Timeline



Dec 7, 2022:

6:22 PM Ticket #8076 (Unnecessary restart required when new file formats installed) closed by Eric Pettersen
fixed: Installing an uninstalled bundle was creating a duplicate copy of the …
2:13 PM Ticket #5055 (Allow BLAST gui to use a sequence viewer id and direct sequence input) reopened by Zach Pearson
Adding or rewording labels is fine. Is there a particular reason other …
1:24 PM ChangeLog edited by Elaine Meng
(diff)
12:57 PM Ticket #8148 (Dead Structure Measurement tool trying to show status) created by Eric Pettersen
[…]
12:45 PM Ticket #8147 (Unknown crash) created by chimerax-bug-report@…
[…]
11:38 AM Ticket #8146 (Testing that Mac ARM platform is reported on M1 Macs with ChimeraX 1.5 ...) closed by Tom Goddard
not a bug: Correctly reports platform. Did this test to see why #8135 reported …
11:34 AM Ticket #8146 (Testing that Mac ARM platform is reported on M1 Macs with ChimeraX 1.5 ...) created by goddard@…
[…]
10:31 AM Ticket #8145 (Crash in QMainWindow::removeDockWidget) created by chimerax-bug-report@…
[…]
9:56 AM Ticket #8144 (Crash showing Rapid Access at startup) closed by Eric Pettersen
can't reproduce: Linux
9:54 AM Ticket #8143 (Crash running modal dialog) closed by Eric Pettersen
can't reproduce
9:52 AM Ticket #8141 (Crash showing Rapid Access at startup) closed by Eric Pettersen
can't reproduce: Linux
9:52 AM Ticket #8140 (Crash showing Rapid Access at startup) closed by Eric Pettersen
can't reproduce
9:20 AM Ticket #8144 (Crash showing Rapid Access at startup) created by chimerax-bug-report@…
[…]
4:54 AM Ticket #8143 (Crash running modal dialog) created by chimerax-bug-report@…
[…]
1:59 AM Ticket #8142 (Qt shim broken in Dec 6 daily builds) created by Tristan Croll
Trying to launch ChimeraX daily just gives a traceback: NOTE: …
12:40 AM Ticket #8141 (Crash showing Rapid Access at startup) created by chimerax-bug-report@…
[…]
12:38 AM Ticket #8140 (Crash showing Rapid Access at startup) created by chimerax-bug-report@…
[…]

Dec 6, 2022:

1:49 PM Ticket #8074 (After other presets: Nonstandard name for heavy atom) closed by Eric Pettersen
nonchimerax: The RCSB is correcting this entry.
1:47 PM Ticket #8112 (sequence layout: list index out of range) closed by Eric Pettersen
can't reproduce
1:31 PM Ticket #8139 (Missing bond) created by kristen.browne@…
[…]
12:22 PM Ticket #8138 (Fatal error: maxassem 1 has no models in it) created by kristen.browne@…
[…]
12:11 PM Ticket #8137 (1.5 not starting) closed by Greg Couch
limitation: Try the RHEL/CentOS 9 rpm. We don't test on FC36, but I expect it to …
11:46 AM Ticket #8137 (1.5 not starting) created by gerwald_jogl@…
[…] startlog.txt​
11:30 AM Ticket #8136 (Toolshed search does not find some bundles) closed by Greg Couch
fixed: Fixed.
10:57 AM Ticket #8135 (Crash in event loop) closed by Eric Pettersen
can't reproduce
10:54 AM Ticket #8134 (Crash showing Rapid Access at startup) closed by Eric Pettersen
can't reproduce: Hi David, Thanks for reporting this problem. We recommend upgrading …
10:23 AM 2022-12-8 created by Tom Goddard
10:21 AM DeveloperMeetings edited by Tom Goddard
(diff)
10:20 AM Ticket #8132 (Old presets) closed by Eric Pettersen
duplicate
10:19 AM Ticket #8128 (Crash in QWindowSystemInterface::handleScreenRemoved) closed by Tom Goddard
nonchimerax: Great that you could reproduce it. In fact it is a long standing Qt …
9:35 AM Ticket #8136 (Toolshed search does not find some bundles) created by dcliebschner@…
Using the search field, searching for "phenix" or "phenixui" does not …
7:09 AM Ticket #8135 (Crash in event loop) created by chimerax-bug-report@…
[…]
5:37 AM Ticket #8134 (Crash showing Rapid Access at startup) created by david.teran@…
[…]
5:16 AM Ticket #8133 (printable ribbon: "No atoms specifified" error) created by kristen.browne@…
[…] pdb1bfp_0.ent​
12:57 AM Ticket #8117 (Crash in OpenMM find_clashing_atoms()) closed by Tristan Croll
fixed: This would happen in 1.3 if the user hit the simulation stop button …

Dec 5, 2022:

4:23 PM Ticket #8132 (Old presets) created by kristen.browne@…
[…]
4:20 PM Dev2022-12-5 edited by Tom Goddard
(diff)
4:20 PM Dev2022-12-5 edited by Tom Goddard
(diff)
4:13 PM Dev2022-12-5 edited by Tom Goddard
(diff)
3:11 PM Dev2022-12-5 edited by Tom Goddard
(diff)
3:05 PM Dev2022-12-5 edited by Tom Goddard
(diff)
3:04 PM Ticket #8131 (SDF charge Index out of bounds) created by kristen.browne@…
[…] Furfural aminoguanidine bicarbonate.sdf​
3:03 PM Dev2022-12-5 created by Tom Goddard
3:01 PM DeveloperMeetings edited by Tom Goddard
(diff)
1:52 PM Ticket #8130 ('VolumeViewer' object has no attribute 'tool_window') closed by Tom Goddard
can't reproduce: Not sure how the tool_window attribute can be gone. It is set when …
1:46 PM Ticket #8125 (Qt fatal error: Failed to initialize graphics backend for OpenGL) closed by Tom Goddard
can't reproduce: Same as #8123, #8124 but different computer, this report with NVIDIA …
1:43 PM Ticket #8123 (Qt fatal error: Failed to initialize graphics backend for OpenGL) closed by Tom Goddard
can't reproduce: Same as #8124, but different computer, this report with GeForce RTX …
1:38 PM Ticket #8124 (Qt fatal error: Failed to initialize graphics backend for OpenGL) closed by Tom Goddard
can't reproduce: This message "Qt fatal error: Failed to initialize graphics backend …
1:08 PM Ticket #8130 ('VolumeViewer' object has no attribute 'tool_window') created by chimerax-bug-report@…
[…]
12:58 PM Ticket #8127 (Crash showing Rapid Access at startup) closed by Eric Pettersen
can't reproduce: Linux
12:56 PM Ticket #8126 (hbonds: More than 2 coplanar positions specified) closed by Eric Pettersen
not a bug: Almost certainly bad connectivity
12:50 PM Ticket #8122 (Crash showing Rapid Access at startup) closed by Eric Pettersen
can't reproduce: Hi Venkatareddy, We aren't able to reproduce this problem ourselves. …
11:47 AM Ticket #8121 (Negative decimal places for distance format) closed by Eric Pettersen
can't reproduce: Duplicate #7881 Early versions of "distance style" or its settings …
11:38 AM Ticket #8129 (Allow Quest 2 or other standalone headsets to join ChimeraX VR meetings) created by Tom Goddard
Allow researchers to use ChimeraX virtual reality and join meetings …
11:27 AM Ticket #8119 (Movie encode: No space left on device) closed by Tom Goddard
nonchimerax: The error when saving a movie says OSError: [Errno 28] No space …
11:23 AM Ticket #8120 (Restore new session in old ChimeraX) closed by Eric Pettersen
not a bug: Hi Shauna! Though old sessions are guaranteed to restore in new …
8:06 AM Ticket #8128 (Crash in QWindowSystemInterface::handleScreenRemoved) created by Tristan Croll
[…]
7:29 AM Ticket #8127 (Crash showing Rapid Access at startup) created by chimerax-bug-report@…
[…]

Dec 4, 2022:

11:30 PM Ticket #8126 (hbonds: More than 2 coplanar positions specified) created by chimerax-bug-report@…
[…]
9:03 PM Ticket #8125 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by chimerax-bug-report@…
[…]
8:49 AM Ticket #8124 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by chimerax-bug-report@…
[…]
7:29 AM Ticket #8123 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by chimerax-bug-report@…
[…]

Dec 3, 2022:

9:03 PM Ticket #8122 (Crash showing Rapid Access at startup) created by venkatareddy@…
[…]
5:07 PM Ticket #8121 (Negative decimal places for distance format) created by chimerax-bug-report@…
[…]
12:16 PM Ticket #8120 (Restore new session in old ChimeraX) created by shauna.farr-jones@…
[…] BoNT G mutants HN.cxs​
3:07 AM Ticket #8119 (Movie encode: No space left on device) created by semchonok@…
[…]
1:49 AM Ticket #8118 (Crash with segidChains true) created by chimerax-bug-report@…
[…]

Dec 2, 2022:

11:46 PM Ticket #8117 (Crash in OpenMM find_clashing_atoms()) created by chimerax-bug-report@…
[…]
4:24 PM Ticket #8110 (Wrong channel names opening second copy of 3-channel microscopy) closed by Tom Goddard
fixed: Fixed. ImageJ tiff grid data was not assigning the grid_id for the …
3:46 PM Ticket #7968 (Try OpenMM 8.0 in daily builds) closed by Tom Goddard
fixed: Done. Updated Mac ARM and Intel and Windows and Linux to use OpenMM …
2:51 PM Ticket #8109 (pyproject.toml-based "make install" should reinstall) closed by Zach Pearson
not a bug: Works for the version of setuptools shipped with 1.5 (and hopefully …
2:23 PM Ticket #8115 (libGLU.so.1: cannot open shared object file: No such file or directory) closed by Eric Pettersen
duplicate
2:20 PM Ticket #8113 (Crash in event loop) closed by Eric Pettersen
can't reproduce
1:37 PM Ticket #5055 (Allow BLAST gui to use a sequence viewer id and direct sequence input) closed by Zach Pearson
fixed: seq_view …
1:04 PM Ticket #3014 (Blast Protein tool: threading) closed by Zach Pearson
fixed: They do. :)
12:49 PM Ticket #8107 (Map→Style→Transparent surface not toggling transparency) closed by Tom Goddard
fixed: Fixed. Made map transparency toolbar button ignore hidden models even …
12:47 PM 2022-12-1 edited by Elaine Meng
(diff)
12:37 PM 2022-12-1 edited by Elaine Meng
(diff)
12:20 PM 2022-12-1 edited by Tom Goddard
(diff)
11:41 AM Ticket #8116 (Crash in QMenu::clear()) created by msanzmurillo@…
[…]
11:03 AM Ticket #8115 (libGLU.so.1: cannot open shared object file: No such file or directory) created by chimerax-bug-report@…
[…]
9:36 AM Ticket #8114 (read_xyz: elements: list index out of range) created by bdharding@…
[…]
8:09 AM ChangeLog edited by Elaine Meng
(diff)
8:08 AM ChangeLog edited by Elaine Meng
(diff)

Dec 1, 2022:

11:25 PM Ticket #8113 (Crash in event loop) created by chimerax-bug-report@…
[…]
9:54 PM Ticket #8112 (sequence layout: list index out of range) created by chimerax-bug-report@…
[…]
6:20 PM Ticket #8111 (AlphaFold prediction broken with energy minimization or pdb templates) closed by Tom Goddard
fixed: Fixed. Updated ChimeraX colabfold script to install dependencies for …
6:04 PM Ticket #8111 (AlphaFold prediction broken with energy minimization or pdb templates) created by Tom Goddard
Google Colab update from python 3.7 to 3.8 breaking ChimeraX AlphaFold …
5:36 PM Ticket #8110 (Wrong channel names opening second copy of 3-channel microscopy) created by goddard@…
[…]
5:15 PM Ticket #8109 (pyproject.toml-based "make install" should reinstall) created by Eric Pettersen
For bundle_info.xml-based bundles, "make install" forces a reinstall …
3:28 PM Ticket #8106 (Possibly provide event to double-click criteria() call) closed by Eric Pettersen
fixed: Okay, off the same logic now all methods (label/criteria/callback) of …
1:16 PM Ticket #8108 (Help Viewer doesn't agree with MGnify entry page opened from Blast ...) closed by Zach Pearson
nonchimerax: Works on my machine; both on the daily build and my current developer …
12:57 PM Ticket #8108 (Help Viewer doesn't agree with MGnify entry page opened from Blast ...) created by Elaine Meng
When I do a blast search of ESMFold database and then in the Blast …
12:04 PM Ticket #5056 (Allow blastprotein command to use a UniProt name or id) closed by Zach Pearson
fixed: [​https://github.com/RBVI/ChimeraX/commit/05f11de2ccb9226f6ab3ccd5120c36 …
9:47 AM Ticket #8107 (Map→Style→Transparent surface not toggling transparency) created by bta4001@…
[…]
8:12 AM Ticket #8106 (Possibly provide event to double-click criteria() call) created by Tristan Croll
[…]
5:01 AM Ticket #8105 (ChimeraX/lib not on library path) created by Tristan Croll
[…]
1:26 AM Ticket #8104 (TmplResidue SMILES string) closed by Greg Couch
fixed: Added. To get the information use …

Nov 30, 2022:

6:56 PM ChangeLog edited by Elaine Meng
(diff)
5:53 PM Ticket #8077 (coulombic → ribbon → coulombic: structure gone) closed by Eric Pettersen
can't reproduce: I assume that you will just file a new ticket if this happens again …
11:49 AM Ticket #7970 (Allow running ESMFold structure prediction and kmer and blast search ...) closed by Tom Goddard
fixed: Done. Hooked up the ESMFold gui search button which runs a blast search.
10:06 AM Ticket #8097 (Error initializing VR: KeyError: 1002 "Oculus Link Not Enabled") closed by Tom Goddard
duplicate: Duplicate of #7774 Missing pyopenvr error code "Oculus Link Not …
9:56 AM ChangeLog edited by Tom Goddard
(diff)
9:55 AM ChangeLog edited by Tom Goddard
(diff)
9:55 AM ChangeLog edited by Tom Goddard
(diff)
9:53 AM ChangeLog edited by Tom Goddard
(diff)
9:35 AM Ticket #7961 (Clipper fails to build in Windows - Nov 3 release candidate) closed by Zach Pearson
fixed: Tristan reported this morning that his bundle builds without his …
8:42 AM Ticket #8102 (Crash during selection-promotion process) closed by Eric Pettersen
can't reproduce
8:40 AM Ticket #8101 (Crash using File→Open on Windows and/or in return statement) closed by Eric Pettersen
can't reproduce
8:39 AM Ticket #8100 (Crash using File→Open on Windows and/or in return statement) closed by Eric Pettersen
can't reproduce
8:32 AM Ticket #8104 (TmplResidue SMILES string) created by Tristan Croll
[…]
8:00 AM Ticket #8103 (Shell tool: Qt enum vs. int) created by Tristan Croll
[…]
7:58 AM Ticket #8102 (Crash during selection-promotion process) created by chimerax-bug-report@…
[…]
5:23 AM Ticket #8101 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
5:02 AM Ticket #8100 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
4:47 AM Ticket #8099 (ISOLDE: close session: 'AtomicStructure' object has no attribute ...) created by maf95@…
[…]
2:12 AM Ticket #8098 (ISOLDE: 'AtomicStructure' object has no attribute 'session') created by leofrancalima@…
[…]

Nov 29, 2022:

6:54 PM Ticket #8041 (Add ESMFold database to BlastProtein) closed by Zach Pearson
fixed: Thanks for your patience. As you said, …
4:56 PM ChangeLog edited by Elaine Meng
(diff)
10:41 AM Ticket #8097 (Error initializing VR: KeyError: 1002 "Oculus Link Not Enabled") created by chimerax-bug-report@…
[…]
10:40 AM Ticket #8059 (chimeraX freezing) closed by Greg Couch
limitation: Yeah! Thank you for letting us know.
10:07 AM 2022-12-1 created by Tom Goddard
10:06 AM DeveloperMeetings edited by Tom Goddard
(diff)
9:51 AM Milestone 1.5 completed
== Released == * November 29, 2022 == Feature Freeze and Branch == …
9:06 AM Ticket #8095 (Crash in event loop) closed by Eric Pettersen
can't reproduce
9:03 AM Ticket #8093 (Restore new session in old ChimeraX) closed by Eric Pettersen
not a bug
7:37 AM Ticket #8096 (Antechamber on M2: Bad CPU type in executable) created by chimerax-bug-report@…
[…]
6:48 AM Ticket #8095 (Crash in event loop) created by chimerax-bug-report@…
[…]
6:20 AM Ticket #8094 (ArtiaX session save: Unknown class name 'MarkerSetPlus') created by chimerax-bug-report@…
[…]
6:16 AM ChangeLog edited by Elaine Meng
(diff)
3:59 AM Ticket #8093 (Restore new session in old ChimeraX) created by rishi.raj@…
[…]

Nov 28, 2022:

5:39 PM ChangeLog edited by Elaine Meng
(diff)
3:56 PM Ticket #8092 (Reading 2D ImageJ microscopy: IndexError: index out of range) closed by Tom Goddard
fixed: Fixed. The code was using zsize equal to the number of tiff pages …
3:50 PM Ticket #8092 (Reading 2D ImageJ microscopy: IndexError: index out of range) created by goddard@…
[…]
3:41 PM Dev2022-11-28 edited by Tom Goddard
(diff)
3:40 PM Dev2022-11-28 edited by Tom Goddard
(diff)
3:38 PM Dev2022-11-28 edited by Tom Goddard
(diff)
3:36 PM Dev2022-11-28 created by Tom Goddard
3:34 PM DeveloperMeetings edited by Tom Goddard
(diff)
3:00 PM Ticket #8086 (AlphaFold predict: ValueError: could not broadcast input array from shape) closed by Tom Goddard
nonchimerax: This error is in ColabFold, we did not write that code. Colabfold is …
2:46 PM Ticket #7301 (Freeze on Ubuntu 22.04 + registration date/time error) closed by Greg Couch
duplicate: Duplicate of #8059
2:13 PM Ticket #8090 (Graphics crash, macOS 12.4, Intel Iris Plus Graphics 645) closed by Tom Goddard
nonchimerax: Apple Intel graphics driver crash
1:40 PM Ticket #8091 (UniProt fetch: HTTP Error 405: Not Allowed) closed by Eric Pettersen
duplicate: Hi Federica, Thanks for reporting this problem. UniProt changed the …
1:32 PM Ticket #8081 (Graphics crash, macOS 10.15.7, NVIDIA GeForce GTX 780M) closed by Tom Goddard
nonchimerax: Apple Intel graphics driver crash.
1:30 PM Ticket #8088 (Crash using File→Open on Windows and/or in return statement) closed by Eric Pettersen
can't reproduce: 1.3
1:29 PM Ticket #8087 (Crash using File→Open on Windows and/or in return statement) closed by Eric Pettersen
can't reproduce: 1.3
1:24 PM Ticket #8085 (Modeller target is None) closed by Eric Pettersen
duplicate: This a duplicate of #7992 and is fixed on the develop branch. Should …
1:18 PM Ticket #8084 (Crash during screen changed) closed by Eric Pettersen
duplicate
1:09 PM Ticket #8082 (Volume not in Surface Color volume menu) closed by Eric Pettersen
can't reproduce: Seems to imply that the map is not in session.models or that it is not …
11:56 AM Ticket #8079 (Crash in event loop) closed by Eric Pettersen
can't reproduce
1:48 AM Ticket #8091 (UniProt fetch: HTTP Error 405: Not Allowed) created by federica.souto.trinei@…
[…] Captura de Pantalla 2022-11-28 a las 10.46.58.png

Nov 27, 2022:

5:38 PM Ticket #8090 (Graphics crash, macOS 12.4, Intel Iris Plus Graphics 645) created by chimerax-bug-report@…
[…]
2:17 AM Ticket #8089 (Clipper: AttributeError: 'NoneType' object has no attribute ...) created by chimerax-bug-report@…
[…]
2:03 AM Ticket #8088 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]

Nov 25, 2022:

11:08 PM Ticket #8070 (libGLU.so.1: cannot open shared object file: No such file or directory) closed by Greg Couch
worksforme: The fix is to install libGLU. On RHEL derived systems, that is in the …
10:48 AM Ticket #8087 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
9:57 AM Ticket #8086 (AlphaFold predict: ValueError: could not broadcast input array from shape) created by blemire@…
[…] Screen Shot 2022-11-25 at 10.53.39 AM.png​
8:42 AM Ticket #8085 (Modeller target is None) created by chimerax-bug-report@…
[…]
7:32 AM Ticket #8084 (Crash during screen changed) created by chimerax-bug-report@…
[…]

Nov 24, 2022:

7:53 AM Ticket #8083 (ISOLDE session restore: 'AtomicStructure' object has no attribute 'session') created by michal.ponczek@…
[…]
7:41 AM Ticket #8082 (Volume not in Surface Color volume menu) created by chimerax-bug-report@…
[…]
4:51 AM Ticket #8081 (Graphics crash, macOS 10.15.7, NVIDIA GeForce GTX 780M) created by chimerax-bug-report@…
[…]
3:25 AM Ticket #8080 (Crash repeating "style ball" command) created by andreapellegrini6698@…
[…]

Nov 23, 2022:

9:45 PM Ticket #8079 (Crash in event loop) created by chimerax-bug-report@…
[…]
5:58 PM ChangeLog edited by Eric Pettersen
(diff)
4:07 PM Ticket #8078 (DICOM tools: please hook up help to context menu) closed by Zach Pearson
fixed: I also cherry-picked your documentation changes into the release branch.
3:13 PM Ticket #3014 (Blast Protein tool: threading) reopened by Elaine Meng
1:44 PM Ticket #8073 (Could not come up with unique atom name in mega-residue) closed by Eric Pettersen
limitation: The entire 40-residue nucleic acid moiety in 4r8i is composed of …
11:37 AM Ticket #8078 (DICOM tools: please hook up help to context menu) created by Elaine Meng
DICOM tools look good, just need to hook documentation up to context …
11:19 AM Ticket #8077 (coulombic → ribbon → coulombic: structure gone) created by kristen.browne@…
[…]
9:20 AM Ticket #8071 (Crash using File→Open on Windows and/or in return statement) closed by Eric Pettersen
can't reproduce: 1.3
9:09 AM Ticket #8076 (Unnecessary restart required when new file formats installed) created by tony.schaefer@…
e.g. when SEQCROW installed to read .xyz files
7:51 AM Ticket #8075 (Printable ribbon preset hangs) created by kristen.browne@…
[…]
7:41 AM Ticket #8074 (After other presets: Nonstandard name for heavy atom) created by kristen.browne@…
[…]
6:50 AM Ticket #8073 (Could not come up with unique atom name in mega-residue) created by kristen.browne@…
[…]

Nov 22, 2022:

5:20 PM Ticket #8072 (AlphaFold coloring panel does not list AlphaFold models in menu) closed by Tom Goddard
fixed: Fixed. Show all structures in alphafold coloring gui but set the menu …
4:48 PM Ticket #8072 (AlphaFold coloring panel does not list AlphaFold models in menu) created by goddard@…
[…]
4:31 PM Ticket #8056 (Problem opening Gaussian output: Unknown element detected: Variables) closed by Eric Pettersen
fixed
3:14 PM Ticket #8071 (Crash using File→Open on Windows and/or in return statement) created by chimerax-bug-report@…
[…]
2:35 PM Ticket #8070 (libGLU.so.1: cannot open shared object file: No such file or directory) created by chimerax-bug-report@…
[…]
1:42 PM Ticket #8069 (BlastProtein: cannot import name '_log_alphafold_sequence_info') closed by Tom Goddard
fixed: Fixed. I changed the AlphaFold private method that Blast Protein was …
1:29 PM Ticket #8069 (BlastProtein: cannot import name '_log_alphafold_sequence_info') created by goddard@…
[…]
11:35 AM Ticket #8068 (Make selection, coloring, mesh and dot styles work on BILD models) created by Tom Goddard
None of the standard operations work on BILD models. I made a single …
11:05 AM Ticket #8067 (Save independent rotation mouse mode in sessions) created by hassan@…
[…]
9:35 AM Ticket #8052 (limit formats in Save dialog to ones appropriate for current models) closed by Eric Pettersen
wontfix: Given that, as Tom points out, there may be as many downsides as …
9:20 AM Ticket #8066 (saving attribute values) closed by Eric Pettersen
fixed: Hi Björn, Thanks for reporting this problem. The problem is that the …
3:27 AM Ticket #8066 (saving attribute values) created by bjorn.forsberg@…
[…]

Nov 21, 2022:

6:59 PM Ticket #6774 (Unknown crash) closed by Tom Goddard
can't reproduce: This looks like a crash in the Qt window toolkit, but there is not …
6:57 PM Ticket #6924 (QXcbConnection: XCB error:) closed by Tom Goddard
nonchimerax: No reply from reporter.
6:57 PM Ticket #6961 (AlphaFold prediction: A UTF-8 locale is required. Got ANSI_X3.4-1968) closed by Tom Goddard
can't reproduce: I have not seen this error in 6 months. Maybe our switch to using …
6:55 PM Ticket #7209 (Mac notarization fails about 1/4 of the time: "A timestamp was ...) closed by Tom Goddard
fixed: I increased the number of notarization retries from 1 to 4 and …
6:51 PM Ticket #7417 ("cofr" info misleading) closed by Tom Goddard
limitation
6:50 PM Ticket #7428 (Inconsistent stack trace information) closed by Tom Goddard
limitation: I may improve the log handling in the future to allow for multiple …
6:46 PM Ticket #7524 (Save image to desktop: permission denied) closed by Tom Goddard
duplicate: ChimeraX was changed more than a year ago so it will not set the …
6:42 PM Ticket #7678 (Crashes creating QWebEngineProfile on Windows) closed by Tom Goddard
nonchimerax
6:41 PM Ticket #7739 (QPainter::begin: Paint device returned engine == 0, type: 2) closed by Tom Goddard
can't reproduce
6:40 PM Ticket #7878 ('show' unexpectedly showing whole chains) closed by Tom Goddard
can't reproduce: No reply from reporter.
6:38 PM Ticket #8010 (Image stack:tuple index out of range) closed by Tom Goddard
can't reproduce: Probably requires an incomplete set of files to reproduce this.
5:18 PM Ticket #8064 (clicking Model Panel Info to show DICOM Browser either gives traceback ...) closed by Zach Pearson
fixed: This should be fixed tomorrow. The DICOM browser was rewritten to make …
4:58 PM Ticket #8065 (Log chain table with RMSD for AlphaFold multimer predictions) created by goddard@…
[…]
4:44 PM Ticket #8015 ('DICOMBrowserTool' object has no attribute '_see_what_happened') closed by Zach Pearson
fixed: Should be fixed in tomorrow's daily build and release candidate.
2:42 PM Ticket #8019 (Bad alternate locations) closed by Eric Pettersen
limitation: Okay, I submitted a pull request that will skip a preset when these …
1:26 PM Ticket #8055 (AlphaFold: I/O operation on closed file) closed by Tom Goddard
fixed
1:25 PM Ticket #8055 (AlphaFold: I/O operation on closed file) reopened by Tom Goddard
Fixed. The release of jax 0.3.25 broke ColabFold. Unfortunately …
11:58 AM Ticket #8064 (clicking Model Panel Info to show DICOM Browser either gives traceback ...) created by Elaine Meng
[…]
10:30 AM Ticket #8063 (Crash running AlphaFold prediction) closed by Tom Goddard
can't reproduce
10:29 AM Ticket #8062 (Status bar: wrapped C/C++ object of type QScreen has been deleted) closed by Tom Goddard
duplicate: This bug was fixed about a year ago. It happens when running ChimeraX …
10:23 AM Ticket #8055 (AlphaFold: I/O operation on closed file) closed by Tom Goddard
nonchimerax: That is an error in AlphaFold code, not in ChimeraX. It says it is …
10:21 AM Ticket #8061 (MD viewer: No self.atomLocations) closed by Eric Pettersen
not a bug: Not a trajectory (self.atomLocations only set on ENDMDL record).
10:19 AM Ticket #8063 (Crash running AlphaFold prediction) created by chimerax-bug-report@…
[…]
9:29 AM Ticket #8060 (crash running modal dialog) closed by Eric Pettersen
can't reproduce
9:26 AM Ticket #8058 (Crash using File→Open on Windows and/or in return statement) closed by Eric Pettersen
can't reproduce: Hi Uzay, Thanks for reporting this problem. We believe it is fixed …
9:21 AM Ticket #8057 (Save session: Basic Actions: 'QEventLoop' object has no attribute 'exec_') closed by Eric Pettersen
duplicate
9:14 AM Ticket #8054 (Crash processing geometry change) closed by Eric Pettersen
can't reproduce
9:12 AM Ticket #8053 (Crash creating QTimer) closed by Eric Pettersen
can't reproduce
8:58 AM Ticket #8050 (Crash in event loop) closed by Eric Pettersen
can't reproduce
6:10 AM Ticket #8062 (Status bar: wrapped C/C++ object of type QScreen has been deleted) created by nadine.hellmold@…
[…]
5:43 AM Ticket #8061 (MD viewer: No self.atomLocations) created by chimerax-bug-report@…
[…]
3:03 AM Ticket #8060 (crash running modal dialog) created by chimerax-bug-report@…
[…]
2:51 AM Ticket #8059 (chimeraX freezing) created by francois.hoh@…
[…]

Nov 20, 2022:

5:47 PM Ticket #8058 (Crash using File→Open on Windows and/or in return statement) created by uzay.sezen@…
[…]
10:58 AM Ticket #8057 (Save session: Basic Actions: 'QEventLoop' object has no attribute 'exec_') created by chimerax-bug-report@…
[…]

Nov 19, 2022:

9:05 PM Ticket #8056 (Problem opening Gaussian output: Unknown element detected: Variables) created by matthew.graneri@…
[…] gau_ma.h2s-opt-freq-b3lyp-d3-qzvppd.log​
10:04 AM Ticket #8055 (AlphaFold: I/O operation on closed file) created by blemire@…
[…] Screen Shot 2022-11-19 at 11.00.32 AM.png​
7:17 AM Ticket #8054 (Crash processing geometry change) created by chimerax-bug-report@…
[…]
6:45 AM Ticket #8053 (Crash creating QTimer) created by chimerax-bug-report@…
[…]

Nov 18, 2022:

5:04 PM Ticket #7997 (Add Charges: Nonstandard name for heavy atom) closed by Eric Pettersen
fixed: Tomorrow's daily build will handle phosphorylated 5' termini.
3:13 PM Ticket #8052 (limit formats in Save dialog to ones appropriate for current models) created by Greg Couch
It would be nice if the list of output formats in the Save dialog …
1:14 PM Ticket #8051 (ISOLDE: matplotlib: 'box_aspect' and 'fig_aspect' must be positive + ...) created by mille153@…
[…]
10:41 AM Ticket #8049 (MemoryError saving large image) closed by Tom Goddard
nonchimerax: Ran out of memory trying to save an 6000 x 4000 image. PIL tried to …
10:01 AM Ticket #8050 (Crash in event loop) created by chimerax-bug-report@…
[…]

Nov 17, 2022:

11:23 PM Ticket #8049 (MemoryError saving large image) created by chimerax-bug-report@…
[…]
3:40 PM 2022-11-17 edited by Tom Goddard
(diff)
3:40 PM 2022-11-17 edited by Tom Goddard
(diff)
3:02 PM Dev2022-11-17 created by Tom Goddard
2:54 PM DeveloperMeetings edited by Tom Goddard
(diff)
1:25 PM Ticket #7992 (Modeller target is None) closed by Eric Pettersen
fixed: Fix: …
1:23 PM Ticket #8048 (Crash in timer callback) created by tshar017@…
[…]
10:36 AM ChangeLog edited by Elaine Meng
(diff)
10:22 AM 2022-11-17 edited by Tom Goddard
(diff)
9:53 AM Ticket #8047 (Crash using File→Open dialog on Windows and/or returning from function) closed by Eric Pettersen
can't reproduce: 1.3
9:51 AM Ticket #8046 (Crash in garbage collection after showing 30000+ pseudobonds) closed by Eric Pettersen
can't reproduce
4:39 AM Ticket #8047 (Crash using File→Open dialog on Windows and/or returning from function) created by chimerax-bug-report@…
[…]

Nov 16, 2022:

4:18 PM Ticket #7769 (Crash reading mmCIF) closed by Greg Couch
can't reproduce: Learned on 11 October 2022 that the .cif file had been deleted.
4:02 PM Ticket #3534 (Parsing complaint about Ligand Expo cif files) closed by Greg Couch
nonchimerax: Yes, that is illegal according to the CIF standard, …
3:45 PM Ticket #7925 (DICOM Browser: bundle forgot to override start_tool method) closed by Zach Pearson
fixed
2:54 PM Ticket #8045 (Bad symmetry table entries) closed by Tom Goddard
fixed
2:42 PM Ticket #8034 ("make clean" compiles bundle) closed by Zach Pearson
fixed: Should be fixed by …
1:35 PM Ticket #8022 (Bad residue names from Mol2 file) closed by Eric Pettersen
fixed: The Mol2 reader wasn't adding missing-structure pseudobonds when …
1:23 PM Ticket #8046 (Crash in garbage collection after showing 30000+ pseudobonds) created by chimerax-bug-report@…
[…]
1:02 PM Ticket #8045 (Bad symmetry table entries) created by Eric Pettersen
Click on entry 1 of the symmetry table for the attached file works …
12:06 PM 2022-11-17 edited by Tom Goddard
(diff)
10:32 AM Ticket #8043 (glGetFramebufferAttachmentParameteriv: invalid enumerant) closed by Tom Goddard
limitation: ChimeraX requires Windows 10 or 11. Maybe it will run on Windows 7 …
9:26 AM Ticket #8037 (Charge-determination failure for CAS in 1fyw) closed by Eric Pettersen
limitation: Neither charge-determination method can handle the arsenic in the CAS …
8:56 AM Ticket #8044 (glGetFramebufferAttachmentParameteriv: invalid enumerant) closed by Eric Pettersen
duplicate
8:53 AM Ticket #8042 (Unknown crash) closed by Eric Pettersen
can't reproduce
8:51 AM Ticket #8039 (Charge-determination convergence failure for 4pk2) closed by Eric Pettersen
limitation: The charge determination works with the Gasteiger method, and …
7:49 AM Ticket #8044 (glGetFramebufferAttachmentParameteriv: invalid enumerant) created by zengqh99@…
[…]
6:52 AM Ticket #8043 (glGetFramebufferAttachmentParameteriv: invalid enumerant) created by zengqh99@…
[…]

Nov 15, 2022:

11:10 PM Ticket #7993 (Mesa-Utils package required) closed by Greg Couch
can't reproduce: I don't know where those errors are coming from. But if you uninstall …
6:24 PM Ticket #8040 (alphafold pae command with no structure gives AttributeError) closed by Tom Goddard
fixed: Fixed in ChimeraX 1.5 and daily build. The chain divider lines on the …
6:20 PM Ticket #8042 (Unknown crash) created by chimerax-bug-report@…
[…]
6:11 PM Ticket #8041 (Add ESMFold database to BlastProtein) created by Tom Goddard
The ESMFold metagenomic atlas is very similar to the AlphaFold …
5:49 PM Ticket #7945 (Read PAE matrix: No module named 'jax') closed by Tom Goddard
fixed: Duplicate of #8032. Fixed.
5:36 PM Ticket #8023 (All white coulombic) closed by Eric Pettersen
not a bug: The PDB has a spurious TER card in the middle of chain A, between …
5:28 PM Ticket #8032 (Read PAE matrix: No module named 'jax') closed by Tom Goddard
fixed: Fixed in ChimeraX 1.5 release candidate and daily build. I put in a …
5:16 PM Ticket #8024 (PubChem: #charges != #atoms) closed by Eric Pettersen
fixed: Now in addition to a missing charges section of the SDF file meaning …
5:04 PM Ticket #7967 (Ubuntu 22 ChimeraX installer is replacing symlinks by copies of libraries) closed by Greg Couch
fixed: Needed syslinks=True argument to shutil.copytree()
4:57 PM Ticket #8036 (Not able to sign in to Google Colab for AlphaFold prediction) closed by Tom Goddard
worksforme
4:40 PM Ticket #8026 (sqm failure on all-nonstandard nucleic acid) closed by Eric Pettersen
fixed: Switched the coulombic preset to use Gasteiger charge-determination …
4:40 PM Ticket #8040 (alphafold pae command with no structure gives AttributeError) created by goddard@…
[…]
4:03 PM Ticket #8028 (microheterogeneity) closed by Eric Pettersen
limitation: ChimeraX simply does not handle microheterogeneity (e.g residue 782 in …
2:38 PM Ticket #8029 (non-standard C-terminal oxygen name) closed by Eric Pettersen
fixed: Add Charge will allow 1OCT and 2OCT as C-terminal oxygen names …
2:05 PM ChangeLog edited by Elaine Meng
(diff)
2:04 PM ChangeLog edited by Elaine Meng
(diff)
1:54 PM Ticket #8039 (Charge-determination convergence failure for 4pk2) created by kristen.browne@…
[…] 4pk2.pdb​
1:53 PM ChangeLog edited by Elaine Meng
(diff)
1:22 PM Ticket #8038 (Compressed .cif without .gz suffix) created by kristen.browne@…
[…] 2fae-assembly-1.cif​
1:16 PM Ticket #8037 (Charge-determination failure for CAS in 1fyw) created by kristen.browne@…
[…]
12:01 PM Ticket #8031 (Incorrect element column in PDB file) closed by Eric Pettersen
not a bug: The input PDB file is just bad. The "element' column is *mostly* the …
11:35 AM Ticket #8035 (Bad formal charge estimate) closed by Eric Pettersen
limitation: The ChargeError does get caught by the command processing code, but …
10:14 AM Ticket #8036 (Not able to sign in to Google Colab for AlphaFold prediction) created by Tom Goddard
[…]
10:02 AM 2022-11-17 created by Tom Goddard
10:01 AM DeveloperMeetings edited by Tom Goddard
(diff)
9:56 AM Ticket #8035 (Bad formal charge estimate) created by kristen.browne@…
[…] 1av7.pdb​

Nov 14, 2022:

6:09 PM Ticket #8034 ("make clean" compiles bundle) created by Greg Couch
When doing "make clean" in the mmcif bundle with an error in …[…]
5:26 PM Ticket #8033 (SEQCROW: memory reporting: unsupported operand type(s) for *: ...) created by neryvillegas@…
[…]
3:07 PM Ticket #8030 (PDB file reader accepts "nan" coordinates without warning) closed by Eric Pettersen
fixed: Use numpy.isnan() to check the coordinates coming from the PDB reader. …
2:17 PM Ticket #8032 (Read PAE matrix: No module named 'jax') created by sclassen@…
[…]
2:01 PM Ticket #8025 (Small molecule CIF) closed by Eric Pettersen
duplicate: Duplicate of #4479 -- will add Kristen to recipient list for that ticket
1:14 PM Ticket #8031 (Incorrect element column in PDB file) created by kristen.browne@…
[…] 2.5F phyre prediction.pdb​
11:31 AM Ticket #8020 (Encode movie: Output directory does not exist) closed by Tom Goddard
duplicate: You probably are using Microsoft OneDrive which relocates your Desktop …
11:16 AM Ticket #8014 (Surface computation: cannot convert float NaN to integer) closed by Tom Goddard
nonchimerax: Probable bad PDB file with NaN atom coordinates. User opened a file …
11:14 AM Ticket #8030 (PDB file reader accepts "nan" coordinates without warning) created by Tom Goddard
A few times we have seen users open PDB files which have coordinates …
10:58 AM Ticket #8011 (Movie encoding: No space left on device) closed by Tom Goddard
nonchimerax: Making a spin movie of 180 frames, temp directory had no disk space. …
10:52 AM Ticket #8029 (non-standard C-terminal oxygen name) created by kristen.browne@…
[…] 3ZG6-SIRT6.pdb​
10:48 AM Ticket #8007 (Picking: Singular matrix) closed by Tom Goddard
nonchimerax: Opened 7ud4.pdb then "sym #1 biomt" then mouse over causes an error …
10:33 AM Ticket #8028 (microheterogeneity) created by kristen.browne@…
[…] 4gfh.pdb​
10:29 AM Ticket #8027 (Add "save image" context menu entry for AlphaFold PAE plots) closed by Tom Goddard
fixed: Added to daily build, not in 1.5.
10:27 AM Ticket #8027 (Add "save image" context menu entry for AlphaFold PAE plots) created by goddard@…
[…]
10:19 AM Ticket #8018 (Crash showing Rapid Access at startup) closed by Eric Pettersen
can't reproduce
10:09 AM Ticket #8026 (sqm failure on all-nonstandard nucleic acid) created by kristen.browne@…
[…]
9:44 AM Ticket #8008 (ISOLDE: dead Structure model) closed by Tristan Croll
fixed: ... what. Why on earth would a user be installing ISOLDE into ChimeraX …
9:42 AM Ticket #8012 (Crash using File→Save on Windows and/or in return statement) closed by Eric Pettersen
can't reproduce: Hi Andrew, We believe this problem is fixed in the latest release of …
9:35 AM Ticket #8009 (ISOLDE: dead Structure model) closed by Eric Pettersen
duplicate: Same as #8008, except additional follow-on errors.
9:26 AM Ticket #8025 (Small molecule CIF) created by kristen.browne@…
[…] 168875.cif​
9:22 AM Ticket #8003 (Crash adjusting window sizes) closed by Eric Pettersen
can't reproduce: Hi Chai, Thanks for reporting this problem. From the code traceback, …
9:21 AM Ticket #8024 (PubChem: #charges != #atoms) created by kristen.browne@…
[…]
9:11 AM Ticket #8023 (All white coulombic) created by kristen.browne@…
[…] NTD_CCD_CTD_pymol_1-coot-0_modified.pdb​
9:06 AM Ticket #8022 (Bad residue names from Mol2 file) created by kristen.browne@…
[…] CCR5.mol2​
9:01 AM Ticket #8021 (Coulombic all white) created by kristen.browne@…
[…] dyn1_dimer.pdb​
8:46 AM Ticket #8020 (Encode movie: Output directory does not exist) created by zhf4001@…
[…]
7:15 AM Ticket #8019 (Bad alternate locations) created by kristen.browne@…
[…] out_15898.pdb​
4:46 AM Ticket #8018 (Crash showing Rapid Access at startup) created by chimerax-bug-report@…
[…]
4:12 AM Ticket #8017 (Clipper: Spgr_descr: No such HM symbol) created by chimerax-bug-report@…
[…]
4:12 AM Ticket #8016 (Clipper: Unrecognised space group string (empty string)) created by chimerax-bug-report@…
[…]

Nov 13, 2022:

2:58 PM Ticket #8015 ('DICOMBrowserTool' object has no attribute '_see_what_happened') created by henriquecsj@…
[…]
10:22 AM Ticket #8014 (Surface computation: cannot convert float NaN to integer) created by chimerax-bug-report@…
[…]

Nov 12, 2022:

2:59 PM Ticket #8013 (Compare alphafold database structure conformations for all sequences ...) created by Tom Goddard
It might be informative to see the different conformations AlphaFold …
1:25 PM Ticket #8012 (Crash using File→Save on Windows and/or in return statement) created by anmugo@…
[…]
11:46 AM Ticket #8011 (Movie encoding: No space left on device) created by chimerax-bug-report@…
[…]
8:23 AM Ticket #8010 (Image stack:tuple index out of range) created by dakoner@…
[…]
1:07 AM Ticket #8009 (ISOLDE: dead Structure model) created by chimerax-bug-report@…
[…]
1:06 AM Ticket #8008 (ISOLDE: dead Structure model) created by chimerax-bug-report@…
[…]

Nov 11, 2022:

5:47 PM Ticket #7725 (Update to AlphaFold database version 4) closed by Tom Goddard
fixed: Fixed in 1.5 and daily build. I've updated the alphafold and …
5:28 PM ChangeLog edited by Tom Goddard
(diff)
5:27 PM ChangeLog edited by Tom Goddard
(diff)
5:19 PM ChangeLog edited by Tom Goddard
(diff)
2:36 PM Ticket #8007 (Picking: Singular matrix) created by chimerax-bug-report@…
[…]
1:51 PM Ticket #8006 (Improve granularity of webservice poll timing) created by Tom Goddard
We use client-side polling to determine when webservice jobs are …
12:58 PM Ticket #7984 (Segger: Color array dimension 3 must be one more than index array ...) closed by Tom Goddard
fixed
12:50 AM Ticket #7976 (Toolshed upload internal server error) closed by Greg Couch
fixed: I put a fix in, please try uploading again and confirm that it works. …

Nov 10, 2022:

6:29 PM 2022-11-10 edited by Tom Goddard
(diff)
6:25 PM Ticket #8005 (Make a mouse mode to extract non-axis aligned volume subregions) created by Tom Goddard
For extracting features from electron tomograms it is useful to drag a …
6:16 PM NIAID2022 edited by Tom Goddard
(diff)
6:15 PM NIAID2022 edited by Tom Goddard
(diff)
6:07 PM Ticket #7989 (Graphics crash, macOS 12.4, Intel Iris Plus Graphics 645) closed by Tom Goddard
nonchimerax: Apple Intel graphics driver crash.
5:43 PM Ticket #8004 (ChimeraX sometimes very slow to start) created by Tom Goddard
ChimeraX sometimes takes 30 seconds to a minute to startup. We should …
5:38 PM Ticket #8003 (Crash adjusting window sizes) created by chai.gopalasingam@…
[…]
5:30 PM Ticket #7801 (Out of memory opening 7f1q) closed by Greg Couch
can't reproduce
5:08 PM Ticket #8002 (Blast error searching Alphafold database version 4) closed by Tom Goddard
duplicate
5:07 PM Ticket #8002 (Blast error searching Alphafold database version 4) reopened by Tom Goddard
5:05 PM Ticket #8002 (Blast error searching Alphafold database version 4) closed by Tom Goddard
duplicate: Testing alphafold database version 4 blast search for ticket #7725. …
4:45 PM Ticket #8002 (Blast error searching Alphafold database version 4) created by goddard@…
[…]
3:22 PM Ticket #7988 (chimerax.add_charge.settings missing) closed by Eric Pettersen
fixed: Yay!
3:19 PM Ticket #8001 (H-bonds: More than 2 coplanar positions specified) closed by Eric Pettersen
not a bug: Hi Phil, It looks like several residues are missing alternate …
3:05 PM Ticket #8000 (Crash showing Rapid Access at startup) closed by Eric Pettersen