Timeline



Mar 8, 2023:

11:47 PM Ticket #8622 (Graphics crash, macOS 13.2.1, Intel Iris Plus Graphics 640) created by chimerax-bug-report@…
[…]
9:59 PM Ticket #8621 (Have to change step to get NRRD images to render at the right size) created by Zach Pearson
Just as the title says; NRRD images occasionally initially display as …
5:41 PM Ticket #8620 ('ModellerScoringJob' object has no attribute 'results') created by chimerax-bug-report@…
[…]
1:55 PM Ticket #8619 (Move "ribbon" from experimental commands) created by Tom Goddard
Ugh. I see the ribbon command is also in exp_cmds. Should fix that …
1:53 PM Ticket #7825 (Make getcrd give a warning or error if no atoms are specified.) closed by pett
fixed: Will open separate ticket for moving "ribbon" from experimental commands.
1:40 PM Ticket #8618 (Adding a mouse mode to DICOM rearranges the medical image toolbar) created by Zach Pearson
Trying to add an experimental mouse mode to perform segmentations …
1:22 PM Ticket #8617 (Crash clearing aniso_u6) created by chimerax-bug-report@…
[…]
1:12 PM Ticket #8616 (Multiple swapaa/na swaps) created by matthias.vorlaender@…
Allow swapaa/na to make multiple different swaps at once (they already …
1:05 PM Ticket #8615 (Crash clearing aniso_u6) closed by pett
duplicate
12:58 PM Ticket #8615 (Crash clearing aniso_u6) created by chimerax-bug-report@…
[…]
12:13 PM Ticket #8614 (Crash in Atom::effective_coord playing RMF coordset) created by chimerax-bug-report@…
[…]
12:10 PM ChangeLog edited by Elaine Meng
(diff)
12:05 PM ChangeLog edited by Elaine Meng
(diff)
9:44 AM Ticket #1045 (Nucleic matchmaker error) closed by pett
fixed
9:42 AM Ticket #8613 (Crash in garbage collection) closed by pett
duplicate
8:48 AM Ticket #8613 (Crash in garbage collection) created by chimerax-bug-report@…
[…]
3:04 AM Ticket #8612 (Graphics crash, macOS 11.6, Intel Iris Plus Graphics 650) created by chimerax-bug-report@…
[…]

Mar 7, 2023:

5:01 PM 2023-3-9 created by Tom Goddard
5:00 PM DeveloperMeetings edited by Tom Goddard
(diff)
4:59 PM Ticket #8610 (Surface calculation: cannot convert float NaN to integer) closed by Tom Goddard
nonchimerax: Appears that the PDB file has NaN coordinates. I think our PDB file …
4:55 PM Ticket #8608 (Crash creating QWebEngineProfile at startup) closed by Tom Goddard
can't reproduce
11:16 AM Ticket #8606 (No sequences in file) closed by pett
fixed: Converted no-sequences error to UserError
10:25 AM Ticket #8611 (Graphics crash, macOS 13.0.1, Intel Iris Plus Graphics) created by chimerax-bug-report@…
[…]
9:03 AM Ticket #8609 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: 1.3
8:55 AM Ticket #8604 (Crash showing Rapid Access at startup) closed by pett
can't reproduce: Linux
8:02 AM Ticket #8610 (Surface calculation: cannot convert float NaN to integer) created by chimerax-bug-report@…
[…]
6:14 AM Ticket #8609 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
4:43 AM Ticket #8608 (Crash creating QWebEngineProfile at startup) created by chimerax-bug-report@…
[…]
1:52 AM Ticket #8607 (SEQCROW sticks preset sets key_light_color to 4 values instead of 3) created by joegair@…
[…]
12:41 AM Ticket #8606 (No sequences in file) created by chimerax-bug-report@…
[…]

Mar 6, 2023:

11:44 PM Ticket #8605 (Various surface errors) created by chimerax-bug-report@…
[…]
11:41 PM Ticket #8604 (Crash showing Rapid Access at startup) created by chimerax-bug-report@…
[…]
1:39 PM Ticket #8602 (Crash creating QWebEngineProfile at startup) closed by Tom Goddard
can't reproduce: We've seen 39 crashes reported in create_chimerax_profile() crashing …
1:26 PM Ticket #8598 (Crash in calculate_surface_geometry) closed by Tom Goddard
can't reproduce: Crashed in sharp edge code during a molecular surface recalculation. …
1:23 PM Ticket #8597 (Opening JSON: KeyError: 'Channels') closed by Tom Goddard
duplicate: Fixed several months ago by warning about wrong file type. Trying to …
1:19 PM Ticket #8596 ("label listfonts": QFontDatabase(QFontDatabase): not enough arguments) closed by Tom Goddard
fixed: Fixed in tomorrow's daily build. The Qt window toolkit call to list …
11:28 AM Ticket #8603 (Crash creating QWebEngineProfile at startup) closed by pett
duplicate
11:22 AM Ticket #8601 (Crash using File→Open dialog on Windows and/or returning from function) closed by pett
can't reproduce: 1.3
11:21 AM Ticket #8600 (Crash closing window while XMAS in use) closed by pett
duplicate: Duplicate of #8575
10:57 AM Ticket #8599 (Crash in calculate_surface_geometry) closed by pett
duplicate
10:36 AM Ticket #8595 (Crash in copy_from_framebuffer) closed by pett
can't reproduce: 1.2.5
10:34 AM Ticket #8594 (Crash in event loop) closed by pett
can't reproduce
1:02 AM Ticket #8603 (Crash creating QWebEngineProfile at startup) created by chimerax-bug-report@…
[…]
12:58 AM Ticket #8602 (Crash creating QWebEngineProfile at startup) created by chimerax-bug-report@…
[…]

Mar 5, 2023:

8:13 PM Ticket #8601 (Crash using File→Open dialog on Windows and/or returning from function) created by chimerax-bug-report@…
[…]
12:12 PM Ticket #8600 (Crash closing window while XMAS in use) created by chimerax-bug-report@…
[…]
8:25 AM Ticket #8599 (Crash in calculate_surface_geometry) created by chimerax-bug-report@…
[…]
8:25 AM Ticket #8598 (Crash in calculate_surface_geometry) created by chimerax-bug-report@…
[…]
6:45 AM Ticket #8597 (Opening JSON: KeyError: 'Channels') created by chimerax-bug-report@…
[…]
12:43 AM Ticket #8596 ("label listfonts": QFontDatabase(QFontDatabase): not enough arguments) created by zrh15@…
[…]

Mar 4, 2023:

9:00 AM Ticket #8595 (Crash in copy_from_framebuffer) created by chimerax-bug-report@…
[…]

Mar 3, 2023:

5:22 AM Ticket #8594 (Crash in event loop) created by chimerax-bug-report@…
[…]

Mar 2, 2023:

5:03 PM Ticket #8590 (Graphics crash, macOS 11.6, Intel Iris Plus Graphics) closed by Tom Goddard
nonchimerax: Apple Intel graphics crash.
4:59 PM Ticket #8592 (Graphics crash, macOS 13.1, Intel Iris Plus Graphics 645, dual display) closed by Tom Goddard
nonchimerax: Apple Intel graphics driver crash.
4:40 PM Ticket #8587 (Crash saving image) closed by Tom Goddard
nonchimerax: I've seen this crash saving an image with ChimeraX 1.3 on CentOS 7. …
3:22 PM Ticket #8518 (Implement a NRRD file reader) closed by Zach Pearson
fixed: There is now …
2:02 PM Ticket #8593 (Cannot install bundles) created by bonneau@…
Just to let you know, in case this ends up being useful info for you, …
1:54 PM NIAID2022 edited by Elaine Meng
(diff)
1:34 PM NIAID2022 edited by Elaine Meng
(diff)
12:51 PM Ticket #8530 (Crash clearing aniso_u6) closed by pett
fixed: Fix will be in tomorrow's daily build.
12:49 PM Ticket #8457 (Crash clearing aniso_u6) closed by pett
fixed: The ctypes call of clear_atom_aniso_u6 wasn't specifying the type of …
10:23 AM Ticket #8589 (Unknown crash after selection) closed by pett
can't reproduce
10:19 AM Ticket #8588 (Crash clearing aniso_u6) closed by pett
duplicate
9:37 AM Ticket #8592 (Graphics crash, macOS 13.1, Intel Iris Plus Graphics 645, dual display) created by chimerax-bug-report@…
[…]
9:34 AM Ticket #8591 (Crash in garbage collection from timer after structure closed) created by ppratap@…
[…]
3:10 AM Ticket #8590 (Graphics crash, macOS 11.6, Intel Iris Plus Graphics) created by chimerax-bug-report@…
[…]
2:06 AM Ticket #8589 (Unknown crash after selection) created by chimerax-bug-report@…
[…]

Mar 1, 2023:

4:32 PM Ticket #8588 (Crash clearing aniso_u6) created by chimerax-bug-report@…
[…]
1:35 PM Ticket #8587 (Crash saving image) created by aleksandr.sverzhinsky@…
[…]
11:19 AM Ticket #8586 ("view matrix" given degenerate matrix) created by chimerax-bug-report@…
[…]
10:28 AM Ticket #8585 (Graphics crash, macOS 11.7, Intel Iris) created by chimerax-bug-report@…
[…]
9:30 AM Ticket #8584 (sym: Tried to get the position of deleted drawing) closed by pett
duplicate
9:20 AM Ticket #8582 (Crash during text input) closed by pett
can't reproduce
9:18 AM Ticket #8581 (Crash in QMainWindow::removeDockWidget) closed by pett
can't reproduce
7:38 AM Ticket #8584 (sym: Tried to get the position of deleted drawing) created by chimerax-bug-report@…
[…]
7:38 AM Ticket #8583 (sym: Tried to get the position of deleted drawing) created by chimerax-bug-report@…
[…]

Feb 28, 2023:

9:55 PM Ticket #8580 (Qt fatal error: Failed to initialize graphics backend for OpenGL) closed by Tom Goddard
nonchimerax: ChimeraX did not start because the Qt window toolkit could not …
9:46 PM Ticket #8577 (glDrawBuffer: invalid operation) closed by Tom Goddard
can't reproduce: Probably a graphics driver bug. RTX 3090 with Nvidia driver 520.61.05 …
8:36 PM Ticket #8582 (Crash during text input) created by chimerax-bug-report@…
[…]
8:24 PM Ticket #8581 (Crash in QMainWindow::removeDockWidget) created by chimerax-bug-report@…
[…]
5:42 PM Ticket #8580 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by Paul.Harris@…
The following bug report has been submitted: Platform: …
5:41 PM Ticket #8579 (Crash clearing aniso_u6) closed by pett
duplicate: Duplicate of #8457
5:40 PM Ticket #8579 (Crash clearing aniso_u6) created by chimerax-bug-report@…
The following bug report has been submitted: Platform: …
5:34 PM Ticket #8578 (Haphazard tool tips) created by Tristan Croll
The following bug report has been submitted: Platform: …
5:32 PM Ticket #8577 (glDrawBuffer: invalid operation) created by chimerax-bug-report@…
The following bug report has been submitted: Platform: …
5:31 PM Ticket #8576 (ChargeError produces traceback) closed by pett
fixed
5:30 PM Ticket #8576 (ChargeError produces traceback) created by chimerax-bug-report@…
The following bug report has been submitted: Platform: …
5:07 PM Ticket #8574 (Graphics crash, macOS 12.5.1, Intel HD Graphics 6000) closed by Tom Goddard
nonchimerax: Apple Intel graphics driver crash.
5:04 PM Ticket #8575 (Crash closing window while XMAS in use) created by bonneau@…
The following bug report has been submitted: Platform: …
4:55 PM Ticket #8574 (Graphics crash, macOS 12.5.1, Intel HD Graphics 6000) created by chimerax-bug-report@…
The following bug report has been submitted: Platform: …
4:53 PM Ticket #8573 (Additional EMDB entry info) created by Tristan Croll
The following bug report has been submitted: Platform: …
4:39 PM Ticket #8572 (test) closed by pett
not a bug
4:39 PM Ticket #8571 (test) closed by pett
not a bug
4:12 PM 2023-3-2 created by Tom Goddard
4:10 PM DeveloperMeetings edited by Tom Goddard
(diff)
4:04 PM Ticket #8569 (Unknown crash) closed by pett
can't reproduce
2:49 PM Ticket #8572 (test) created by pett
[…]
2:45 PM Ticket #8571 (test) created by Greg Couch
[…]
9:49 AM ChangeLog edited by Elaine Meng
(diff)
9:40 AM ChangeLog edited by Elaine Meng
(diff)
9:35 AM ChangeLog edited by Elaine Meng
(diff)

Feb 27, 2023:

8:25 PM Ticket #8566 (AlphaFold/Blast: Needleman-Wunsch being passed structure, not sequence) closed by Tom Goddard
fixed: Fixed in tomorrow's daily build (Feb 28, 2023). Using the AlphaFold
7:50 PM Ticket #8563 (Graphics crash, macOS 10.15.7, Intel Iris Plus Graphics) closed by Tom Goddard
nonchimerax: Apple Intel graphics driver crash. Two displays.
6:58 PM Ticket #8565 (Crash in event loop after showing many pseudobonds) closed by pett
can't reproduce
6:43 PM Ticket #8554 (MatchMaker: wrapped C/C++ object of type QPushButton has been deleted) closed by pett
fixed: sys.last_traceback was holding the reference! Fix: …
1:12 AM Ticket #8570 (Must run from installer) created by zstuwdc@…
[…]

Feb 26, 2023:

10:28 PM Ticket #8569 (Unknown crash) created by chimerax-bug-report@…
[…]

Feb 25, 2023:

2:39 PM Ticket #8568 ('overloadable' attribute missing) created by rish.23@…
[…]
1:08 PM Ticket #8567 (Clipper missing) created by rish.23@…
[…]
5:10 AM Ticket #8566 (AlphaFold/Blast: Needleman-Wunsch being passed structure, not sequence) created by ubaumann@…
[…]

Feb 24, 2023:

11:19 PM Ticket #8565 (Crash in event loop after showing many pseudobonds) created by chimerax-bug-report@…
[…]
9:11 PM Ticket #8564 (installation issue) created by venkatareddy@…
[…]
5:30 PM Ticket #8563 (Graphics crash, macOS 10.15.7, Intel Iris Plus Graphics) created by chimerax-bug-report@…
[…]
12:01 PM Ticket #8557 (Reading AlphaFold JSON as MOLE; shader syntax error) closed by Tom Goddard
duplicate: The graphics error is a driver problem. The error opening AlphaFold
11:57 AM Ticket #8556 (Crash in molarray.LookupTable._delete_table) closed by Tom Goddard
can't reproduce: ChimeraX crashed trying to release some memory. This was probably …
11:55 AM Ticket #8562 (QQuickWidget: Failed to make context current when creating FBO) created by lochuynh@…
[…]
11:35 AM Ticket #8553 (AddH problem) closed by pett
duplicate: Hi Shana, This is the same issue, you either need to delete the …
11:29 AM Ticket #8552 (AddH problem) closed by pett
fixed: Hi Shana, You're not running addh, you are running addcharge. Do you …
11:28 AM Ticket #8555 (glClear: invalid operation) closed by Tom Goddard
nonchimerax: This error at ChimeraX startup indicates that your graphics driver is …
11:00 AM Ticket #8539 (Download DICOM tool: need to segregate by collection when drilling ...) closed by Zach Pearson
fixed: [https://github.com/RBVI/ChimeraX/commit/b73def018082fb884b61013a2c9443
10:25 AM Ticket #8561 (Session restore: invalid load key) closed by pett
duplicate
10:22 AM Ticket #8560 (QWindowsWindow:setDarkBorderToWindow: Unable to set dark window border) closed by pett
duplicate: Duplicate of #8541; adding Tristan to recipient list for that ticket
10:21 AM Ticket #8437 (QWindowsWindow::setDarkBorderToWindow: Unable to set dark window border) closed by pett
duplicate: Duplicate of #8541
9:59 AM Ticket #8558 (Crash showing Rapid Access at startup(?)) closed by pett
can't reproduce: Linux; the Python traceback implies the crash happened at startup …
8:24 AM Ticket #8561 (Session restore: invalid load key) created by chimerax-bug-report@…
[…]
6:36 AM Ticket #8560 (QWindowsWindow:setDarkBorderToWindow: Unable to set dark window border) created by Tristan Croll
[…]
6:23 AM Ticket #8559 (Difficult morphing scenario) created by Tristan Croll
[…] 8em7_8em4_rebuilt.zip
5:56 AM Ticket #8558 (Crash showing Rapid Access at startup(?)) created by chimerax-bug-report@…
[…]
3:57 AM Ticket #8557 (Reading AlphaFold JSON as MOLE; shader syntax error) created by chimerax-bug-report@…
[…]
3:52 AM Ticket #8556 (Crash in molarray.LookupTable._delete_table) created by irene.vercellino@…
[…]

Feb 23, 2023:

11:04 PM Ticket #8555 (glClear: invalid operation) created by S.Reischauer@…
[…]
10:32 PM Ticket #8554 (MatchMaker: wrapped C/C++ object of type QPushButton has been deleted) created by chimerax-bug-report@…
[…]
6:44 PM Ticket #8547 (Window black) closed by Tom Goddard
nonchimerax: ChimeraX and the Qt window toolkit it uses cannot display correctly …
3:34 PM Ticket #8503 (DICOM: minor text change request on DICOM Browser and Download DICOM tools) closed by Zach Pearson
fixed: OK, …
11:37 AM Ticket #8553 (AddH problem) created by stoddards@…
[…] Keppra21MBO-webina_out.pdbqt
11:33 AM Ticket #8552 (AddH problem) created by stoddards@…
[…] 1EVE-Docking-webina_out.pdbqt
10:57 AM Ticket #8536 (Atomic/session memory leak) closed by pett
fixed: Was under the misapprehension that appending to a list works the same …
9:05 AM Ticket #8548 (ISOLDE: Unparameterised residue detected) closed by Tristan Croll
duplicate: Ancient - ChimeraX 1.0.
8:58 AM Ticket #8550 (Unknown crash at startup) closed by pett
can't reproduce
8:40 AM Ticket #8546 (Crash in event loop) closed by pett
can't reproduce
8:37 AM Ticket #8545 (Restore new session in old ChimeraX) closed by pett
limitation
8:30 AM Ticket #8543 (Crash destroying QGridLayout) closed by pett
can't reproduce: XMAS was installed
7:40 AM Ticket #8551 (Volume Viewer does not update for 'rename') created by matt.jaremko@…
[…]
4:55 AM Ticket #8550 (Unknown crash at startup) created by chimerax-bug-report@…
[…]
2:27 AM Ticket #8549 (Various surface errors) created by chimerax-bug-report@…
[…]

Feb 22, 2023:

6:55 PM Ticket #8548 (ISOLDE: Unparameterised residue detected) created by chimerax-bug-report@…
[…]
6:36 PM Ticket #8547 (Window black) created by heziyan@…
[…]
4:39 PM Ticket #8534 (Qt fatal error: Failed to initialize graphics backend for OpenGL) closed by Tom Goddard
nonchimerax: Aha! Thanks for that info. Displaying 3D graphics (OpenGL) using a …
3:06 PM Ticket #8546 (Crash in event loop) created by chimerax-bug-report@…
[…]
2:12 PM Ticket #8545 (Restore new session in old ChimeraX) created by chimerax-bug-report@…
[…]
12:24 PM Ticket #8544 (ISOLDE: after session restore 'mgr' is None) created by chimerax-bug-report@…
[…]
10:51 AM Ticket #8543 (Crash destroying QGridLayout) created by chimerax-bug-report@…
[…]
10:32 AM Ticket #8542 (Add molmap option to specify grid size) created by joshua.denson@…
Would be convenient of the molmap command could specify a grid size …
9:31 AM Ticket #8538 (Add Charges: Could not come up with unique atom name in mega-residue) closed by pett
duplicate

Feb 21, 2023:

9:13 PM Ticket #8540 (Remove CONFINCLUDEDIR, CONFINCLUDEPY, INCLUDEPY, INCLUDEDIR, etc from ...) closed by Zach Pearson
fixed: I bumped setuptools after clearing those values from _sysconfigdata.
7:01 PM Ticket #8541 (QWindowsWindow::setDarkBorderToWindow: Unable to set dark window border) created by Tony Schaefer
[…]
5:19 PM Ticket #8540 (Remove CONFINCLUDEDIR, CONFINCLUDEPY, INCLUDEPY, INCLUDEDIR, etc from ...) created by Zach Pearson
We pinned setuptools to version 65.1.1 to avoid a change in distutils …
5:01 PM Ticket #8389 (Implement a NifTI File Reader) closed by Zach Pearson
fixed: Enabled the NifTI reader for tomorrow's (02/22/23) daily build.
4:47 PM Ticket #8503 (DICOM: minor text change request on DICOM Browser and Download DICOM tools) reopened by Elaine Meng
Not quite done. Although both initial tool dialogs (DICOM Browser, …
4:12 PM Ticket #8539 (Download DICOM tool: need to segregate by collection when drilling ...) created by Elaine Meng
Need to segregate studies by collection (if drilling down from >1 …
2:53 PM Ticket #8538 (Add Charges: Could not come up with unique atom name in mega-residue) created by chimerax-bug-report@…
[…]
2:33 PM Ticket #8532 (Region past end of alignment) closed by pett
fixed: Ensure that created regions (e.g. SCF coloring) don't extend past ends …
12:25 PM Ticket #8523 (Cruft in API reference) closed by Zach Pearson
fixed: [https://github.com/RBVI/ChimeraX/commit/248109bd8f8231c946020d0b0c85f0
10:52 AM Ticket #8535 (Crash creating HTML profile) closed by pett
duplicate
10:34 AM Ticket #8527 (Error in glGetFramebufferAttachmentParameteriv) closed by Tom Goddard
nonchimerax: Broken OpenGL graphics driver. Also using Windows 7 which ChimeraX …
10:30 AM Ticket #8520 (View matrix issue) closed by Tom Goddard
not a bug: Glad we figured it out. I made a request to add a camera command …
10:29 AM Ticket #8537 (Add a camera command option to set ortho camera field width) created by Tom Goddard
In ticket #8520 the problem was that the view matrix command does not …
10:26 AM Ticket #8524 (Qt fatal error: Failed to initialize graphics backend for OpenGL) closed by Tom Goddard
nonchimerax: There are a variety of Qt bug reports about this "failed to initialize …
10:11 AM Ticket #8533 (Issue opening pdb files from ZDOCK) closed by pett
duplicate: Hi Shawn, The ZDOCK "PDB" file does not conform to the PDB standard …
9:12 AM Ticket #8529 (Crash in glGetFramebufferAttachmentParameteriv) closed by pett
duplicate
9:11 AM Ticket #8528 (Crash in glGetFramebufferAttachmentParameteriv) closed by pett
duplicate
9:06 AM Ticket #8526 (Crash clearing aniso_u6) closed by pett
duplicate: ARM, and running directly from .dmg (though we know the latter isn't …
8:06 AM Ticket #8536 (Atomic/session memory leak) created by Tristan Croll
[…]
4:44 AM Ticket #8535 (Crash creating HTML profile) created by chimerax-bug-report@…
[…]
1:13 AM Ticket #8534 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by nikhil.bharambe@…
[…]

Feb 20, 2023:

2:58 PM Ticket #8533 (Issue opening pdb files from ZDOCK) created by shawn.owen@…
[…] [[Image(...)]] complex.1.pdb
6:43 AM Ticket #8532 (Region past end of alignment) created by chimerax-bug-report@…
[…]
6:40 AM Ticket #8531 (Crash asking for registration after opening old session) created by chimerax-bug-report@…
[…]
4:14 AM Ticket #8530 (Crash clearing aniso_u6) created by 21122748r@…
[…]

Feb 19, 2023:

10:03 PM Ticket #8529 (Crash in glGetFramebufferAttachmentParameteriv) created by chimerax-bug-report@…
[…]
9:49 PM Ticket #8528 (Crash in glGetFramebufferAttachmentParameteriv) created by chimerax-bug-report@…
[…]
9:21 PM Ticket #8527 (Error in glGetFramebufferAttachmentParameteriv) created by chimerax-bug-report@…
[…]

Feb 18, 2023:

5:06 PM Ticket #8526 (Crash clearing aniso_u6) created by chimerax-bug-report@…
[…]
3:20 AM Ticket #8525 (Session restore: Compressed file ended before the end-of-stream marker ...) created by disha-gajanan.hiregange@…
[…]

Feb 17, 2023:

7:59 PM Ticket #8524 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by chimerax-bug-report@…
[…]
5:30 PM Ticket #8523 (Cruft in API reference) created by pett
The listings in the Programmer's Guide / API Reference / Python …
11:24 AM Dev2022-2-20 edited by Tom Goddard
(diff)
11:04 AM Ticket #8519 (Crash coloring ribbon) closed by Tom Goddard
can't reproduce: I have never seen a report of ChimeraX crashing on ribbon coloring. …
10:41 AM Ticket #8521 (PermissionError saving command history) closed by pett
duplicate: Various fixes have been applied since then.
10:15 AM Ticket #8522 (Crash opening mmCIF on Linux) created by audreyo@…
[…] I53-50_marshmallow_half_shell_trimer_centered.cif
9:55 AM Ticket #8521 (PermissionError saving command history) created by chimerax-bug-report@…
[…]
8:01 AM Ticket #8520 (View matrix issue) created by matt.jaremko@…
[…]
1:26 AM Ticket #8519 (Crash coloring ribbon) created by laura.rotilio@…
[…]

Feb 16, 2023:

5:48 PM Ticket #7904 (RCSB biological unit: PDBx/mmCIF styling lost) closed by Greg Couch
fixed: Done for #8484.
5:47 PM Ticket #8484 ("styling lost" in hand-edited mmCIF) closed by Greg Couch
fixed: Added fallback path to read the mmCIF file without PDBx/mmCIF styling …
4:32 PM Ticket #4479 (Read small-molecule CIF files) closed by Greg Couch
fixed: Any further work on small molecule CIF files should be on a new ticket.
4:26 PM Ticket #8506 (Saving GLTF of mesh surface actually saves a filled surface) closed by Tom Goddard
fixed: Done. GLTF save and load now handle mesh and dot surfaces.
4:17 PM Ticket #4342 (mmCIF format-compliance issues) closed by Greg Couch
fixed: The molecular data in the session file was unexpected by the mmCIF …
3:50 PM Ticket #8518 (Implement a NRRD file reader) created by Zach Pearson
Part of the NIAID contract
3:49 PM Ticket #8517 (Some TCIA dicoms open at an angle that makes them look invisible) created by Zach Pearson
Sometimes when a DICOM file is downloaded from TCIA and opened, …
3:09 PM Ticket #8511 (Make GLTF save volume image rendering) closed by Tom Goddard
fixed: Done. It can be pretty slow to save a GLTF with a volume image I …
1:54 PM 2023-2-16 edited by Elaine Meng
(diff)
1:21 PM 2023-2-16 edited by Tom Goddard
(diff)
1:21 PM 2023-2-16 edited by Tom Goddard
(diff)
12:26 PM Ticket #8515 (Map fit: Tried to get the position of deleted drawing) closed by Tom Goddard
fixed: Fixed. Added error message saying deleted fit structures cannot be saved.
12:12 PM Ticket #8516 (glClear: invalid framebuffer operation) closed by Tom Goddard
nonchimerax: Probably related to removing a second display […]
10:29 AM Ticket #8514 (Map not visible when Side View showing) closed by Tom Goddard
can't reproduce: This works fine for me using ChimeraX 1.5 on an Intel Mac with macOS …
9:59 AM Ticket #8513 (self.structure is None) closed by pett
duplicate: From 0.91!
6:54 AM Ticket #8516 (glClear: invalid framebuffer operation) created by chimerax-bug-report@…
[…]
5:03 AM Ticket #8515 (Map fit: Tried to get the position of deleted drawing) created by chimerax-bug-report@…
[…]
4:13 AM Ticket #8514 (Map not visible when Side View showing) created by lvhailiyaohui@…
[…]

Feb 15, 2023:

11:15 PM Ticket #8513 (self.structure is None) created by chimerax-bug-report@…
[…]
8:02 PM Ticket #8512 (Crash in msgpack_deserialize) created by agautam@…
[…]
1:51 PM Ticket #8510 (Crash reading 6V9V) closed by Greg Couch
can't reproduce: This might be a hardware bug. See …
1:23 PM Ticket #8511 (Make GLTF save volume image rendering) created by Tom Goddard
Would like the GLTF writer to save volume image rendering as a stack …
1:13 PM Ticket #8507 (Saving a GLTF file of a transparent surface shows as opaque in BabylonJS) closed by Tom Goddard
fixed: Fixed. Made gltf writer set material alphaMode to blend if drawing is …
12:50 PM Ticket #8510 (Crash reading 6V9V) created by rohou.alexis@…
[…]
12:41 PM Ticket #8509 (Write GLTF files directly to Quest 2 headset) created by Tom Goddard
I'd like to have ChimeraX able to write GLTF files directly to a Quest …
12:24 PM Ticket #8503 (DICOM: minor text change request on DICOM Browser and Download DICOM tools) closed by Zach Pearson
fixed: OK, I got …
10:58 AM Ticket #8508 (Crash in removeDockWidget) created by cesar.segura@…
[…]
10:40 AM Ticket #8507 (Saving a GLTF file of a transparent surface shows as opaque in BabylonJS) created by goddard@…
[…]
10:31 AM Ticket #8506 (Saving GLTF of mesh surface actually saves a filled surface) created by goddard@…
[…]
9:34 AM Ticket #8505 (Crash using File→Open on Windows and/or in return statement) closed by pett
can't reproduce: 1.3
9:33 AM Ticket #8504 (Crash in event loop) closed by pett
can't reproduce
8:05 AM Ticket #8505 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]

Feb 14, 2023:

6:27 PM Ticket #8504 (Crash in event loop) created by chimerax-bug-report@…
[…]
4:14 PM Ticket #8503 (DICOM: minor text change request on DICOM Browser and Download DICOM tools) created by Elaine Meng
To be consistent with the Blast Protein results dialog (hobgoblin of …
3:57 PM Ticket #8502 (Add metallic and roughness options for GLTF output) closed by Tom Goddard
fixed: Done. The option names are metallicFactor and roughnessFactor and the …
3:53 PM Ticket #8502 (Add metallic and roughness options for GLTF output) created by goddard@…
[…]
2:26 PM Ticket #8476 (Matchmaker: 'NoneType' object has no attribute 'setChecked') closed by pett
fixed: Since I cannot reproduce this, have the settings handler deregister …
1:08 PM Ticket #8501 (swapna) closed by pett
not a bug: Hi Sarah, The swapna command was only implemented fairly recently, so …
1:08 PM Ticket #8500 (swapna) closed by pett
not a bug
12:38 PM Ticket #8501 (swapna) created by sarah.smaga@…
[…]
12:34 PM Ticket #8500 (swapna) created by hl.torresvera@…
[…]
12:28 PM Ticket #8499 (Collate details about DICOM collections from series) created by Zach Pearson
The nbia api is much more detailed at the study level than the …
11:32 AM ChangeLog edited by Elaine Meng
(diff)
10:44 AM Ticket #8498 (Crash clearing aniso_u6) closed by pett
duplicate: Duplicate of #8457
10:18 AM Ticket #8495 (Graphics crash, macOS 10.15.7, Intel Iris Plus Graphics) closed by Tom Goddard
nonchimerax: Apple Intel graphics driver crash.
10:17 AM Ticket #8493 (Crash Reporter: Permission denied) closed by Tom Goddard
duplicate: This problem was fixed a few years ago. Update to the current …
10:15 AM Dev2022-2-20 created by Tom Goddard
10:14 AM DeveloperMeetings edited by Tom Goddard
(diff)
10:13 AM 2023-2-16 edited by Tom Goddard
(diff)
10:13 AM 2023-2-16 created by Tom Goddard
10:10 AM Ticket #8498 (Crash clearing aniso_u6) created by chimerax-bug-report@…
[…]
10:10 AM DeveloperMeetings edited by Tom Goddard
(diff)
9:38 AM Ticket #8474 (SEQCROW: crash forming tsbond) closed by pett
fixed: The PseudobondGroup constructor for structure-associated groups adds …
9:01 AM Ticket #8497 (ArtiaX: rotate selected particles: arrays used as indices must be of ...) created by chimerax-bug-report@…
[…]
8:32 AM Ticket #8494 (Session restore: invalid load key) closed by pett
duplicate: Hi Hannah, We believe this error occurs when you try to restore a …
8:16 AM Ticket #8490 (Crash opening PDB) closed by pett
can't reproduce
7:48 AM Ticket #8496 (Crash in event loop) created by bhishem.thakur@…
[…]
7:47 AM Ticket #8495 (Graphics crash, macOS 10.15.7, Intel Iris Plus Graphics) created by chimerax-bug-report@…
[…]
4:15 AM Ticket #8494 (Session restore: invalid load key) created by hrb@…
[…]
4:14 AM Ticket #8493 (Crash Reporter: Permission denied) created by hrb@…
[…]

Feb 13, 2023:

11:37 PM Ticket #8492 (ISOLDE: Can't install package: invalid requirement specified) created by ichcharisma@…
[…] SCR-20230214-n2k.png
6:45 PM Dev2022-2-13 edited by Tom Goddard
(diff)
6:39 PM Ticket #8491 (Opening ORCA file: could not broadcast input array from shape) created by mhvg1994@…
[…] ma.h2s-opt-freq-ccsdt-tz-mo2.out
6:15 PM Ticket #1902 (RFE: surface should update during trajectory playback) closed by Tom Goddard
fixed: Molecular surfaces automatically update when atoms move or are …
5:52 PM Ticket #8473 (Show chain sequence: TypeError: __init__() got an unexpected keyword ...) closed by pett
fixed: Hi Michael, Thanks for reporting the problem with the sequence …
5:45 PM Ticket #8487 (Move selected model moving other models) closed by Tom Goddard
not a bug: The mouse mode called "Drag model" in the toolbar (command 'ui right …
5:44 PM Ticket #8478 (Add Charges: hydrogen bonded to atom that should not have hydrogens) closed by pett
fixed: Need to use templates (of GLY) for UNK residue if backbone atoms …
5:16 PM Dev2022-2-13 edited by Tom Goddard
(diff)
4:36 PM Ticket #8490 (Crash opening PDB) created by chimerax-bug-report@…
[…]
2:37 PM Ticket #8489 (Crash using File→Open dialog on Windows and/or returning from function) closed by pett
can't reproduce: 1.3
2:36 PM Ticket #8488 (Crash destroying tool) closed by pett
can't reproduce: User dropped a session onto a ChimeraX where an AlphaFold prediction …
1:54 PM Ticket #8489 (Crash using File→Open dialog on Windows and/or returning from function) created by chimerax-bug-report@…
[…]
1:09 PM Ticket #8488 (Crash destroying tool) created by chimerax-bug-report@…
[…]
12:51 PM Ticket #8487 (Move selected model moving other models) created by cchen@…
[…]
12:17 PM Ticket #8470 (KeyError formatting blast results) closed by Zach Pearson
fixed: Based on the KeyError I think this happens when the BLAST results come …
11:20 AM Ticket #8486 (After session restore: wrapped C/C++ object of type ChainListWidget ...) closed by pett
duplicate
11:19 AM Ticket #8485 (After session restore: wrapped C/C++ object of type ChainListWidget ...) closed by pett
can't reproduce: Would need the session file to have a shot
11:12 AM Ticket #8481 (Cannot find Python library) closed by pett
can't reproduce: 1.2.5
11:07 AM Ticket #8479 (Out of memory reading trajectory) closed by pett
limitation: Hi Sergio, ChimeraX is trying to read your entire trajectory. I …
10:46 AM Ticket #8475 (MatchMaker: 'NoneType' object has no attribute 'setChecked') closed by pett
duplicate
10:38 AM Ticket #8468 (Change Google account for AlphaFold) closed by Tom Goddard
nonchimerax: Here is a description of how to change your Google sign-in for …
10:23 AM Ticket #8471 (Crash handling pointer in numpy) closed by pett
can't reproduce: 1.3
10:18 AM Ticket #8469 (Crash using File→Open dialog on Windows and/or returning from function) closed by pett
can't reproduce: 1.3
9:20 AM Ticket #8486 (After session restore: wrapped C/C++ object of type ChainListWidget ...) created by chimerax-bug-report@…
[…]
9:20 AM Ticket #8485 (After session restore: wrapped C/C++ object of type ChainListWidget ...) created by chimerax-bug-report@…
[…]
7:43 AM Ticket #8484 ("styling lost" in hand-edited mmCIF) created by cathy.lawson@…
[…]
7:01 AM Ticket #8483 (Merging fragments issues) created by Tristan Croll
[…]
6:31 AM Ticket #8482 (Update OpenMM to 8.0.0 for 1.6) created by Tristan Croll
[…] OpenMM-8.0.0-Linux.tgz
3:19 AM Ticket #8481 (Cannot find Python library) created by chimerax-bug-report@…
[…]

Feb 12, 2023:

3:47 AM Ticket #8480 (Tried to get the position of deleted drawing "VR UI panel") created by chimerax-bug-report@…
[…]

Feb 11, 2023:

9:03 PM Ticket #8479 (Out of memory reading trajectory) created by hassan@…
[…]
2:26 PM Ticket #8478 (Add Charges: hydrogen bonded to atom that should not have hydrogens) created by goddard@…
[…]
1:59 PM Ticket #8477 (Fetch PDB fails in Python 3.11 ChimeraX) closed by Tom Goddard
fixed: Fixed in python311 branch. Standard Python module email.utils …
1:51 PM Ticket #8477 (Fetch PDB fails in Python 3.11 ChimeraX) created by goddard@…
[…]
2:35 AM Ticket #8476 (Matchmaker: 'NoneType' object has no attribute 'setChecked') created by xwu@…
[…]
2:27 AM Ticket #8475 (MatchMaker: 'NoneType' object has no attribute 'setChecked') created by xwu@…
[…]
2:11 AM Ticket #8474 (SEQCROW: crash forming tsbond) created by andreapellegrini6698@…
[…]

Feb 10, 2023:

12:56 PM Dev2022-2-13 created by Tom Goddard
12:54 PM DeveloperMeetings edited by Tom Goddard
(diff)
12:50 PM 2023-2-9 edited by Tom Goddard
(diff)
9:18 AM Ticket #8473 (Show chain sequence: TypeError: __init__() got an unexpected keyword ...) created by weberm@…
[…]
8:01 AM Ticket #8472 (Various simulation errors) created by chimerax-bug-report@…
[…]
4:15 AM Ticket #8471 (Crash handling pointer in numpy) created by chimerax-bug-report@…
[…]
4:08 AM Ticket #8470 (KeyError formatting blast results) created by chimerax-bug-report@…
[…]
3:55 AM Ticket #8464 (ISOLDE: Unparameterised residue detected) closed by Tristan Croll
duplicate: Updating to ISOLDE 1.5 (by first updating to ChimeraX 1.5) should take …
1:01 AM Ticket #8469 (Crash using File→Open dialog on Windows and/or returning from function) created by chimerax-bug-report@…
[…]

Feb 9, 2023:

9:38 PM Ticket #8468 (Change Google account for AlphaFold) created by jeehokim84@…
[…]
7:27 PM Ticket #8465 (Marker surface does not move with marker) closed by Tom Goddard
worksforme: The molecular surface updates as expected for me in the current …
6:53 PM Ticket #8466 (Graphics crash, macOS 13.0.1, Intel Iris Plus Graphics 645) closed by Tom Goddard
nonchimerax: Apple Intel graphics driver crash.
4:25 PM Ticket #8462 (Graphics crash, macOS 11.5.2, Intel Iris Plus Graphics 640) closed by pett
can't reproduce: 1.2.5
4:22 PM Ticket #8467 (need to vary number of dashes in missing segments psuedobond depending ...) created by Greg Couch
6xra_rebuilt_glycan_chains_reassigned.cif​ in #4342 has a really long, …
4:18 PM Ticket #8461 (Crash in event loop) closed by pett
can't reproduce
2:18 PM NIAID2022 edited by Elaine Meng
(diff)
2:01 PM NIAID2022 edited by Elaine Meng
(diff)
1:33 PM NIAID2022 edited by Elaine Meng
(diff)
1:25 PM NIAID2022 edited by Elaine Meng
(diff)
11:04 AM Ticket #8466 (Graphics crash, macOS 13.0.1, Intel Iris Plus Graphics 645) created by chimerax-bug-report@…
[…]
10:57 AM Ticket #8465 (Marker surface does not move with marker) created by Elaine Meng
[…] disconnect.cxs
10:12 AM Ticket #8308 (Crash opening mmCIF) closed by Greg Couch
can't reproduce: Need the mmCIF file to reproduce the problem.
5:29 AM Ticket #8464 (ISOLDE: Unparameterised residue detected) created by emcrae@…
[…]
2:02 AM Ticket #8463 (XMAS: 'Tabular' object has no attribute 'peptide_pairs') created by chimerax-bug-report@…
[…]

Feb 8, 2023:

6:08 PM Ticket #8459 (mmCIF "more info" shows raw HTML) closed by Greg Couch
fixed: Fixed.
3:45 PM Ticket #8462 (Graphics crash, macOS 11.5.2, Intel Iris Plus Graphics 640) created by chimerax-bug-report@…
[…]
3:30 PM Ticket #8451 (Load a default database with Download DICOM tool) closed by Zach Pearson
fixed: In …
1:52 PM Ticket #8461 (Crash in event loop) created by chimerax-bug-report@…
[…]
11:21 AM Ticket #8456 (alphafold pae: 'NoneType' object has no attribute 'residues') closed by Tom Goddard
duplicate: This error was fixed in ChimeraX 1.5. You are opening AlphaFold PAE …
11:18 AM Ticket #8460 (self._current_reference is None) created by mille153@…
[…]
9:39 AM Ticket #8458 (Save mmCIF: 'SaveOptionsWidget' object has no attribute 'compute_sheets') closed by pett
duplicate: Hi Haaris, Thanks for reporting this problem. It was fixed in the …
8:59 AM Ticket #8459 (mmCIF "more info" shows raw HTML) created by Tristan Croll
[…]
4:29 AM Ticket #8458 (Save mmCIF: 'SaveOptionsWidget' object has no attribute 'compute_sheets') created by haaris.safdari@…
[…]

Feb 7, 2023:

11:33 PM Ticket #8457 (Crash clearing aniso_u6) created by chimerax-bug-report@…
[…]
6:34 PM Ticket #8456 (alphafold pae: 'NoneType' object has no attribute 'residues') created by jose.soto@…
[…]
5:56 PM Ticket #8455 (Crash in garbage collection) closed by pett
duplicate: Hi Haoyang, Thanks for reporting this problem. Please upgrade to the …
5:02 PM Ticket #3871 (Add zone selection panel option to omit original selection) closed by pett
fixed: Available in next daily build. Subject to Elaine tweaking.
3:01 PM Ticket #8455 (Crash in garbage collection) created by hyli.pasteur@…
[…]
2:19 PM Ticket #3387 (Render By Attribute tool) closed by pett
duplicate
2:07 PM Ticket #4794 (Dock Prep) closed by pett
fixed
1:22 PM Ticket #8452 (Fix labelling errors in the Download DICOM tool) closed by Zach Pearson
fixed: [https://github.com/RBVI/ChimeraX/commit/4bfbc63551fab092c50243a83774f5
11:43 AM Ticket #8454 (Token starts with space) created by chimerax-bug-report@…
[…]
11:20 AM Ticket #8453 (Associate Download DICOM entries with corresponding TCIA webpage) created by Zach Pearson
(6) If possible, I would like this additional action available for …
11:19 AM Ticket #8452 (Fix labelling errors in the Download DICOM tool) created by Zach Pearson
From an email sent by Elaine: (5b) The "Back to Databases" button …
11:17 AM Ticket #8451 (Load a default database with Download DICOM tool) created by Zach Pearson
From an email from Elaine: (1) Tool starts up with Database: None. …
10:39 AM 2023-2-9 edited by Tom Goddard
(diff)
10:38 AM 2023-2-9 created by Tom Goddard
10:37 AM DeveloperMeetings edited by Tom Goddard
(diff)
9:52 AM Ticket #8445 (Help Viewer, authorize: 'PasswordDialog' object has no attribute 'exec_') closed by Greg Couch
fixed: This problem was due to a missed change from PyQt 5 to PyQt 6. It's …
9:37 AM Ticket #8450 (MatchMaker: 'NoneType' object has no attribute 'setChecked') closed by pett
can't reproduce
9:25 AM Ticket #8448 ('CentroidModel' object has no attribute 'distance') closed by pett
duplicate: Duplicate of #8449
4:45 AM Ticket #8450 (MatchMaker: 'NoneType' object has no attribute 'setChecked') created by chimerax-bug-report@…
[…]
4:38 AM Ticket #8449 ('CentroidModel' object has no attribute 'distance') created by kuretklara@…
[…]
4:36 AM Ticket #8448 ('CentroidModel' object has no attribute 'distance') created by chimerax-bug-report@…
[…]

Feb 6, 2023:

12:47 PM Ticket #8447 (Crash closing tool window) created by chidambareswaren.mahadevan@…
[…]
11:37 AM Ticket #8443 (No checkwaters command) closed by pett
fixed: Removed references to non-existent "checkwaters" command
11:12 AM Ticket #8434 (Rainbow and color sequential) closed by Tom Goddard
not a bug: The rainbow chain or color sequential chain command colors only the …
10:55 AM Ticket #8446 (Cartoon of large 7y5e is slow, takes 30 seconds first time, 4 seconds ...) created by goddard@…
[…]
10:48 AM Ticket #8435 (Crash computing ribbons) closed by Tom Goddard
can't reproduce: That 7y5e PDB model is a monster with 1.2 million atoms and 150,000 …
10:28 AM Ticket #8444 (invalid parameter not satisfying: !isnan(newOrigin.y)) closed by pett
can't reproduce: Hi TJ, You should drag ChimeraX from the .dmg window into your …
10:10 AM Ticket #8440 (Clipper: crash setting aniso_u6) closed by pett
can't reproduce: Right. We hope to make it more obvious that you need to drag the app …
9:45 AM Ticket #8445 (Help Viewer, authorize: 'PasswordDialog' object has no attribute 'exec_') created by shabir.najmudin@…
[…]
9:42 AM Ticket #8442 (Crash opening PDB) closed by pett
can't reproduce
9:41 AM Ticket #8441 (Incorrectly installed CUDA) closed by pett
fixed: Hi Saverio, Glad you were able to get it working. --Eric Eric …
9:37 AM Ticket #8390 (Allow opening (downloading) DICOM files from tcia) closed by Zach Pearson
fixed: This was implemented in a …
9:26 AM Ticket #8439 (Crash in event loop) closed by pett
can't reproduce: Hi Cesar, I recommend upgrading to ChimeraX 1.5, which will provide …
Note: See TracTimeline for information about the timeline view.