #7444 (Graphics crash, macOS 11.6.8, Intel Iris Plus Graphics 645) created by
- […]
- 4:50 PM Ticket #7443 (Make easy shadowed transparent surface mode) created by
- It is common to show transparent surfaces (cryoEM or molecular) with …
- 3:40 PM Ticket #7441 (Graphics crash, macOS 12.5, Intel Iris Plus Graphics 655) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 3:36 PM Ticket #7407 (ArtiaX error after closing all models and opening new particle list) closed by
- fixed: I'll close this ticket since you don't have an account on our system …
- 3:30 PM Ticket #7442 (Toolshed web server logs are mostly missing after May 2022) created by
- It looks like the Toolshed web server logs are mostly missing from May …
- 2:46 PM Ticket #7437 (Crash starting ISOLDE simulation) closed by
- can't reproduce: Crashed in numpy making a triangulation for an atom sphere (a few …
- 10:49 AM Ticket #7435 (Speed up Blast Protein search by using 4 threads) closed by
- fixed: I've made the change. :) Glad you found a way to make this faster.
- 10:34 AM Ticket #7439 (Crash in AtomSearchTree) closed by
- duplicate: Probable duplicate of #7256
- 10:11 AM Ticket #7441 (Graphics crash, macOS 12.5, Intel Iris Plus Graphics 655) created by
- […]
- 9:50 AM Ticket #7440 (Emulate Chimera per-helix coloring) created by
- In Chimera if you rainbow the ribbon and then make perhelix axes, they …
- 9:32 AM Ticket #7439 (Crash in AtomSearchTree) created by
- […]
- 9:14 AM Ticket #7436 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: Early 1.4, before moving to the fixed version of Python
- 9:11 AM Ticket #7434 (Crash or hang at startup) closed by
- can't reproduce
- 8:08 AM Ticket #7438 (Toolshed bot traffic?) created by
- […]
Aug 11, 2022:
- 9:01 PM Ticket #7437 (Crash starting ISOLDE simulation) created by
- […]
- 7:47 PM Ticket #7436 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 7:01 PM Ticket #7435 (Speed up Blast Protein search by using 4 threads) created by
- Have blastp use 4 threads instead of the default 1 thread when running …
- 5:08 PM Ticket #7434 (Crash or hang at startup) created by
- […]
- 4:42 PM Ticket #7433 (Destruction of status bar during session restore: wrapped C/C++ object ...) closed by
- duplicate: Hi Maria, Thanks for reporting this problem. It has been fixed in …
- 4:36 PM Ticket #7432 (Crash using File→Open dialog on Windows and/or returning from function) closed by
- can't reproduce: 1.3
- 4:33 PM Ticket #7429 (Crash showing Rapid Access at startup) closed by
- can't reproduce: Maybe, maybe not.
- 4:28 PM Ticket #7427 (QMainWindowLayout::tabPosition called with out-of-bounds value) closed by
- can't reproduce: Seemed to occur after "Destroying pre-existing alignment with …
- 3:07 PM Ticket #7433 (Destruction of status bar during session restore: wrapped C/C++ object ...) created by
- […]
- 2:33 PM 2022-8-11 edited by
- (diff)
- 2:26 PM DeveloperMeetings edited by
- (diff)
- 2:03 PM Ticket #7431 ("close session" does not reset volume model color rotation) closed by
- fixed: Fixed. I made it reset the volume colors whenever you open a volume …
- 1:46 PM Ticket #7430 (why does this script show DICOM as surface style?) closed by
- fixed: Fixed. The code that made volumes update surfaces immediately in …
- 11:18 AM Ticket #7432 (Crash using File→Open dialog on Windows and/or returning from function) created by
- […]
- 10:41 AM ChangeLog edited by
- (diff)
- 10:10 AM Ticket #7431 ("close session" does not reset volume model color rotation) created by
- If I open a map, then use "close session", then reopen the map, it is …
- 10:08 AM Ticket #7430 (why does this script show DICOM as surface style?) created by
- In older versions of ChimeraX (e.g. 0.9) this short script given …
- 5:05 AM Ticket #7429 (Crash showing Rapid Access at startup) created by
- […]
- 1:49 AM Ticket #7428 (Inconsistent stack trace information) created by
- […]
Aug 10, 2022:
- 1:39 PM Ticket #7427 (QMainWindowLayout::tabPosition called with out-of-bounds value) created by
- […]
- 11:29 AM Ticket #7426 (BlastProtein giving a warning when an error should be reported) created by
- […]
- 11:04 AM Dev2022-8-8 edited by
- (diff)
- 10:47 AM Ticket #7424 (ISOLDE color button: __init__() got an unexpected keyword argument ...) closed by
- duplicate: This is another instance of #7381. The ChimeraX 1.5.dev... daily …
- 10:34 AM Ticket #7423 (Crash deleting structures) closed by
- can't reproduce
- 10:33 AM Ticket #7422 (MatchMaker: 'NoneType' object has no attribute 'setChecked') closed by
- can't reproduce: I'm not sure how this is possible. The user restores a session and …
- 10:13 AM Ticket #7425 (SEQCROW: wrapped C/C++ object of type DelayForcePrint has been deleted) closed by
- fixed
- 10:09 AM Ticket #7425 (SEQCROW: wrapped C/C++ object of type DelayForcePrint has been deleted) created by
- […]
- 9:08 AM Ticket #7418 (BLAST AlphaFold database version 3: Bad Request) closed by
- fixed: Bumped the allowable database versions on webservices; should be good …
- 2:25 AM Ticket #7424 (ISOLDE color button: __init__() got an unexpected keyword argument ...) created by
- […]
Aug 9, 2022:
- 9:05 PM Ticket #7423 (Crash deleting structures) created by
- […]
- 1:34 PM Ticket #7422 (MatchMaker: 'NoneType' object has no attribute 'setChecked') created by
- […]
- 12:38 PM 2022-8-11 created by
- 12:37 PM DeveloperMeetings edited by
- (diff)
- 12:16 PM Ticket #7410 (Crash creating SEQCROW QMenuBar in ARM tech preview) closed by
- fixed: Sounds like your fake menus are a reasonable work-around. It might be …
- 10:30 AM Dev2022-8-8 edited by
- (diff)
- 10:23 AM Ticket #7360 (Crash in atom-spec parser) closed by
- can't reproduce: We intend to change our command parser anyway, which will probably …
- 9:57 AM Ticket #7421 ([ChimeraX] error) created by
- […]
- 9:16 AM Ticket #7420 (Scrollable Segger segment saving?) created by
- […]
Aug 8, 2022:
- 8:30 PM Ticket #7015 (DICOM: was "airways" preset always so dim?) closed by
- not a bug: The VR dicom lung image you link to appears to be maybe 5 or more …
- 7:53 PM Ticket #7205 (Morph: index out of bounds) closed by
- can't reproduce: No response from reporter.
- 7:52 PM Ticket #7239 (Log link to associated EMDB entry when PDB model opened) closed by
- fixed
- 7:51 PM Ticket #7290 (Crash loading dylib) closed by
- can't reproduce: No response from reporter.
- 7:50 PM Ticket #7296 (Crash loading dylib) closed by
- can't reproduce: No response from reporter.
- 7:49 PM Ticket #7309 (volume sel step 1: index out of range for ImageJ TIFF stack) closed by
- can't reproduce: No response from reporter.
- 7:48 PM Ticket #7069 (Surface session restore: updaters is None) closed by
- duplicate
- 7:46 PM Ticket #7405 (Revert rotate independent mouse mode to normal rotation when models closed) closed by
- fixed
- 7:10 PM Ticket #7414 (develop example bundles: missing bundle_api for bundle) closed by
- not a bug: Glad I could help. If there's anything of general utility we can do …
- 6:14 PM phenix-8-11-22 edited by
- (diff)
- 6:12 PM phenix-8-11-22 edited by
- (diff)
- 6:03 PM phenix-8-11-22 edited by
- (diff)
- 5:50 PM phenix-8-11-22 edited by
- (diff)
- 5:30 PM Ticket #7419 (Drag select blacks out graphics) created by
- […]
- 5:28 PM phenix-8-11-22 created by
- 5:25 PM Features edited by
- (diff)
- 5:19 PM Ticket #7418 (BLAST AlphaFold database version 3: Bad Request) created by
- […]
- 4:19 PM Dev2022-8-8 created by
- 4:18 PM Ticket #7417 ("cofr" info misleading) created by
- […]
- 4:13 PM ChangeLog edited by
- (diff)
- 4:11 PM DeveloperMeetings edited by
- (diff)
- 3:42 PM Ticket #7416 (SEQCROW: crash in Tools / Quantum Chemistry / Build QM Input) created by
- […]
- 3:22 PM Ticket #7415 (SEQCROW: argument 2 has unexpected type 'MatchFlag') created by
- […]
- 2:37 PM Ticket #7414 (develop example bundles: missing bundle_api for bundle) created by
- […]
- 1:55 PM Ticket #7395 (Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with ...) closed by
- nonchimerax: I tried pressing all manner of modifier keys and home, and other non …
- 1:53 PM Ticket #7412 (Crash in set_matrix after sym command) closed by
- can't reproduce: Maybe a graphics driver crash. Was setting a shader variable which …
- 1:26 PM Ticket #7402 (Crash at startup showing Rapid Access) closed by
- can't reproduce: The formats that ViewDockX can read are near the top of its Help page: …
- 11:21 AM Ticket #7411 (Timeout for Opal model-loops web service) closed by
- can't reproduce: Working now.
- 11:19 AM Ticket #7408 (Graphics crash, macOS 12.5, AMD Radeon R9 M395) closed by
- nonchimerax: Apple Intel graphics driver crash.
Aug 7, 2022:
Aug 6, 2022:
- 6:25 AM Ticket #7412 (Crash in set_matrix after sym command) created by
- […]
- 4:24 AM Ticket #7411 (Timeout for Opal model-loops web service) created by
- […]
Aug 5, 2022:
- 7:27 PM Ticket #7410 (Crash creating SEQCROW QMenuBar in ARM tech preview) created by
- […]
- 6:05 PM Ticket #7409 (Probable SEQCROW/Qt crash) closed by
- can't reproduce: SEQCROW makes extensive use of QMenuBar widgets whereas they are not …
- 5:53 PM Ticket #7409 (Probable SEQCROW/Qt crash) created by
- […]
- 5:26 PM Ticket #7406 (Make the "close session" command reset to default graphics settings) closed by
- fixed: Fixed. Using command "close session" instead of "close" will now …
- 5:02 PM Ticket #7066 (Douse tool enhancements) closed by
- fixed: Launcher implemented
- 3:17 PM Ticket #7408 (Graphics crash, macOS 12.5, AMD Radeon R9 M395) created by
- […]
- 2:09 PM Ticket #7401 (Maps not aligned) closed by
- not a bug: Ok. I hope to put in a fix soon (next week?) that will automatically …
- 1:58 PM Ticket #7407 (ArtiaX error after closing all models and opening new particle list) created by
- […]
- 1:34 PM Ticket #7404 (Rotate models: Require contiguous n x 3 x 4 array) closed by
- duplicate: Fixed a few days ago. Super annoying that numpy 1.23 changed the …
- 1:25 PM Ticket #7403 (Pseudobond drawing: Cylinder end point, radii or rotation array not ...) closed by
- duplicate
- 1:05 PM Ticket #3863 (Linking two chains merges them) closed by
- wontfix: Upon further review, I have decided to do nothing about this. I want …
- 12:18 PM Ticket #7406 (Make the "close session" command reset to default graphics settings) created by
- Moritz requests command to reset clipping / lighting / background / …
- 12:15 PM Ticket #7405 (Revert rotate independent mouse mode to normal rotation when models closed) created by
- […]
- 10:58 AM Ticket #7404 (Rotate models: Require contiguous n x 3 x 4 array) created by
- […]
- 10:31 AM Ticket #7403 (Pseudobond drawing: Cylinder end point, radii or rotation array not ...) created by
- […]
- 10:15 AM Ticket #7402 (Crash at startup showing Rapid Access) created by
- […]
- 9:32 AM Ticket #7401 (Maps not aligned) created by
- […] Screen Shot 2022-08-05 at 9.25.29 AM.png
- 9:00 AM Ticket #7399 (Pseudobond drawing: Cylinder end point, radii or rotation array not ...) closed by
- duplicate
- 4:43 AM Ticket #7400 (Crash at startup showing Rapid Access) created by
- […]
- 1:11 AM Ticket #7399 (Pseudobond drawing: Cylinder end point, radii or rotation array not ...) created by
- […]
Aug 4, 2022:
- 6:38 PM Ticket #7397 (vop: 'Place' object has no attribute 'position') closed by
- fixed: Fixed. The volume unroll command center option parsing was broken. A …
- 6:30 PM Ticket #166 (Side view display for orthographic camera) closed by
- fixed: Fixed. Side view scaling and bounding lines are now correct in …
- 5:38 PM Ticket #7398 (Crash showing Rapid Access at startup) closed by
- can't reproduce
- 5:26 PM Ticket #2739 (Poor visibility for side view clip planes) closed by
- fixed: Fixed. Made line colors match Chimera. Also eye and clip planes turn …
- 5:01 PM Ticket #7362 (Side view not going away) closed by
- fixed: Fixed. Seems this bug was introduced by Qt 6.3.1. The side view …
- 4:35 PM Ticket #7344 (MemoryError saving session) closed by
- nonchimerax: I'm surprised the ran out of memory lz4 compressing the ChimeraX …
- 4:20 PM Ticket #7396 (Make bug reporter distinguish Mac Intel and ARM ChimeraX versions) closed by
- worksforme: Not needed. The "Platform" line at the top of the bug report …
- 4:19 PM Ticket #7398 (Crash showing Rapid Access at startup) created by
- […]
- 3:02 PM 2022-8-4 edited by
- (diff)
- 2:22 PM Ticket #7397 (vop: 'Place' object has no attribute 'position') created by
- […]
- 2:19 PM Ticket #6191 (QT bug?) closed by
- can't reproduce: Insufficient information to reproduce.
- 2:08 PM Ticket #6669 (This copy of PyQt is unlicensed on macOS arm64) closed by
- nonchimerax: Fixed by Riverbank after prodding from Tom Goddard.
- 2:04 PM NIAID2022 edited by
- (diff)
- 2:02 PM NIAID2022 edited by
- (diff)
- 1:24 PM NIAID2022 edited by
- (diff)
- 12:26 PM Ticket #7396 (Make bug reporter distinguish Mac Intel and ARM ChimeraX versions) created by
- Currently bug reporter gives no indication if the Intel or ARM …
- 12:22 PM Ticket #7395 (Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with ...) created by
- Mac ARM ChimeraX is logging many warnings […] in ticket #7393.
- 10:30 AM Ticket #7389 (Freeze accessing Toolshed) closed by
- can't reproduce: Are you having network problems? "More Tools..." uses an internal web …
- 10:29 AM Ticket #7394 (Stop simulation: model is None) created by
- […]
- 10:26 AM Ticket #7393 (Pseudobond drawing: Cylinder end point, radii or rotation array not ...) closed by
- duplicate
- 10:13 AM Ticket #7392 (Crash in QApplication.quit()) closed by
- can't reproduce
- 9:41 AM Ticket #7393 (Pseudobond drawing: Cylinder end point, radii or rotation array not ...) created by
- […]
- 9:40 AM Ticket #7386 (Crash showing Rapid Access at startup) closed by
- can't reproduce
- 8:37 AM Ticket #7392 (Crash in QApplication.quit()) created by
- […]
- 8:33 AM Ticket #7391 (ArtiaX: ValueError: Unknown class name 'MarkerSetPlus') created by
- […]
- 6:16 AM Ticket #7390 (Crash in color button code) created by
- […]
- 5:56 AM Ticket #7389 (Freeze accessing Toolshed) created by
- […]
Aug 3, 2022:
- 8:16 PM Ticket #7388 (BLAST of NR database uses 180 Gbytes of resident memory on server) created by
- This ticket is about high server memory use by BLAST searches of NR …
- 6:57 PM Ticket #7384 (Pseudobond drawing: Cylinder end point, radii or rotation array not ...) closed by
- fixed: Fixed. Changed the arrays C++ code is_contiguous() method to accept 0 …
- 6:09 PM Ticket #7387 (BLAST of Uniref50, UniRef90, UniRef100 appears to be using old ...) created by
- Not sure if these are the uniref databases being used by blast …
- 6:07 PM Ticket #7386 (Crash showing Rapid Access at startup) created by
- […]
- 6:03 PM Ticket #7385 (Crash showing Rapid Access at startup) closed by
- can't reproduce
- 6:00 PM Ticket #7383 (UnicodeDecodeError reading PDB file) closed by
- can't reproduce: I am totally mystified by this stack trace. When reading a normal …
- 3:32 PM Ticket #7385 (Crash showing Rapid Access at startup) created by
- […]
- 12:33 PM Ticket #7384 (Pseudobond drawing: Cylinder end point, radii or rotation array not ...) created by
- […]
- 11:47 AM Ticket #7383 (UnicodeDecodeError reading PDB file) created by
- […]
- 10:34 AM Ticket #7382 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 10:33 AM Ticket #7377 (Crash reporter: ~/Library/Logs/DiagnosticReports permission denied) closed by
- duplicate: This error happens when ChimeraX checks to see if it crashed the last …
- 10:31 AM Ticket #7380 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 10:29 AM Ticket #7379 (Crash during partial structure deletion) closed by
- can't reproduce
- 10:26 AM Ticket #7378 (Crash deleting structure during session close) closed by
- can't reproduce: Not enough info to reproduce. Could well already be fixed.
- 10:21 AM Ticket #7376 (Crash in fork) closed by
- limitation: Was using 8.1GB at the time.
- 10:19 AM Ticket #7375 (Unknown crash after "volume level" command) closed by
- can't reproduce: Was using 8.6GB at the time
- 10:04 AM Ticket #7382 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 8:54 AM Ticket #7381 (ISOLDE GUI startup: __init__() got an unexpected keyword argument ...) created by
- […]
- 6:24 AM Ticket #7380 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 5:31 AM Ticket #7379 (Crash during partial structure deletion) created by
- […]
- 4:53 AM Ticket #7378 (Crash deleting structure during session close) created by
- […]
- 12:17 AM Ticket #7377 (Crash reporter: ~/Library/Logs/DiagnosticReports permission denied) created by
- […]
Aug 2, 2022:
- 11:11 PM Ticket #7322 (PAE data not opened) closed by
- fixed: Fixed. I finally figured this out. A change to ChimeraX on July 8 to …
- 10:02 PM Ticket #7376 (Crash in fork) created by
- […]
- 3:44 PM Ticket #7375 (Unknown crash after "volume level" command) created by
- […]
- 2:10 PM Ticket #7374 (Crash destroying tool during garbage collection) created by
- […]
- 11:56 AM Ticket #7369 ("close" fails to close models in certain situations) closed by
- fixed: Objects.invert() was failing to account for pseudobond groups. Fix: …
- 11:51 AM Ticket #7373 (Make segmentations overlap DICOM volumes properly) created by
- It took forever to figure out how to create a segmentation, and to my …
- 10:21 AM 2022-7-28 edited by
- (diff)
- 10:21 AM 2022-8-4 created by
- 10:19 AM DeveloperMeetings edited by
- (diff)
- 10:10 AM Ticket #7372 (Unknown crash) closed by
- can't reproduce: Was using 8.4GB at the time
- 10:06 AM Ticket #7370 (Problem reading IMOD file) closed by
- duplicate: Fixed 7 months ago. Ticket #5892.
- 8:14 AM Ticket #7368 (Crash handling symmetry) closed by
- duplicate: Back in the system. Thanks Scooter!
- 6:34 AM Ticket #7372 (Unknown crash) created by
- […]
- 3:43 AM Ticket #7371 (Toolshed installing wrong version) created by
- […]
Aug 1, 2022:
- 6:10 PM Ticket #7370 (Problem reading IMOD file) created by
- […]
- 5:58 PM Ticket #7369 ("close" fails to close models in certain situations) created by
- With 1nwd open (NMR ensemble with metal coordination groups), "close …
- 5:40 PM Ticket #7367 (Session save: function 'set_pbgroup_py_instance' not found) closed by
- duplicate: Hi Janice, Thanks for reporting this problem. It was fixed about a …
- 4:41 PM Ticket #7368 (Crash handling symmetry) created by
- […]
- 2:02 PM Ticket #7367 (Session save: function 'set_pbgroup_py_instance' not found) created by
- […]
- 1:06 PM Ticket #7366 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 11:25 AM Dev2022-8-1 edited by
- (diff)
- 11:23 AM Dev2022-8-1 edited by
- (diff)
- 11:18 AM Dev2022-8-1 edited by
- (diff)
- 11:09 AM Ticket #7366 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 10:56 AM Dev2022-7-25 edited by
- (diff)
- 10:56 AM Dev2022-7-26 edited by
- (diff)
- 10:55 AM Dev2022-8-1 edited by
- (diff)
- 10:55 AM Dev2022-8-1 created by
- 10:51 AM DeveloperMeetings edited by
- (diff)
- 10:51 AM DeveloperMeetings edited by
- (diff)
- 10:47 AM Ticket #7365 (Crash in garbage collection during new object allocation) closed by
- duplicate: Hi Soneya, Thanks for reporting this problem. Please upgrade to the …
- 10:41 AM Ticket #7364 (Draw status line: Attempt to retrieve context when no valid context) closed by
- can't reproduce: Status line redraw on expose event, no valid OpenGL context. Have …
- 10:33 AM Ticket #7363 (Crash in custom bundle initialization) closed by
- can't reproduce: Without access to this "Wiggle" bundle source, I don't know that …
- 10:26 AM Ticket #7361 (Crash using File→Open on Windows) closed by
- can't reproduce: 1.3
- 9:47 AM Ticket #7357 (glClear: invalid framebuffer operation) closed by
- can't reproduce: Same as #7356, same reporter.
- 9:46 AM Ticket #7356 (glClear: invalid framebuffer operation) closed by
- can't reproduce: OpenGL error on expose event of status line. I guess it is related to …
- 9:40 AM Ticket #7355 (Save dead dock widget shown state in session) closed by
- can't reproduce
- 9:36 AM Ticket #7351 (Restoring new session in old version) closed by
- not a bug
- 9:29 AM Ticket #7349 (Crash in event loop) closed by
- can't reproduce
- 9:27 AM Ticket #7348 (KeyError deleting 2D arrow) closed by
- duplicate: Hi Eduardo, Thanks for reporting this problem. It was fixed about …
- 9:17 AM Ticket #7347 (Crash using File→Open on Windows) closed by
- can't reproduce: 1.3
- 9:04 AM Ticket #7345 (Crash in event loop) closed by
- can't reproduce
- 8:04 AM Ticket #7365 (Crash in garbage collection during new object allocation) created by
- […]
- 6:33 AM Ticket #7364 (Draw status line: Attempt to retrieve context when no valid context) created by
- […]
Jul 31, 2022:
- 7:23 PM Ticket #7363 (Crash in custom bundle initialization) created by
- […]
- 9:32 AM Ticket #7362 (Side view not going away) created by
- […] Screen Shot 2022-07-31 at 9.30.51 AM.png
- 3:37 AM Ticket #7361 (Crash using File→Open on Windows) created by
- […]
Jul 30, 2022:
Jul 29, 2022:
- 5:12 PM Ticket #7359 (Implement Match→Align) created by
- […]
- 3:35 PM Ticket #7358 (Update AlphaFold database sequence searches for July 2022 release of ...) created by
- The EBI released an update to the AlphaFold database increasing from 1 …
- 2:12 PM Ticket #7357 (glClear: invalid framebuffer operation) created by
- […]
- 2:12 PM Ticket #7356 (glClear: invalid framebuffer operation) created by
- […]
- 2:02 PM Ticket #7355 (Save dead dock widget shown state in session) created by
- […]
- 1:48 PM Ticket #7353 (AlphaFold Error Plot gui may fetch PAE with the wrong database version) closed by
- fixed: Fixed. I made the AlphaFold Error Plot tool look at the structure …
- 12:21 PM Ticket #7354 (AlphaFold database "version" number differs from "release" number ...) created by
- AlphaFold database has had 4 releases numbered 1,2,3,4 on their FAQ …
- 11:55 AM Ticket #7353 (AlphaFold Error Plot gui may fetch PAE with the wrong database version) created by
- […]
- 11:45 AM Ticket #7352 (alphafold fetch command ignores version option when fetching PAE data) closed by
- fixed: Fixed. I also added a "version" option to the "alphafold pae" command …
- 11:39 AM Ticket #7336 (AlphaFold reporting old files) closed by
- fixed: Fixed. Does not require new ChimeraX since fix was in script fetched …
- 11:30 AM Ticket #7352 (alphafold fetch command ignores version option when fetching PAE data) created by
- […]
- 11:26 AM Ticket #7351 (Restoring new session in old version) created by
- […]
- 11:10 AM Ticket #7350 (AlphaFold PAE domains divide by zero with AlphaFold database version 3) closed by
- fixed: Fixed. Made minimum PAE value 0.2 when computing domains.
- 10:49 AM Ticket #7350 (AlphaFold PAE domains divide by zero with AlphaFold database version 3) created by
- […]
- 7:19 AM Ticket #7349 (Crash in event loop) created by
- […]
- 7:18 AM Ticket #7348 (KeyError deleting 2D arrow) created by
- […]
- 4:19 AM Ticket #7347 (Crash using File→Open on Windows) created by
- […]
- 2:23 AM Ticket #7346 (Make alphafold fetch and pae commands work with version 3 of the ...) created by
- […] alphafold.diff
Jul 28, 2022:
- 11:12 PM Ticket #7345 (Crash in event loop) created by
- […]
- 6:16 PM Ticket #7344 (MemoryError saving session) created by
- […]
- 6:05 PM 2022-7-28 edited by
- (diff)
- 5:15 PM Ticket #7343 (Avoid pages of intimidating orange warning text on Toolshed install) created by
- […]
- 5:01 PM Ticket #7337 (Selection demotion: Values array length does not match objects array length) closed by
- fixed: Fixed. If the number of atoms has changed the select up/down will …
- 4:43 PM Ticket #7341 (Crash importing numpy) closed by
- can't reproduce: No clues. Unlikely that numpy was the actual cause of the crash. …
- 3:43 PM Ticket #4749 (Specify first, last, skip when reading MD frames) closed by
- fixed: Available as start/end/skip keywords
- 3:41 PM Ticket #5874 (Renumber residues) closed by
- fixed: Command and tool available in current daily builds.
- 3:39 PM Ticket #3197 (command to change chain IDs) closed by
- fixed: Command and tool available in current daily builds.
- 2:00 PM Ticket #7338 (Volume histogram: cannot convert float NaN to integer) closed by
- nonchimerax: It looks like the hdf data file opened contained NaN values. …
- 1:46 PM Ticket #7340 (initial 'visibility false' not honored for 2D arrow) closed by
- fixed
- 1:14 PM Ticket #7342 (Axes/Planes/Centroids tool) created by
- ticket created for purposed of milestoning
- 12:32 PM 2022-7-28 edited by
- (diff)
- 10:57 AM Ticket #7341 (Crash importing numpy) created by
- […]
- 9:33 AM Ticket #7340 (initial 'visibility false' not honored for 2D arrow) created by
- As per summary
- 9:09 AM Ticket #7339 (Crash in event loop) closed by
- can't reproduce: Had just opened a session; was using 15GB at the time.
- 6:04 AM Ticket #7339 (Crash in event loop) created by
- […]
- 12:28 AM Ticket #7338 (Volume histogram: cannot convert float NaN to integer) created by
- […]
Jul 27, 2022:
- 9:54 PM Ticket #7337 (Selection demotion: Values array length does not match objects array length) created by
- […]
- 2:28 PM Ticket #7335 (Crash showing Rapid Access at startup) closed by
- can't reproduce
- 2:24 PM Ticket #7336 (AlphaFold reporting old files) created by
- […]
- 12:07 PM Ticket #7335 (Crash showing Rapid Access at startup) created by
- […]
- 11:56 AM Ticket #7334 (Add command option to fitmap to write fit positions and metrics to a ...) closed by
- fixed: Done. I added a logFits option to the fitmap command that takes a …
- 11:49 AM Ticket #7334 (Add command option to fitmap to write fit positions and metrics to a ...) created by
- Begin forwarded message: From: Christian Tüting via ChimeraX-users …
- 1:50 AM Ticket #7333 (Problem confirming SSL certificate for PyPi) created by
- […]
Jul 26, 2022:
- 7:30 PM Ticket #7332 (Gaussian molecular surface selection outline not shown) closed by
- fixed: Fixed. Surface code did not correctly display highlight if surface …
- 4:33 PM Ticket #7328 (Mouse select of low res molecular surface does not select it) closed by
- fixed: I made a separate ticket #7332 for Gaussian surfaces not showing a …
- 4:32 PM Ticket #7332 (Gaussian molecular surface selection outline not shown) created by
- […]
- 10:14 AM 2022-7-21 edited by
- (diff)
- 10:13 AM 2022-7-28 created by
- 10:12 AM DeveloperMeetings edited by
- (diff)
- 9:53 AM Dev2022-7-26 created by
- 9:45 AM DeveloperMeetings edited by
- (diff)
- 9:28 AM Ticket #7330 (Crash during fork) closed by
- can't reproduce: Hi Margot, Thank for reporting this problem. ChimeraX 1.3 and 1.4 …
- 9:17 AM Ticket #7329 (Volume Viewer after session restore: wrapped C/C++ object of type ...) closed by
- duplicate: Duplicate of #7103
- 9:04 AM Ticket #7331 (Opening ORCA output file: could not broadcast input array) created by
- […] 16101896_MnCO3_tBuNHC_Ph_THF_optfreq.out
- 4:35 AM Ticket #7330 (Crash during fork) created by
- […]
Jul 25, 2022:
- 6:36 PM Ticket #7329 (Volume Viewer after session restore: wrapped C/C++ object of type ...) created by
- […]
- 4:22 PM Ticket #7314 (Crash in mapFromGlobal(QCursor.pos())) closed by
- can't reproduce: Seems like a Qt 6 bug.
- 4:20 PM Ticket #7313 (Graphics crash, macOS 12.3.1, Intel Iris Graphics 6100) closed by
- nonchimerax: Apple graphics driver crash.
- 3:48 PM Ticket #7328 (Mouse select of low res molecular surface does not select it) created by
- […]
- 3:44 PM Ticket #7325 (Update surface selection: index is out of bounds for axis) closed by
- fixed: Fixed. Use no vertex to atom map if surface geometry was replaced by …
- 3:07 PM Dev2022-7-25 edited by
- (diff)
- 3:00 PM Dev2022-7-25 created by
- 2:52 PM DeveloperMeetings edited by
- (diff)
- 10:51 AM Ticket #7320 (Crash creating QWebEngineProfile at startup) closed by
- can't reproduce: This ChimeraX crash seems to be a bug in the Qt window toolkit. We …
- 10:48 AM Ticket #7323 (Graphics crash, macOS 11.6.7, Intel Iris Plus Graphics 650) closed by
- nonchimerax: Apple graphics driver crash.
- 9:59 AM Ticket #7327 (Index error opening regular PDB in MD Viewer) closed by
- limitation
- 9:57 AM Ticket #7326 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: Hi Julia, Thanks for reporting this problem. We believe it is fixed …
- 9:45 AM Ticket #7324 (QWebEngine crash: Calling windowShouldClose: on the delegate for the ...) closed by
- can't reproduce: Hi Carina, I'm not certain this will help but you shouldn't run …
- 9:34 AM Ticket #7321 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 8:11 AM Ticket #7327 (Index error opening regular PDB in MD Viewer) created by
- […]
- 2:12 AM Ticket #7326 (Crash using File→Open on Windows and/or in return statement) created by
- […]
Jul 24, 2022:
Jul 23, 2022:
Note:
See TracTimeline
for information about the timeline view.
