![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Dec 18, 2022:
- 11:12 PM Ticket #8215 (Linux: QAccessibleTree::indexFromLogical: invalid index) created by
- […]
- 1:54 AM Ticket #8214 (ChimeraX deb compatible with Debian?) created by
- […] smime.p7s
Dec 16, 2022:
- 11:37 PM Ticket #8213 (Linux: QAccessibleTable::indexOfChild invalid child) created by
- […]
- 4:20 PM Ticket #8212 (Can two AlphaFold predictions be run at the same time with Colab Pro) created by
- Rayees Mattoo asked this on the chimerax user mailing list. I found …
- 12:25 PM Ticket #8211 (Error running second AlphaFold job before first completes) created by
- […]
- 12:17 PM Ticket #8210 (Crash running two AlphaFold predictions in two ChimeraX instances) created by
- […] crash_report.txt
- 12:06 PM Ticket #8209 (Graphics crash, macOS 12.5.1, Intel Iris Graphics 6100) created by
- […]
- 10:47 AM Ticket #8194 (chimerax.build_structure.bond.CreateBondError: Must specify two or ...) closed by
- fixed: Okay, I have submitted a pull request that "fixes" this problem. I …
- 10:10 AM Ticket #8208 (Session restore: rotamer model not child of parent) created by
- […]
- 10:06 AM Ticket #8207 (Fake Atom Error) created by
- […] 4hhb-max-hemoglobin.pdb …
- 9:49 AM Ticket #8205 (Abort from Qt) closed by
- can't reproduce
- 9:43 AM Ticket #8200 (Hydrogen bonded to atom that should not have hydrogens) closed by
- not a bug
- 6:56 AM Ticket #8206 (hbonds: acc_phi_psi() takes 8 positional arguments but 10 were given) created by
- […]
- 6:47 AM Ticket #8205 (Abort from Qt) created by
- […]
- 3:28 AM Ticket #8204 ('close' after paused simulation: 'AtomicStructure' object has no ...) created by
- […]
Dec 15, 2022:
- 4:51 PM Ticket #8199 (TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given) closed by
- fixed: Okay, bundle now does not check H-bonds as part of hydrogen addition. …
- 4:24 PM 2022-12-15 edited by
- (diff)
- 3:22 PM Ticket #8201 (Save mouse undo info: models is None) closed by
- fixed: Appears that the user was using rotate selected models mouse mode, …
- 2:00 PM Ticket #8203 (Save mouse undo info: models is None) closed by
- duplicate
- 1:59 PM Ticket #8202 (Save mouse undo info: models is None) closed by
- duplicate
- 1:52 PM Ticket #8197 (mmCIF: 'SaveOptionsWidget' object has no attribute 'compute_sheets') closed by
- duplicate
- 1:41 PM Ticket #8191 (AttributeError: 'SeqCanvas' object has no attribute 'lead_block') closed by
- can't reproduce: I can't figure out a scenario where a redraw occurs before the initial …
- 11:57 AM Ticket #8203 (Save mouse undo info: models is None) created by
- […]
- 11:56 AM Ticket #8202 (Save mouse undo info: models is None) created by
- […]
- 11:56 AM Ticket #8201 (Save mouse undo info: models is None) created by
- […]
- 11:23 AM Ticket #8200 (Hydrogen bonded to atom that should not have hydrogens) created by
- […]
- 11:11 AM Ticket #8199 (TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given) created by
- […]
- 11:07 AM Ticket #8198 (Index Error: list index out of range) created by
- […] HAG1.pdb
- 10:57 AM Ticket #8197 (mmCIF: 'SaveOptionsWidget' object has no attribute 'compute_sheets') created by
- […]
- 10:44 AM Ticket #8189 (TimeoutError fetching version information) closed by
- can't reproduce: Possibly due to the period of plato downtime yesterday.
- 10:39 AM Ticket #8196 (Volume disappears) created by
- […] emd_7037_0 (1).map
- 10:12 AM Ticket #8195 (raise ValueError("z_align endpoints must be distinct")) created by
- […] MARCpeptide.mol2
- 9:45 AM Ticket #8194 (chimerax.build_structure.bond.CreateBondError: Must specify two or ...) created by
- […]
- 9:11 AM Ticket #8193 (Ribbon structure missing) created by
- […] [[Image(...)]] [[Image(...)]]
- 2:19 AM Ticket #8192 (Update coordinates: RuntimeError: Release Object) created by
- […]
- 12:18 AM Ticket #8191 (AttributeError: 'SeqCanvas' object has no attribute 'lead_block') created by
- […]
Dec 14, 2022:
- 5:13 PM Ticket #8190 (Have web services use HTTPS proxy if set) created by
- Though cxservices supports a proxy_url, chimerax.webservices makes no …
- 3:54 PM Ticket #8189 (TimeoutError fetching version information) created by
- […]
- 1:25 PM Ticket #8180 (Restore new session in old ChimeraX) closed by
- limitation: Yes, you would need to upgrade your Mac or use another (newer) Mac to …
- 1:07 PM Ticket #8188 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 1:01 PM Ticket #8188 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 12:06 PM Ticket #8186 (Crash in event loop possibly saving large image) closed by
- can't reproduce: I'd guess it is an Apple Intel graphics driver crash. The image being …
- 12:04 PM Ticket #8184 (Crash in ses_surface_geometry) closed by
- duplicate: Tried to compute SES surface for 500,000 or more atoms and machine …
- 11:57 AM Ticket #8185 (Unable to open file for writing) closed by
- not a bug: User probably in non-writable folder
- 11:36 AM Ticket #7577 (Atomspec /A-B sometimes orders chains B,A breaking commands where ...) closed by
- fixed: I looked at fixing this "generically" (i.e. any /A-F atom spec comes …
- 11:31 AM Ticket #8187 (put flatpak build for the generic Linux release in daily builds) created by
- We currently create packages RHEL 8/9 and Ubuntu 20.04/22.04. That …
- 6:05 AM Ticket #8186 (Crash in event loop possibly saving large image) created by
- […]
- 3:04 AM Ticket #8185 (Unable to open file for writing) created by
- […]
- 1:47 AM Ticket #8184 (Crash in ses_surface_geometry) created by
- […]
Dec 13, 2022:
- 6:21 PM Ticket #8183 (Volume image opacity is too sensitive where brightness curve is near ...) created by
- […]
- 5:14 PM Ticket #7999 (Marker operations don't work through transparent surfaces) closed by
- fixed: Fixed. Picking markers was not ignoring transparent surfaces.
- 4:52 PM Ticket #8165 (EMDB quicksubmit (database id) to NIH 3D failing: wwpdb mirror missing file) closed by
- fixed: Okay, I added a fallback to EMDB Europe and have submitted it as a …
- 1:25 PM Ticket #8167 (Matchmaker behavior changed) closed by
- fixed: Okay, this is fixed now and your script will work the same as 1.4 in …
- 1:08 PM Ticket #8182 (Update AlphaFold prediction to use version 2.3.0 which handles larger ...) created by
- The AlphaFold 2.3.0 release made December 13, 2022 has memory …
- 11:44 AM 2022-12-15 created by
- 11:43 AM DeveloperMeetings edited by
- (diff)
- 11:38 AM Ticket #8178 (Picking: numpy.linalg.LinAlgError: Singular matrix) closed by
- fixed: Fixed. The error is because a tether cone had a singular matrix …
- 10:48 AM Ticket #8180 (Restore new session in old ChimeraX) reopened by
- I find this slightly perplexing. If 1.4 actually crashes, then the …
- 10:23 AM Ticket #8181 (Restore new session in old ChimeraX) closed by
- duplicate: Duplicate of #8180
- 9:42 AM Ticket #8180 (Restore new session in old ChimeraX) closed by
- limitation: Hi, Though old sessions are guaranteed to restore in newer versions …
- 9:38 AM Ticket #8179 (Crash opening mmCIF) closed by
- can't reproduce
- 9:12 AM Ticket #8181 (Restore new session in old ChimeraX) created by
- […]
- 8:42 AM Ticket #8180 (Restore new session in old ChimeraX) created by
- […]
- 3:02 AM Ticket #8179 (Crash opening mmCIF) created by
- […]
- 12:59 AM Ticket #8178 (Picking: numpy.linalg.LinAlgError: Singular matrix) created by
- […]
- 12:49 AM Ticket #8177 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by
- […]
Dec 12, 2022:
- 6:00 PM Ticket #8176 (Drag model mouse mode does not work on volume tilted slab) closed by
- fixed: Fixed. Mouse intercept was only being computed for image style region …
- 5:43 PM Ticket #8176 (Drag model mouse mode does not work on volume tilted slab) created by
- […]
- 4:44 PM Dev2022-12-12 edited by
- (diff)
- 4:42 PM Dev2022-12-12 edited by
- (diff)
- 4:41 PM Dev2022-12-12 edited by
- (diff)
- 4:31 PM ChangeLog edited by
- (diff)
- 4:31 PM ChangeLog edited by
- (diff)
- 2:41 PM Ticket #8142 (Qt shim broken in Dec 6 daily builds) closed by
- fixed: Fixed Linux daily builds. There were two problems. One was the PyQt …
- 2:38 PM Ticket #8175 (Linux CentOS 8 import test fails, cannot import libQt6Core.so) created by
- The CentOS 8 daily builds fails importing many modules because …
- 2:33 PM Ticket #8174 (Broken linux daily builds installed when prereq wheels fail to sync to ...) created by
- The Linux daily builds were put on the download page even when syncing …
- 2:29 PM Ticket #8173 (Linux daily build is released even when PyQt install fails) created by
- The Linux daily builds ended up on the download page even though PyQt …
- 2:29 PM Ticket #8171 (Modeller not keeping all requested residues frozen) closed by
- fixed: Okay, this is fixed in both and will be in tomorrow's daily build for …
- 2:22 PM Dev2022-12-12 edited by
- (diff)
- 2:20 PM Dev2022-12-12 created by
- 2:19 PM DeveloperMeetings edited by
- (diff)
- 1:11 PM Ticket #8172 (Read MOLE format: KeyError: 'Channels') closed by
- fixed: The user tried to open a PubChem 3D structure file in JSON format. …
- 12:29 PM Ticket #8172 (Read MOLE format: KeyError: 'Channels') created by
- […]
- 11:29 AM Ticket #8171 (Modeller not keeping all requested residues frozen) created by
- Problem exists in both ChimeraX and Chimera. Fix in ChimeraX first …
- 11:23 AM Ticket #8168 (numpy: Windows fatal exception: access violation) closed by
- wontfix: In old version of ChimeraX. numpy is version 1.21.2. Upgrading numpy …
- 10:56 AM Ticket #8160 (Web services not returning output) closed by
- fixed: This is happening because the clustalo webservice is writing files …
- 10:54 AM Ticket #8169 (Check Waters referencing dead pseudobond group?) closed by
- fixed: Close the tool if the user independently closes the H-bond groups, …
- 9:55 AM Ticket #8166 (Graphic crash, macOS 11.2.3, Intel HD Graphics 6000) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 9:54 AM Ticket #8161 (Crash saving PNG) closed by
- can't reproduce: This crash in Pillow saving the image file has been reported several …
- 9:25 AM Ticket #8164 (Crash opening PDB) closed by
- can't reproduce
- 9:24 AM Ticket #8163 (Crash opening PDB) closed by
- can't reproduce
- 9:10 AM Ticket #8159 (Restore new session in old ChimeraX) closed by
- limitation
- 9:09 AM Ticket #8158 (Restore new session in old ChimeraX) closed by
- not a bug
- 8:54 AM Ticket #8170 (Files should use symmetry information if available) created by
- […]
- 7:21 AM Ticket #8169 (Check Waters referencing dead pseudobond group?) created by
- […]
Dec 11, 2022:
Dec 10, 2022:
Dec 9, 2022:
- 4:07 PM Ticket #8154 (ImportError: libGLU.so.1: cannot open shared object file: No such file ...) closed by
- limitation: You are running CentOS 7. My guess is that you tried to install the …
- 3:45 PM Ticket #8166 (Graphic crash, macOS 11.2.3, Intel HD Graphics 6000) created by
- […]
- 3:05 PM Ticket #8157 (Installing Linux ChimeraX daily build gives: Custom initialization of ...) closed by
- can't reproduce: OK, hopefully this was fixed as part of the other build system …
- 3:04 PM Ticket #7173 (RFE: Get optional dependencies from the Toolshed and/or pip) closed by
- fixed: Just wanted to give everyone the opportunity to object to its closure, …
- 12:53 PM Ticket #7426 (BlastProtein giving a warning when an error should be reported) closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/93c299d5784ca0177115de60337042 …
- 12:28 PM Ticket #8165 (EMDB quicksubmit (database id) to NIH 3D failing: wwpdb mirror missing file) created by
- […]
- 10:13 AM Ticket #8164 (Crash opening PDB) created by
- […]
- 10:03 AM Ticket #8163 (Crash opening PDB) created by
- […]
- 9:12 AM Ticket #8162 (AttributeError: 'BlastProteinFormWidget' object has no attribute ...) closed by
- fixed
- 8:44 AM Ticket #8162 (AttributeError: 'BlastProteinFormWidget' object has no attribute ...) created by
- […]
- 7:04 AM Ticket #8161 (Crash saving PNG) created by
- […]
- 3:14 AM Ticket #8160 (Web services not returning output) created by
- […]
- 2:40 AM Ticket #5055 (Allow BLAST gui to use a sequence viewer id and direct sequence input) closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/55298924d24c067dc83112c6d0826a …
- 1:30 AM Ticket #8159 (Restore new session in old ChimeraX) created by
- […]
- 1:29 AM Ticket #8158 (Restore new session in old ChimeraX) created by
- […]
Dec 8, 2022:
- 7:59 PM Ticket #8157 (Installing Linux ChimeraX daily build gives: Custom initialization of ...) created by
- [[Image]]{{{ The following bug report has been submitted: Platform: …
- 5:45 PM Ticket #8038 (Compressed .cif without .gz suffix) closed by
- limitation: Didn't hear any squawking, so assuming the status quo is okay.
- 5:09 PM Ticket #8133 (printable ribbon: "No atoms specifified" error) closed by
- fixed: Fixed by removing the @@num_atoms<500 restriction from the struts atom spec
- 5:06 PM Ticket #8138 (Fatal error: maxassem 1 has no models in it) closed by
- limitation: It was decided to use the updated versions of these entries.
- 3:17 PM NIAID2022 edited by
- (diff)
- 2:54 PM Ticket #8148 (Dead Structure Measurement tool trying to show status) closed by
- fixed
- 2:49 PM Ticket #8156 (silhouettes → tiny boxes) closed by
- nonchimerax: The incorrect silhouette edge display in ChimeraX is caused by …
- 2:44 PM Ticket #8155 (Crash saving PNG) closed by
- can't reproduce: Crash is in PIL writing image file in old ChimeraX. Have seen it …
- 2:38 PM NIAID2022 edited by
- (diff)
- 2:37 PM NIAID2022 edited by
- (diff)
- 2:35 PM Ticket #8152 (Crash in QMainWindow::removeDockWidget) closed by
- can't reproduce
- 2:34 PM Ticket #8149 (Crash in event loop after volume step 1 on .mtz data) closed by
- can't reproduce: C++ stack trace has no useful info.
- 2:32 PM Ticket #8151 (Crash creating QWebEngineProfile at startup) closed by
- duplicate
- 2:32 PM Ticket #8150 (Crash with segidChains true) closed by
- duplicate: Duplicate of #8118
- 2:26 PM Ticket #8147 (Unknown crash) closed by
- can't reproduce: Run directly from .dmg
- 2:07 PM NIAID2022 edited by
- (diff)
- 2:02 PM NIAID2022 edited by
- (diff)
- 2:01 PM Ticket #8156 (silhouettes → tiny boxes) created by
- […] Screen Shot 2022-12-08 at 2.01.40 PM.png
- 1:54 PM NIAID2022 edited by
- (diff)
- 1:18 PM Ticket #8155 (Crash saving PNG) created by
- […]
- 12:03 PM Ticket #8145 (Crash in QMainWindow::removeDockWidget) closed by
- can't reproduce: According to the Python stack trace, ToolInstance.delete() is being …
- 11:51 AM WikiStart edited by
- (diff)
- 11:40 AM Ticket #8154 (ImportError: libGLU.so.1: cannot open shared object file: No such file ...) created by
- […]
- 11:39 AM 2022-12-8 edited by
- (diff)
- 11:06 AM Ticket #8153 (Atoms lost reading pdbe_bio file, atoms not grouped by model in mmCIF file) created by
- open pdbe_bio:2MIV maxAssemblies 1 autoStyle false loses the nucleic …
- 8:19 AM Ticket #8152 (Crash in QMainWindow::removeDockWidget) created by
- […]
- 8:18 AM Ticket #8151 (Crash creating QWebEngineProfile at startup) created by
- […]
- 7:26 AM Ticket #8150 (Crash with segidChains true) created by
- […]
- 2:51 AM Ticket #8149 (Crash in event loop after volume step 1 on .mtz data) created by
- […]
Dec 7, 2022:
- 6:22 PM Ticket #8076 (Unnecessary restart required when new file formats installed) closed by
- 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
- Adding or rewording labels is fine. Is there a particular reason other …
- 1:24 PM ChangeLog edited by
- (diff)
- 12:57 PM Ticket #8148 (Dead Structure Measurement tool trying to show status) created by
- […]
- 12:45 PM Ticket #8147 (Unknown crash) created by
- […]
- 11:38 AM Ticket #8146 (Testing that Mac ARM platform is reported on M1 Macs with ChimeraX 1.5 ...) closed by
- 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
- […]
- 10:31 AM Ticket #8145 (Crash in QMainWindow::removeDockWidget) created by
- […]
- 9:56 AM Ticket #8144 (Crash showing Rapid Access at startup) closed by
- can't reproduce: Linux
- 9:54 AM Ticket #8143 (Crash running modal dialog) closed by
- can't reproduce
- 9:52 AM Ticket #8141 (Crash showing Rapid Access at startup) closed by
- can't reproduce: Linux
- 9:52 AM Ticket #8140 (Crash showing Rapid Access at startup) closed by
- can't reproduce
- 9:20 AM Ticket #8144 (Crash showing Rapid Access at startup) created by
- […]
- 4:54 AM Ticket #8143 (Crash running modal dialog) created by
- […]
- 1:59 AM Ticket #8142 (Qt shim broken in Dec 6 daily builds) created by
- Trying to launch ChimeraX daily just gives a traceback: NOTE: …
- 12:40 AM Ticket #8141 (Crash showing Rapid Access at startup) created by
- […]
- 12:38 AM Ticket #8140 (Crash showing Rapid Access at startup) created by
- […]
Dec 6, 2022:
- 1:49 PM Ticket #8074 (After other presets: Nonstandard name for heavy atom) closed by
- nonchimerax: The RCSB is correcting this entry.
- 1:47 PM Ticket #8112 (sequence layout: list index out of range) closed by
- can't reproduce
- 1:31 PM Ticket #8139 (Missing bond) created by
- […]
- 12:22 PM Ticket #8138 (Fatal error: maxassem 1 has no models in it) created by
- […]
- 12:11 PM Ticket #8137 (1.5 not starting) closed by
- 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
- […] startlog.txt
- 11:30 AM Ticket #8136 (Toolshed search does not find some bundles) closed by
- fixed: Fixed.
- 10:57 AM Ticket #8135 (Crash in event loop) closed by
- can't reproduce
- 10:54 AM Ticket #8134 (Crash showing Rapid Access at startup) closed by
- can't reproduce: Hi David, Thanks for reporting this problem. We recommend upgrading …
- 10:23 AM 2022-12-8 created by
- 10:21 AM DeveloperMeetings edited by
- (diff)
- 10:20 AM Ticket #8132 (Old presets) closed by
- duplicate
- 10:19 AM Ticket #8128 (Crash in QWindowSystemInterface::handleScreenRemoved) closed by
- 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
- Using the search field, searching for "phenix" or "phenixui" does not …
- 7:09 AM Ticket #8135 (Crash in event loop) created by
- […]
- 5:37 AM Ticket #8134 (Crash showing Rapid Access at startup) created by
- […]
- 5:16 AM Ticket #8133 (printable ribbon: "No atoms specifified" error) created by
- […] pdb1bfp_0.ent
- 12:57 AM Ticket #8117 (Crash in OpenMM find_clashing_atoms()) closed by
- 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
- […]
- 4:20 PM Dev2022-12-5 edited by
- (diff)
- 4:20 PM Dev2022-12-5 edited by
- (diff)
- 4:13 PM Dev2022-12-5 edited by
- (diff)
- 3:11 PM Dev2022-12-5 edited by
- (diff)
- 3:05 PM Dev2022-12-5 edited by
- (diff)
- 3:04 PM Ticket #8131 (SDF charge Index out of bounds) created by
- […] Furfural aminoguanidine bicarbonate.sdf
- 3:03 PM Dev2022-12-5 created by
- 3:01 PM DeveloperMeetings edited by
- (diff)
- 1:52 PM Ticket #8130 ('VolumeViewer' object has no attribute 'tool_window') closed by
- 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
- 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
- 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
- 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
- […]
- 12:58 PM Ticket #8127 (Crash showing Rapid Access at startup) closed by
- can't reproduce: Linux
- 12:56 PM Ticket #8126 (hbonds: More than 2 coplanar positions specified) closed by
- not a bug: Almost certainly bad connectivity
- 12:50 PM Ticket #8122 (Crash showing Rapid Access at startup) closed by
- 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
- 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
- Allow researchers to use ChimeraX virtual reality and join meetings …
- 11:27 AM Ticket #8119 (Movie encode: No space left on device) closed by
- 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
- 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
- […]
- 7:29 AM Ticket #8127 (Crash showing Rapid Access at startup) created by
- […]
Dec 4, 2022:
- 11:30 PM Ticket #8126 (hbonds: More than 2 coplanar positions specified) created by
- […]
- 9:03 PM Ticket #8125 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by
- […]
- 8:49 AM Ticket #8124 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by
- […]
- 7:29 AM Ticket #8123 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by
- […]
Dec 3, 2022:
- 9:03 PM Ticket #8122 (Crash showing Rapid Access at startup) created by
- […]
- 5:07 PM Ticket #8121 (Negative decimal places for distance format) created by
- […]
- 12:16 PM Ticket #8120 (Restore new session in old ChimeraX) created by
- […] BoNT G mutants HN.cxs
- 3:07 AM Ticket #8119 (Movie encode: No space left on device) created by
- […]
- 1:49 AM Ticket #8118 (Crash with segidChains true) created by
- […]
Dec 2, 2022:
- 11:46 PM Ticket #8117 (Crash in OpenMM find_clashing_atoms()) created by
- […]
- 4:24 PM Ticket #8110 (Wrong channel names opening second copy of 3-channel microscopy) closed by
- 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
- 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
- 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
- duplicate
- 2:20 PM Ticket #8113 (Crash in event loop) closed by
- can't reproduce
- 1:37 PM Ticket #5055 (Allow BLAST gui to use a sequence viewer id and direct sequence input) closed by
-
fixed:
seq_view… - 1:04 PM Ticket #3014 (Blast Protein tool: threading) closed by
- fixed: They do. :)
- 12:49 PM Ticket #8107 (Map→Style→Transparent surface not toggling transparency) closed by
- fixed: Fixed. Made map transparency toolbar button ignore hidden models even …
- 12:47 PM 2022-12-1 edited by
- (diff)
- 12:37 PM 2022-12-1 edited by
- (diff)
- 12:20 PM 2022-12-1 edited by
- (diff)
- 11:41 AM Ticket #8116 (Crash in QMenu::clear()) created by
- […]
- 11:03 AM Ticket #8115 (libGLU.so.1: cannot open shared object file: No such file or directory) created by
- […]
- 9:36 AM Ticket #8114 (read_xyz: elements: list index out of range) created by
- […]
- 8:09 AM ChangeLog edited by
- (diff)
- 8:08 AM ChangeLog edited by
- (diff)
Dec 1, 2022:
- 11:25 PM Ticket #8113 (Crash in event loop) created by
- […]
- 9:54 PM Ticket #8112 (sequence layout: list index out of range) created by
- […]
- 6:20 PM Ticket #8111 (AlphaFold prediction broken with energy minimization or pdb templates) closed by
- 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
- 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
- […]
- 5:15 PM Ticket #8109 (pyproject.toml-based "make install" should reinstall) created by
- 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
- 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
- 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
- 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
- fixed: [https://github.com/RBVI/ChimeraX/commit/05f11de2ccb9226f6ab3ccd5120c36 …
- 9:47 AM Ticket #8107 (Map→Style→Transparent surface not toggling transparency) created by
- […]
- 8:12 AM Ticket #8106 (Possibly provide event to double-click criteria() call) created by
- […]
- 5:01 AM Ticket #8105 (ChimeraX/lib not on library path) created by
- […]
- 1:26 AM Ticket #8104 (TmplResidue SMILES string) closed by
- fixed: Added. To get the information use …
Nov 30, 2022:
- 6:56 PM ChangeLog edited by
- (diff)
- 5:53 PM Ticket #8077 (coulombic → ribbon → coulombic: structure gone) closed by
- 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
- 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
- duplicate: Duplicate of #7774 Missing pyopenvr error code "Oculus Link Not …
- 9:56 AM ChangeLog edited by
- (diff)
- 9:55 AM ChangeLog edited by
- (diff)
- 9:55 AM ChangeLog edited by
- (diff)
- 9:53 AM ChangeLog edited by
- (diff)
- 9:35 AM Ticket #7961 (Clipper fails to build in Windows - Nov 3 release candidate) closed by
- fixed: Tristan reported this morning that his bundle builds without his …
- 8:42 AM Ticket #8102 (Crash during selection-promotion process) closed by
- can't reproduce
- 8:40 AM Ticket #8101 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce
- 8:39 AM Ticket #8100 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce
- 8:32 AM Ticket #8104 (TmplResidue SMILES string) created by
- […]
- 8:00 AM Ticket #8103 (Shell tool: Qt enum vs. int) created by
- […]
- 7:58 AM Ticket #8102 (Crash during selection-promotion process) created by
- […]
- 5:23 AM Ticket #8101 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 5:02 AM Ticket #8100 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 4:47 AM Ticket #8099 (ISOLDE: close session: 'AtomicStructure' object has no attribute ...) created by
- […]
- 2:12 AM Ticket #8098 (ISOLDE: 'AtomicStructure' object has no attribute 'session') created by
- […]
Nov 29, 2022:
- 6:54 PM Ticket #8041 (Add ESMFold database to BlastProtein) closed by
- fixed: Thanks for your patience. As you said, …
- 4:56 PM ChangeLog edited by
- (diff)
- 10:41 AM Ticket #8097 (Error initializing VR: KeyError: 1002 "Oculus Link Not Enabled") created by
- […]
- 10:40 AM Ticket #8059 (chimeraX freezing) closed by
- limitation: Yeah! Thank you for letting us know.
- 10:07 AM 2022-12-1 created by
- 10:06 AM DeveloperMeetings edited by
- (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
- can't reproduce
- 9:03 AM Ticket #8093 (Restore new session in old ChimeraX) closed by
- not a bug
- 7:37 AM Ticket #8096 (Antechamber on M2: Bad CPU type in executable) created by
- […]
- 6:48 AM Ticket #8095 (Crash in event loop) created by
- […]
- 6:20 AM Ticket #8094 (ArtiaX session save: Unknown class name 'MarkerSetPlus') created by
- […]
- 6:16 AM ChangeLog edited by
- (diff)
- 3:59 AM Ticket #8093 (Restore new session in old ChimeraX) created by
- […]
Nov 28, 2022:
- 5:39 PM ChangeLog edited by
- (diff)
- 3:56 PM Ticket #8092 (Reading 2D ImageJ microscopy: IndexError: index out of range) closed by
- 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
- […]
- 3:41 PM Dev2022-11-28 edited by
- (diff)
- 3:40 PM Dev2022-11-28 edited by
- (diff)
- 3:38 PM Dev2022-11-28 edited by
- (diff)
- 3:36 PM Dev2022-11-28 created by
- 3:34 PM DeveloperMeetings edited by
- (diff)
- 3:00 PM Ticket #8086 (AlphaFold predict: ValueError: could not broadcast input array from shape) closed by
- 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
- duplicate: Duplicate of #8059
- 2:13 PM Ticket #8090 (Graphics crash, macOS 12.4, Intel Iris Plus Graphics 645) closed by
- nonchimerax: Apple Intel graphics driver crash
- 1:40 PM Ticket #8091 (UniProt fetch: HTTP Error 405: Not Allowed) closed by
- 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
- nonchimerax: Apple Intel graphics driver crash.
- 1:30 PM Ticket #8088 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 1:29 PM Ticket #8087 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 1:24 PM Ticket #8085 (Modeller target is None) closed by
- 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
- duplicate
- 1:09 PM Ticket #8082 (Volume not in Surface Color volume menu) closed by
- 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
- can't reproduce
- 1:48 AM Ticket #8091 (UniProt fetch: HTTP Error 405: Not Allowed) created by
- […] 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
- […]
- 2:17 AM Ticket #8089 (Clipper: AttributeError: 'NoneType' object has no attribute ...) created by
- […]
- 2:03 AM Ticket #8088 (Crash using File→Open on Windows and/or in return statement) created by
- […]
Nov 25, 2022:
- 11:08 PM Ticket #8070 (libGLU.so.1: cannot open shared object file: No such file or directory) closed by
- 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
- […]
- 9:57 AM Ticket #8086 (AlphaFold predict: ValueError: could not broadcast input array from shape) created by
- […] Screen Shot 2022-11-25 at 10.53.39 AM.png
- 8:42 AM Ticket #8085 (Modeller target is None) created by
- […]
- 7:32 AM Ticket #8084 (Crash during screen changed) created by
- […]
Nov 24, 2022:
- 7:53 AM Ticket #8083 (ISOLDE session restore: 'AtomicStructure' object has no attribute 'session') created by
- […]
- 7:41 AM Ticket #8082 (Volume not in Surface Color volume menu) created by
- […]
- 4:51 AM Ticket #8081 (Graphics crash, macOS 10.15.7, NVIDIA GeForce GTX 780M) created by
- […]
- 3:25 AM Ticket #8080 (Crash repeating "style ball" command) created by
- […]
Nov 23, 2022:
- 9:45 PM Ticket #8079 (Crash in event loop) created by
- […]
- 5:58 PM ChangeLog edited by
- (diff)
- 4:07 PM Ticket #8078 (DICOM tools: please hook up help to context menu) closed by
- fixed: I also cherry-picked your documentation changes into the release branch.
- 3:13 PM Ticket #3014 (Blast Protein tool: threading) reopened by
- 1:44 PM Ticket #8073 (Could not come up with unique atom name in mega-residue) closed by
- 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
- DICOM tools look good, just need to hook documentation up to context …
- 11:19 AM Ticket #8077 (coulombic → ribbon → coulombic: structure gone) created by
- […]
- 9:20 AM Ticket #8071 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 9:09 AM Ticket #8076 (Unnecessary restart required when new file formats installed) created by
- e.g. when SEQCROW installed to read .xyz files
- 7:51 AM Ticket #8075 (Printable ribbon preset hangs) created by
- […]
- 7:41 AM Ticket #8074 (After other presets: Nonstandard name for heavy atom) created by
- […]
- 6:50 AM Ticket #8073 (Could not come up with unique atom name in mega-residue) created by
- […]
Nov 22, 2022:
- 5:20 PM Ticket #8072 (AlphaFold coloring panel does not list AlphaFold models in menu) closed by
- 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
- […]
- 4:31 PM Ticket #8056 (Problem opening Gaussian output: Unknown element detected: Variables) closed by
- fixed
- 3:14 PM Ticket #8071 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 2:35 PM Ticket #8070 (libGLU.so.1: cannot open shared object file: No such file or directory) created by
- […]
- 1:42 PM Ticket #8069 (BlastProtein: cannot import name '_log_alphafold_sequence_info') closed by
- 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
- […]
- 11:35 AM Ticket #8068 (Make selection, coloring, mesh and dot styles work on BILD models) created by
- 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
- […]
- 9:35 AM Ticket #8052 (limit formats in Save dialog to ones appropriate for current models) closed by
- wontfix: Given that, as Tom points out, there may be as many downsides as …
- 9:20 AM Ticket #8066 (saving attribute values) closed by
- fixed: Hi Björn, Thanks for reporting this problem. The problem is that the …
- 3:27 AM Ticket #8066 (saving attribute values) created by
- […]
Nov 21, 2022:
- 6:59 PM Ticket #6774 (Unknown crash) closed by
- 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
- 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
- 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
- fixed: I increased the number of notarization retries from 1 to 4 and …
- 6:51 PM Ticket #7417 ("cofr" info misleading) closed by
- limitation
- 6:50 PM Ticket #7428 (Inconsistent stack trace information) closed by
- 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
- 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
- nonchimerax
- 6:41 PM Ticket #7739 (QPainter::begin: Paint device returned engine == 0, type: 2) closed by
- can't reproduce
- 6:40 PM Ticket #7878 ('show' unexpectedly showing whole chains) closed by
- can't reproduce: No reply from reporter.
- 6:38 PM Ticket #8010 (Image stack:tuple index out of range) closed by
- 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
- 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
- […]
- 4:44 PM Ticket #8015 ('DICOMBrowserTool' object has no attribute '_see_what_happened') closed by
- fixed: Should be fixed in tomorrow's daily build and release candidate.
- 2:42 PM Ticket #8019 (Bad alternate locations) closed by
- 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
- fixed
- 1:25 PM Ticket #8055 (AlphaFold: I/O operation on closed file) reopened by
- 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
- […]
- 10:30 AM Ticket #8063 (Crash running AlphaFold prediction) closed by
- can't reproduce
- 10:29 AM Ticket #8062 (Status bar: wrapped C/C++ object of type QScreen has been deleted) closed by
- 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
- 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
- not a bug: Not a trajectory (self.atomLocations only set on ENDMDL record).
- 10:19 AM Ticket #8063 (Crash running AlphaFold prediction) created by
- […]
- 9:29 AM Ticket #8060 (crash running modal dialog) closed by
- can't reproduce
- 9:26 AM Ticket #8058 (Crash using File→Open on Windows and/or in return statement) closed by
- 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
- duplicate
- 9:14 AM Ticket #8054 (Crash processing geometry change) closed by
- can't reproduce
- 9:12 AM Ticket #8053 (Crash creating QTimer) closed by
- can't reproduce
- 8:58 AM Ticket #8050 (Crash in event loop) closed by
- can't reproduce
- 6:10 AM Ticket #8062 (Status bar: wrapped C/C++ object of type QScreen has been deleted) created by
- […]
- 5:43 AM Ticket #8061 (MD viewer: No self.atomLocations) created by
- […]
- 3:03 AM Ticket #8060 (crash running modal dialog) created by
- […]
- 2:51 AM Ticket #8059 (chimeraX freezing) created by
- […]
Nov 20, 2022:
- 5:47 PM Ticket #8058 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 10:58 AM Ticket #8057 (Save session: Basic Actions: 'QEventLoop' object has no attribute 'exec_') created by
- […]
Nov 19, 2022:
- 9:05 PM Ticket #8056 (Problem opening Gaussian output: Unknown element detected: Variables) created by
- […] gau_ma.h2s-opt-freq-b3lyp-d3-qzvppd.log
- 10:04 AM Ticket #8055 (AlphaFold: I/O operation on closed file) created by
- […] Screen Shot 2022-11-19 at 11.00.32 AM.png
- 7:17 AM Ticket #8054 (Crash processing geometry change) created by
- […]
- 6:45 AM Ticket #8053 (Crash creating QTimer) created by
- […]
Nov 18, 2022:
- 5:04 PM Ticket #7997 (Add Charges: Nonstandard name for heavy atom) closed by
- 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
- 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
- […]
- 10:41 AM Ticket #8049 (MemoryError saving large image) closed by
- 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
- […]
Note:
See TracTimeline
for information about the timeline view.
