![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Aug 30, 2024:
- 2:48 PM Ticket #15843 (RFE: xml2toml function in bundle builder) closed by
- fixed: Bundle builder can now perform rudimentary conversion of …
- 2:32 PM Ticket #15850 (TOML bundle builder doesn't fill out setuptools.packages properly) closed by
- fixed: Should be …
- 1:45 PM Ticket #15857 (Index out of range updating header sequence) created by
- […]
- 1:28 PM Ticket #15854 (Crash on Mac waking from sleep) closed by
- duplicate: Mac Qt 6.6 bug, crash in _NSViewHierarchyDidChangeBackingProperties. …
- 1:15 PM Ticket #15853 (Crash on Mac waking from sleep) closed by
- duplicate: Mac Qt 6.6 bug, crash in displayConfigFinalizedProc. Either plugging …
- 1:13 PM Ticket #15852 (Crash moving window between screens) closed by
- duplicate: Mac Qt 6.6 bug, crash in _NSViewHierarchyDidChangeBackingProperties.
- 1:12 PM Ticket #15849 (Morph: index out of bounds) closed by
- duplicate: Fixed. Duplicate of #15747, trying to morph using a previous morph.
- 1:08 PM Ticket #15856 (Opening PAE json file: not AlphaFold predicted aligned error data, ...) closed by
- fixed
- 1:03 PM Ticket #15856 (Opening PAE json file: not AlphaFold predicted aligned error data, ...) created by
- […]
- 11:45 AM Ticket #15855 (QKeyEvent handled as drop) closed by
- can't reproduce: The type() call on the event returned Drop, despite being a QKeyEvent.
- 11:07 AM Ticket #15855 (QKeyEvent handled as drop) created by
- […]
- 11:01 AM Ticket #15854 (Crash on Mac waking from sleep) created by
- […]
- 9:13 AM Ticket #15853 (Crash on Mac waking from sleep) created by
- […]
- 8:54 AM Ticket #15851 (Crash in garbage collection) closed by
- duplicate
- 8:41 AM Ticket #15848 (Crash in event loop) closed by
- can't reproduce: Hi Moon, Thanks for reporting this problem. It's not really clear …
- 5:17 AM Ticket #15852 (Crash moving window between screens) created by
- […]
- 3:35 AM Ticket #15851 (Crash in garbage collection) created by
- […]
- 2:16 AM Ticket #15850 (TOML bundle builder doesn't fill out setuptools.packages properly) created by
- When building arrays to double check that bundle builder's new …
Aug 29, 2024:
- 7:58 PM ChangeLog edited by
- (diff)
- 7:07 PM Ticket #15849 (Morph: index out of bounds) created by
- […]
- 6:53 PM Ticket #15848 (Crash in event loop) created by
- […]
- 6:32 PM Ticket #15847 (Graphics crash, macOS 13.6.9, Intel UHD Graphics 617) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 4:23 PM Ticket #15840 (addh slow) closed by
- fixed: Some recent-ish code in Residue.add_atom() to possibly adjust …
- 4:22 PM Ticket #15847 (Graphics crash, macOS 13.6.9, Intel UHD Graphics 617) created by
- […]
- 3:38 PM Ticket #15846 (How can the ChimeraX VR coordinates be aligned for 2-person VR with ...) created by
- In the past a two person VR meeting with both headsets in the same …
- 3:17 PM Ticket #15844 (RE: Bug and unable to report) closed by
- can't reproduce: I'm not sure what you mean by "ChimeraX -1.8 is unable to show the …
- 3:13 PM Ticket #15842 (Graphics crash, macOS 14.6.1, Intel Iris Plus Graphics) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 3:12 PM Ticket #15841 (Crash on Mac waking from sleep) closed by
- duplicate: Mac Qt 6.6 crash in _NSViewHierarchyDidChangeBackingProperties, …
- 3:06 PM Ticket #15845 (Test) closed by
- not a bug: Testing bug reporting (really website availability)
- 2:24 PM 2024-8-29 edited by
- (diff)
- 2:23 PM Ticket #15845 (Test) created by
- […]
- 2:18 PM Ticket #15844 (RE: Bug and unable to report) created by
- […] [[Image(...)]] [[Image(...)]]
- 2:07 PM Ticket #15836 (Crash on Mac waking from sleep) closed by
- duplicate: Qt 6.6 bug. Crash in _NSViewHierarchyDidChangeBackingProperties.
- 1:54 PM NIAID2024 edited by
- (diff)
- 1:33 PM NIAID2024 edited by
- (diff)
- 11:12 AM Ticket #15843 (RFE: xml2toml function in bundle builder) created by
- It would be good if bundle builder could use bundle_builder_toml for …
- 10:52 AM Ticket #15835 (Issue Launching ChimeraX) closed by
- nonchimerax: The ChimeraX crash is very likely caused by your current broken …
- 10:50 AM Ticket #15839 ('AtomicStructure' object has no attribute '_alt_loc_changes_handler') closed by
- duplicate
- 10:48 AM Ticket #15838 ('AtomicStructure' object has no attribute '_alt_loc_changes_handler') closed by
- duplicate: Hi Jae-Hun, Thanks for reporting this problem. It is fixed in the …
- 10:45 AM Ticket #15837 ('MarkedHistogram' object has no attribute '_min_val') closed by
- duplicate: Hi Peter, Thanks for reporting this problem. It has been fixed in …
- 10:44 AM Ticket #15826 (patchelf not found on certain Linii) closed by
- fixed: Zach fixed this.
- 8:54 AM phenix-8-26-24 edited by
- (diff)
- 6:57 AM Ticket #15842 (Graphics crash, macOS 14.6.1, Intel Iris Plus Graphics) created by
- […]
- 6:34 AM Ticket #15841 (Crash on Mac waking from sleep) created by
- […]
- 4:10 AM Ticket #15840 (addh slow) created by
- […]
- 12:28 AM Ticket #15839 ('AtomicStructure' object has no attribute '_alt_loc_changes_handler') created by
- […]
Aug 28, 2024:
- 11:29 PM Ticket #15838 ('AtomicStructure' object has no attribute '_alt_loc_changes_handler') created by
- […]
- 4:26 PM Ticket #10036 (Add programming documentation on how to include PyPi dependencies in a ...) closed by
- fixed: Added an explicit mention of declaring dependencies on PyPi packages …
- 2:46 PM Ticket #15837 ('MarkedHistogram' object has no attribute '_min_val') created by
- […]
- 1:22 PM Ticket #15836 (Crash on Mac waking from sleep) created by
- […]
- 10:56 AM Ticket #15835 (Issue Launching ChimeraX) created by
- […] [[Image(...)]] [[Image(...)]]
- 9:13 AM Ticket #15834 (Crash in garbage collection) closed by
- duplicate
- 9:12 AM Ticket #15833 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 7:40 AM Ticket #15834 (Crash in garbage collection) created by
- […]
- 12:22 AM Ticket #15833 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
Aug 27, 2024:
- 1:06 PM Ticket #15559 (Crash opening mmCIF) closed by
- can't reproduce: No response from bug submitter. Need problematic mmCIF file to …
- 12:38 PM Ticket #15832 (Arg sidechains) created by
- […]
- 10:16 AM Ticket #15829 (color radial: ArrayMemoryError) closed by
- limitation: Trying to allocate 233 Mbyte numpy array of 10 million vertex …
- 10:10 AM Ticket #15827 (Volume Viewer menu) closed by
- not a bug: The Volume Viewer panel does not have menus except for the context …
- 9:55 AM Dev20249-2 created by
- 9:54 AM 2024-8-29 created by
- 9:53 AM DeveloperMeetings edited by
- (diff)
- 9:17 AM Ticket #15830 (Crash in python_instances_of_class) closed by
- duplicate: Hi Yoan, Thanks for reporting this problem. We believe it is fixed …
- 6:55 AM Ticket #15831 (SEQCROW: Buried Volume: cannot convert float NaN to integer) created by
- […]
- 6:02 AM Ticket #15830 (Crash in python_instances_of_class) created by
- […]
- 5:13 AM Ticket #15829 (color radial: ArrayMemoryError) created by
- […]
- 3:54 AM Ticket #15828 (ISOLDE: addh step of sim start: z_align endpoints must be distinct) created by
- […]
- 12:03 AM Ticket #15827 (Volume Viewer menu) created by
- […] Volume Viewer_Screenshot 2024-08-27 025252.png
Aug 26, 2024:
- 4:24 PM Ticket #15826 (patchelf not found on certain Linii) created by
- Namely on Flatpak and Ubuntu 20.04 -- and it only fails on the …
- 4:21 PM Ticket #15825 (Add a PDB and AlphaFold database sequence search using RCSB mmseqs2) created by
- It might be useful to add a PDB and AlphaFold database sequence search …
- 3:59 PM Dev2024-8-26 edited by
- (diff)
- 2:19 PM phenix-8-26-24 edited by
- (diff)
- 2:19 PM phenix-8-26-24 edited by
- (diff)
- 2:16 PM phenix-8-26-24 edited by
- (diff)
- 2:14 PM phenix-8-26-24 edited by
- (diff)
- 2:14 PM phenix-8-26-24 edited by
- (diff)
- 1:53 PM Ticket #15824 (Unable to Install Chimerax on Ubuntu 24.04 due to Package Dependencies) created by
- […] Screenshot from 2024-08-26 13-44-53.png
- 1:38 PM phenix-8-26-24 edited by
- (diff)
- 12:10 PM phenix-8-26-24 created by
- 12:10 PM Features edited by
- (diff)
- 11:54 AM Ticket #15822 (Map data: invalid value encountered in multiply) closed by
- duplicate: There are two problems here. The "invalid value encountered in …
- 11:44 AM Ticket #15823 (MemoryError opening mmCIF files) closed by
- duplicate
- 11:35 AM Ticket #15821 (Save mmCIF: 'Residue' object has no attribute 'display') closed by
- duplicate: Hi Disha, Thanks for reporting this problem. It is fixed in the …
- 11:30 AM Ticket #15820 (Bad silhouette outlines) closed by
- duplicate: This is a bug in Apple's Intel graphics driver specific to your …
- 11:28 AM Ticket #15818 (Graphics crash, macOS 14.6.1, AMD Radeon Pro 5300M, in OpenMM) closed by
- duplicate: Duplicate of #15817, same reporter.
- 11:25 AM Ticket #15817 (Graphics crash, macOS 14.6.1, AMD Radeon Pro 5300M, in OpenMM) closed by
- nonchimerax: Crashed in Apple AMD graphics driver using OpenMM with ISOLDE.
- 11:15 AM Ticket #15819 (No space left on device saving settings) closed by
- nonchimerax
- 2:05 AM Ticket #15823 (MemoryError opening mmCIF files) created by
- […]
Aug 25, 2024:
- 5:40 AM Ticket #15822 (Map data: invalid value encountered in multiply) created by
- […]
- 3:54 AM Ticket #15821 (Save mmCIF: 'Residue' object has no attribute 'display') created by
- […]
Aug 24, 2024:
- 5:38 AM Ticket #15820 (Bad silhouette outlines) created by
- […] Screenshot 2024-08-12 at 14.15.01.png
- 3:55 AM Ticket #15819 (No space left on device saving settings) created by
- […]
- 2:42 AM Ticket #15818 (Graphics crash, macOS 14.6.1, AMD Radeon Pro 5300M, in OpenMM) created by
- […]
- 2:31 AM Ticket #15817 (Graphics crash, macOS 14.6.1, AMD Radeon Pro 5300M, in OpenMM) created by
- […]
Aug 23, 2024:
- 11:25 AM Ticket #15815 ('AtomicStructure' object has no attribute '_alt_loc_changes_handler') closed by
- fixed: Fix: …
- 10:56 AM Ticket #15816 (Crash on Mac waking from sleep) closed by
- duplicate: Crash connecting or disconnecting an external display or waking from …
- 7:52 AM Ticket #15816 (Crash on Mac waking from sleep) created by
- […]
Aug 22, 2024:
- 8:37 PM Ticket #15815 ('AtomicStructure' object has no attribute '_alt_loc_changes_handler') created by
- […]
- 3:51 PM Ticket #15814 (ToolInstance.bundle_info is None) created by
- […]
- 3:45 PM Ticket #15805 (ScholAR: bad function declaration) closed by
- fixed: Schol-AR tool will work on ChimeraX versions 1.4+.
- 3:44 PM Ticket #15724 (ChimeraX installed in non-ASCII path on Windows cannot execute al2co) closed by
- can't reproduce: This is a Model Archive #5601 type structure apparently, and opening …
- 3:15 PM Ticket #15812 (AlphaFold Error Plot: listdir: Operation not permitted) closed by
- nonchimerax: ChimeraX did not have permission to list the AlphaFold results …
- 3:12 PM Ticket #15809 (Crash repositioning window (dual display)) closed by
- duplicate: This crash is due to a bug in the Qt window toolkit used by ChimeraX. …
- 2:47 PM Ticket #15813 (Wheel not installing out of bundle dist dir) created by
- […] ChimeraX_ScholAR-0.3.3-py3-none-any.whl
- 2:25 PM Ticket #15812 (AlphaFold Error Plot: listdir: Operation not permitted) created by
- […]
- 2:18 PM Ticket #15811 (Session save: No bundle information for chimerax.core.tasks.Tasks) created by
- […]
- 2:13 PM Ticket #15479 (Could not save clashes to non-ASCII file path) closed by
- fixed: Not a non-ASCII problem -- the folder doesn't exist. Now open_output …
- 12:54 PM Ticket #15810 (RFE: convenient if "color fromatom" could work on atom/residue labels) created by
- As per chimerax-users exchange …
- 12:53 PM 2024-8-22 edited by
- (diff)
- 12:44 PM Ticket #15809 (Crash repositioning window (dual display)) created by
- […]
- 12:34 PM Ticket #15808 (JSON from Mol 2.0 desktop version) closed by
- nonchimerax: Your problems are all with getting proper JSON output from MOLE, not …
- 10:50 AM Ticket #15807 (Graphics crash, macOS 14.5, Intel Iris Plus Graphics) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 10:12 AM Ticket #15808 (JSON from Mol 2.0 desktop version) created by
- Hi Elaine, The desktop version provides an XML file. I converted …
- 10:08 AM Ticket #15806 (testing attachments going to email2trac) closed by
- not a bug
- 8:54 AM Ticket #15807 (Graphics crash, macOS 14.5, Intel Iris Plus Graphics) created by
- […]
- 8:43 AM Ticket #15806 (testing attachments going to email2trac) created by
- […] test_image.png
- 7:31 AM Ticket #15805 (ScholAR: bad function declaration) created by
- […]
- 4:09 AM Ticket #15804 (Log cannot restore session state) created by
- […]
Aug 21, 2024:
- 5:37 PM Ticket #15803 (Crash in garbage collection) closed by
- duplicate
- 4:29 PM Ticket #15797 (alphafold pae file: structure is None) closed by
- fixed: Fixed. I improved the code so it will tell you that you have to open …
- 1:34 PM Ticket #15803 (Crash in garbage collection) created by
- […]
- 1:25 PM Ticket #15802 (Crash on Mac waking from sleep) closed by
- duplicate: Crash in Qt 6.6 in displayConfigFinalizedProc on Intel Mac with AMD …
- 1:23 PM Ticket #15799 (Crash on Mac waking from sleep) closed by
- duplicate: This crash is in the Qt 6.6 window toolkit on Mac. We've seen it many …
- 12:47 PM Ticket #15767 (Fetch IHM entries by 4 character PDB id) closed by
- fixed: Done. The PDB fixed the problem and fetching by 8-digit ids works …
- 12:23 PM Ticket #15785 (Crash moving window between displays) closed by
- can't reproduce: Mac Qt 6.6 crash in _NSViewHierarchyDidChangeBackingProperties. …
- 12:20 PM DeveloperMeetings edited by
- (diff)
- 12:19 PM DeveloperMeetings edited by
- (diff)
- 12:19 PM Dev2024-8-26 created by
- 12:18 PM 2024-8-22 created by
- 12:16 PM DeveloperMeetings edited by
- (diff)
- 12:15 PM DeveloperMeetings edited by
- (diff)
- 12:14 PM Ticket #15782 (ChimeraX downloads all OneDrive files) closed by
- nonchimerax: ChimeraX is not trying to download any files from a OneDrive folder …
- 12:08 PM Ticket #15781 (Crash moving window between displays) closed by
- duplicate: Mac Qt 6.6 crash in _NSViewHierarchyDidChangeBackingProperties. Was …
- 12:05 PM Ticket #15776 (Crash waking Mac up from sleep) closed by
- duplicate: Mac Qt 6.6 bug, crash in _NSViewHierarchyDidChangeBackingProperties. …
- 12:02 PM Ticket #15774 (MemoryError saving map in session) closed by
- limitation: Out of memory trying to copy a volume to a byte array to output into a …
- 11:10 AM Ticket #15769 (ArrayMemoryError in volume splitbyzone) closed by
- limitation: Out of memory using volume splitbyzone. Looks like there were less …
- 9:20 AM Ticket #15798 (Window Device Guard screws everything up) closed by
- nonchimerax
- 7:35 AM Ticket #15802 (Crash on Mac waking from sleep) created by
- […]
- 5:37 AM Ticket #15801 (XMAS: KeyError uploading DisVis outputs) created by
- […]
- 1:48 AM Ticket #15800 (XMAS: "Integrate" -> "create HADDOCK input" does not respond / crashes) created by
- […]
Aug 20, 2024:
- 11:36 PM Ticket #15799 (Crash on Mac waking from sleep) created by
- […]
- 10:37 PM Ticket #15798 (Window Device Guard screws everything up) created by
- […]
- 5:22 PM Ticket #15797 (alphafold pae file: structure is None) created by
- […] …
- 3:05 PM Ticket #15796 (CliX error when preferences file missing) created by
- […]
- 2:02 PM Ticket #15795 (Sequence characters not updated appropriately) created by
- […]
- 11:34 AM Ticket #15794 (Crash in event loop) created by
- […]
- 11:24 AM Ticket #15793 (ViewDockX: cannot convert float infinity to integer) closed by
- fixed: Hi Mojgan, Thanks for reporting this error. I have applied a fix …
- 10:55 AM Ticket #15790 (Unknown crash) closed by
- can't reproduce
- 10:53 AM Ticket #15793 (ViewDockX: cannot convert float infinity to integer) created by
- […]
- 10:41 AM Ticket #15792 (SEQCROW: `y` must contain only finite values) created by
- […]
- 10:41 AM Ticket #15791 (SEQCROW: `y` must contain only finite values) created by
- […]
- 9:38 AM Ticket #15789 (MemoryError opening mmCIF file) closed by
- duplicate
- 9:37 AM Ticket #15788 (pbond adding group to scene twice) closed by
- duplicate: Duplicate of #15770
- 9:25 AM Ticket #15787 (All hydrogen names for taken) closed by
- not a bug: Hi Yue, Thanks for reporting this problem. ChimeraX is not correctly …
- 9:12 AM Ticket #15786 (KeyError (platform) checking for updates) closed by
- duplicate: Duplicate of #15775
- 9:10 AM Ticket #15790 (Unknown crash) created by
- […]
- 1:00 AM Ticket #15789 (MemoryError opening mmCIF file) created by
- […]
Aug 19, 2024:
- 11:52 PM Ticket #15788 (pbond adding group to scene twice) created by
- […]
- 11:52 PM Ticket #15787 (All hydrogen names for taken) created by
- […]
- 10:34 PM Ticket #15786 (KeyError (platform) checking for updates) created by
- […]
- 6:14 PM Ticket #15785 (Crash moving window between displays) created by
- […]
- 5:14 PM Ticket #15758 (IndexError showing MatchMaker alignment) closed by
- fixed: Fix: …
- 4:59 PM Ticket #15784 (Unresponsive on Ubuntu 20.04) closed by
- limitation: Ah ha. You are using the open source NVidia driver. It's slowly …
- 1:31 PM Ticket #15783 (Open CHARMM .crd file) closed by
- not a bug: Hi Mitch, As I understand it, CHARMM-GUI prepares the input for …
- 11:38 AM Ticket #15775 (KeyError (platform) checking for updates) closed by
- fixed: Should be …
- 11:38 AM Ticket #15784 (Unresponsive on Ubuntu 20.04) created by
- […]
- 11:31 AM Ticket #15780 (MatchMaker: circular import of _sw) closed by
- can't reproduce
- 11:22 AM Ticket #15777 (UnicodeDecodeError reading JSON file) closed by
- can't reproduce: Would need the file to make progress.
- 10:30 AM Ticket #15783 (Open CHARMM .crd file) created by
- […] charmm-gui (4).tgz
- 7:43 AM Ticket #15782 (ChimeraX downloads all OneDrive files) created by
- […]
- 7:09 AM Ticket #15781 (Crash moving window between displays) created by
- […]
- 5:34 AM Ticket #15780 (MatchMaker: circular import of _sw) created by
- […]
- 4:52 AM Ticket #15779 (Follow-on error to: 'ClipCap' object has no attribute 'data') created by
- […]
- 4:51 AM Ticket #15778 (Segmentations: 'ClipCap' object has no attribute 'data') created by
- […]
- 2:35 AM Ticket #15777 (UnicodeDecodeError reading JSON file) created by
- […]
Aug 17, 2024:
- 9:53 AM Ticket #15776 (Crash waking Mac up from sleep) created by
- […]
- 1:32 AM Ticket #15775 (KeyError (platform) checking for updates) created by
- […]
Aug 16, 2024:
- 11:30 PM Ticket #15774 (MemoryError saving map in session) created by
- […]
- 11:58 AM Ticket #15773 (Copick: validation_error) created by
- […]
- 9:16 AM Ticket #15771 (Crash in garbage collection) closed by
- duplicate
- 9:05 AM Ticket #15772 (Missing the required parameter `arch` when calling `check_for_updates`) created by
- […]
Aug 15, 2024:
- 4:25 PM Ticket #15770 (pbond adding group to scene twice) closed by
- fixed: Fixed in the next daily. Note that running "pbond" twice with the …
- 2:58 PM Ticket #15771 (Crash in garbage collection) created by
- […]
- 2:33 PM Ticket #15768 (Crash drawing pixmap in Qt interface) closed by
- can't reproduce
- 1:24 PM NIAID2024 edited by
- (diff)
- 11:50 AM 2024-8-15 edited by
- (diff)
- 11:37 AM 2024-8-15 edited by
- (diff)
- 5:51 AM Ticket #15770 (pbond adding group to scene twice) created by
- […]
- 12:17 AM Ticket #15769 (ArrayMemoryError in volume splitbyzone) created by
- […]
- 12:06 AM Ticket #15768 (Crash drawing pixmap in Qt interface) created by
- […]
Aug 14, 2024:
- 2:58 PM Ticket #5401 (Blast Protein: Ligand Formulas (chemical formulas) hard to read) closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/9dfee68f9f16d850b48b92219cd6e0 …
- 12:48 PM Ticket #15767 (Fetch IHM entries by 4 character PDB id) created by
- Fix ChimeraX IHM fetch to work with 4-character PDB codes. It appears …
- 12:35 PM Ticket #15765 (Crash on Mac waking from sleep) closed by
- duplicate: The usual crash in _NSViewHierarchyDidChangeBackingProperties either …
- 12:24 PM Ticket #15766 (Crash in QComboBox.findData()) created by
- […]
- 12:02 PM Ticket #15759 ('MarkedHistogram' object has no attribute '_min_val') closed by
- fixed
- 10:23 AM Ticket #15764 (Crash initializing libarrow) closed by
- can't reproduce: I'm guessing libarrow is part of PyArrow, which is used by pandas and numpy
- 9:56 AM Ticket #15762 (Graphics crash, macOS 11.6, AMD Radeon Pro 5500M) closed by
- can't reproduce
- 5:57 AM Ticket #15765 (Crash on Mac waking from sleep) created by
- […]
- 1:10 AM Ticket #15764 (Crash initializing libarrow) created by
- […]
Aug 13, 2024:
- 5:55 PM Ticket #15760 (Crash on Mac waking from sleep) closed by
- duplicate: ChimeraX crashed in the Qt window toolkit in native macOS call …
- 3:11 PM Ticket #15763 (Output sequences in json format for running alphafold3) closed by
- fixed: Done. There is a new outputJson option for both the alphafold …
- 2:58 PM Ticket #15763 (Output sequences in json format for running alphafold3) created by
- […]
- 1:46 PM Ticket #15762 (Graphics crash, macOS 11.6, AMD Radeon Pro 5500M) created by
- […]
- 1:40 PM Ticket #15761 (Foldseek sequences: IndexError) closed by
- fixed: Fixed. The code did not properly handle the case where a query …
- 1:37 PM Ticket #15761 (Foldseek sequences: IndexError) created by
- […]
- 1:08 PM Ticket #15760 (Crash on Mac waking from sleep) created by
- […]
- 10:42 AM Dev2024-8-12 edited by
- (diff)
- 10:42 AM Dev2024-8-19 created by
- 10:41 AM 2024-8-15 created by
- 10:40 AM 2024-8-8 edited by
- (diff)
- 10:33 AM DeveloperMeetings edited by
- (diff)
Aug 12, 2024:
- 7:09 PM Ticket #15736 (Segger menus not working) closed by
- fixed: Fixed. Tweeked the Qt button padding. Made it the same on Mac, …
- 6:46 PM Ticket #15759 ('MarkedHistogram' object has no attribute '_min_val') created by
- […]
- 5:23 PM Ticket #15612 (PAE surf output problem) closed by
- fixed: The "non-domain" sections are now colored gray in the latest version …
- 4:58 PM Ticket #15557 (mmcif.find_template_residue() fails on Mac for template names ...) closed by
- limitation: The PDB is working on retiring the ligand-expo, so we will need to …
- 4:56 PM Ticket #15754 (toolshed uninstall: 'NoneType' object is not iterable) closed by
- fixed: Should be fixed in next daily build.
- 3:59 PM Dev2024-8-12 edited by
- (diff)
- 1:42 PM Ticket #15753 (Crash in Modeller tool _update_sequence_menus in Qt call ...) closed by
- fixed: Thanks for reporting this problem. Should be fixed in the next daily …
- 12:57 PM Ticket #15758 (IndexError showing MatchMaker alignment) created by
- […]
- 12:02 PM Ticket #15757 (ArrayMemoryError saving molecular surface in session) closed by
- can't reproduce: ChimeraX ran out of memory when trying to save a session. I tried to …
- 11:54 AM Ticket #15755 (Crash in QTimer event callback) closed by
- can't reproduce: Crash in QTimer event callback. Appears the Python callback was …
- 11:48 AM Ticket #15756 (glGetIntegerv: invalid value) closed by
- nonchimerax: Looks like ChimeraX fails to start because your graphics driver is …
- 10:59 AM Ticket #15757 (ArrayMemoryError saving molecular surface in session) created by
- […]
- 10:55 AM Ticket #15756 (glGetIntegerv: invalid value) created by
- […]
- 10:53 AM Ticket #15755 (Crash in QTimer event callback) created by
- […]
Aug 9, 2024:
- 4:36 PM Ticket #15754 (toolshed uninstall: 'NoneType' object is not iterable) created by
- […]
- 3:06 PM Dev2024-8-12 edited by
- (diff)
- 12:28 PM Ticket #15743 (Index out of bounds morphing morphs) closed by
- fixed: Fixed in daily build dated August 9 or newer. Problem was the morph …
- 12:26 PM Ticket #15747 (Morphing from an existing morph: IndexError) closed by
- fixed: Fixed. The morph code copied the first model and since it had …
- 11:49 AM ChangeLog edited by
- (diff)
- 11:36 AM Ticket #15751 (Crash in Qt window toolkit, no Python traceback, no log) closed by
- can't reproduce: ChimeraX crashed in Qt window toolkit call …
- 11:29 AM Ticket #15750 (SEQCROW error: AttributeError: 'NoneType' object has no attribute 'group') closed by
- duplicate: Same as #15749, same reporter.
- 11:28 AM Ticket #15753 (Crash in Modeller tool _update_sequence_menus in Qt call ...) created by
- […]
- 11:26 AM Ticket #15748 (glGetFramebufferAttachmentParameteriv invalid enumerant on startup, Windows) closed by
- nonchimerax: Graphics driver bug with ancient 2011 graphics card: AMD RADEON HD 6350.
- 11:07 AM Ticket #15752 (Better reporting for webservices) created by
- The recent BLAST outage really illustrates the need for more …
- 9:31 AM ChangeLog edited by
- (diff)
- 3:29 AM Ticket #15751 (Crash in Qt window toolkit, no Python traceback, no log) created by
- \{{{ The following bug report has been submitted: Platform: …
- 1:42 AM Ticket #15750 (SEQCROW error: AttributeError: 'NoneType' object has no attribute 'group') created by
- […]
- 1:42 AM Ticket #15749 (SEQCROW error: AttributeError: 'NoneType' object has no attribute 'group') created by
- […]
- 12:25 AM Ticket #15748 (glGetFramebufferAttachmentParameteriv invalid enumerant on startup, Windows) created by
- […]
Aug 8, 2024:
- 7:33 PM Ticket #15747 (Morphing from an existing morph: IndexError) created by
- […]
- 7:15 PM Ticket #15746 (DeepSSETracer installs numpy 2 which causes pip install errors) closed by
- nonchimerax: Hi Jing, When I tried to install DeepSSETracer on my Mac when you …
- 7:03 PM Ticket #15745 (Crash on Mac waking from sleep) closed by
- duplicate: Probable Mac Qt 6.6 bug. Crash in …
- 7:01 PM Ticket #15742 (Crash on Mac waking from sleep) closed by
- duplicate: ChimeraX crashed in _NSViewHierarchyDidChangeBackingProperties. This …
- 6:57 PM Ticket #15740 (Crash on Mac waking from sleep) closed by
- duplicate: Likes Qt 6.6 bug. Have not yet seen it in Qt 6.7. The usual …
- 4:53 PM Ticket #15746 (DeepSSETracer installs numpy 2 which causes pip install errors) created by
- […]
- 3:53 PM Ticket #15745 (Crash on Mac waking from sleep) created by
- […]
- 10:12 AM Ticket #15744 (Crash running open-file dialog) closed by
- can't reproduce
- 8:53 AM Ticket #15741 (QWebEngine crash) closed by
- can't reproduce
- 8:07 AM Ticket #15744 (Crash running open-file dialog) created by
- […]
- 4:57 AM Ticket #15743 (Index out of bounds morphing morphs) created by
- […]
- 1:46 AM Ticket #15742 (Crash on Mac waking from sleep) created by
- […]
Aug 7, 2024:
- 1:53 PM Ticket #15741 (QWebEngine crash) created by
- […]
- 11:48 AM Ticket #15489 (Editable installs broken on latest revision) closed by
- fixed: I forgot to note in this ticket that there was a change to this code. …
- 11:21 AM Ticket #15740 (Crash on Mac waking from sleep) created by
- […]
Aug 6, 2024:
- 6:17 PM Ticket #15739 (Loading an ESMFold BLAST result gives error "Expected a keyword") closed by
- fixed: Fixed. Updated ChimeraX BLAST Protein tool to expect just the MGnify …
- 4:37 PM Ticket #15739 (Loading an ESMFold BLAST result gives error "Expected a keyword") created by
- […]
- 3:23 PM Ticket #7387 (BLAST of Uniref50, UniRef90, UniRef100 appears to be using old ...) reopened by
- yes as Tom G said, I also got failures for uniref(N) and esmfold …
- 2:04 PM Ticket #15738 (SEQCROW: cannot read GTF) created by
- […] bodipy_s1_opt.gjf
- 12:05 PM Dev2024-8-12 created by
- 12:03 PM 2024-8-8 created by
- 12:02 PM DeveloperMeetings edited by
- (diff)
- 11:32 AM Ticket #15737 (AmberTools 24 breaks Mac ChimeraX verification) created by
- […]
- 11:13 AM ChangeLog edited by
- (diff)
- 11:03 AM Ticket #15735 (Various sequence-related session problems) closed by
- can't reproduce: version 0.91
- 10:27 AM Ticket #15736 (Segger menus not working) created by
- […] Screenshot-1.png
- 3:54 AM Ticket #15735 (Various sequence-related session problems) created by
- […]
Aug 5, 2024:
- 10:17 PM Ticket #15733 (ChimeraX check for new versions returns Intel Mac even on ARM Mac computer) closed by
- fixed: Should be fixed in tomorrow's build. To recap: When old versions of …
- 7:26 PM Ticket #15734 (Blast of esmfold database fails, database deleted on server) created by
- […]
- 7:23 PM Ticket #15732 (Checking to see if bug report can distinguish Intel Mac from Universal ...) closed by
- limitation: I did not see any way to recognized universal from intel ChimeraX in …
- 7:22 PM Ticket #15729 (Crash under Rosetta emulation) closed by
- fixed: Glad you got the M1 ChimeraX. It will be much faster. The crash …
- 6:04 PM Ticket #15733 (ChimeraX check for new versions returns Intel Mac even on ARM Mac computer) created by
- […]
- 3:53 PM Dev2024-8-5 edited by
- (diff)
- 3:43 PM Dev2024-8-5 edited by
- (diff)
- 3:02 PM Dev2024-8-5 edited by
- (diff)
- 3:01 PM Dev2024-8-5 edited by
- (diff)
- 3:01 PM Dev2024-8-5 edited by
- (diff)
- 2:53 PM Ticket #7387 (BLAST of Uniref50, UniRef90, UniRef100 appears to be using old ...) closed by
- fixed: As a side effect of all the databases on plato getting nuked, they all …
- 1:24 PM Ticket #15731 (pydantic dependency not installed (on upgrade?)) closed by
- duplicate
- 1:19 PM Ticket #15730 (UnicodeDecodeError opening Mol2 file) closed by
- can't reproduce: Later versions also try UTF-16 and UTF-32
- 12:24 PM Ticket #15732 (Checking to see if bug report can distinguish Intel Mac from Universal ...) created by
- […]
- 11:55 AM Ticket #15728 (Crash in python_instances_of_class) closed by
- can't reproduce
- 11:40 AM Ticket #15727 (Crash in event loop) closed by
- can't reproduce
- 11:36 AM Ticket #15726 (Bad silhouette edges) closed by
- duplicate: Asked and answered on the chimerax-users list
- 11:35 AM Ticket #15725 (Crash getting residue atoms while writing mmCIF) closed by
- can't reproduce
- 10:58 AM Ticket #15723 (Restoring new session in old ChimeraX) closed by
- limitation: Hi Nitesh, While you can open old sessions in new versions of …
- 10:50 AM Ticket #15721 (Crash in garbage collection) closed by
- duplicate
- 7:44 AM Ticket #15731 (pydantic dependency not installed (on upgrade?)) created by
- […]
- 6:50 AM Ticket #15730 (UnicodeDecodeError opening Mol2 file) created by
- […]
- 6:40 AM Ticket #15729 (Crash under Rosetta emulation) created by
- […]
- 5:57 AM Ticket #15728 (Crash in python_instances_of_class) created by
- […]
Aug 3, 2024:
- 3:46 PM Ticket #15727 (Crash in event loop) created by
- […]
- 6:33 AM Ticket #15726 (Bad silhouette edges) created by
- […]
- 5:58 AM Ticket #15725 (Crash getting residue atoms while writing mmCIF) created by
- […]
Aug 2, 2024:
- 7:00 PM Ticket #15724 (ChimeraX installed in non-ASCII path on Windows cannot execute al2co) created by
- […]
- 6:29 PM Ticket #15723 (Restoring new session in old ChimeraX) created by
- […]
- 5:56 PM Ticket #15722 (Improve bundle-installation requirements message) created by
- Installing PhenixUI into ChimeraX 1.5 produces the cryptic and …
- 5:15 PM 2024-8-1 edited by
- (diff)
- 4:48 PM Ticket #15721 (Crash in garbage collection) created by
- […]
- 4:05 PM Ticket #15706 (AlphaFold database missing) closed by
- fixed: Fixed. I restored the AlphaFold k-mer search database from a backup I …
- 4:00 PM Ticket #15718 (Clash attribute not registered) closed by
- fixed: Fixed. Fix will be in tomorrow's daily build.
- 2:26 PM Ticket #15716 (non-MOLE JSON file) closed by
- nonchimerax: Not sure what kind of JSON file you were trying to open in ChimeraX, …
- 2:22 PM Ticket #15720 (Crash in garbage collection) closed by
- duplicate: Hi, Thanks for reporting this problem. It has been fixed in the 1.8 …
- 2:05 PM Ticket #15717 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) closed by
- duplicate
- 12:48 PM Ticket #15697 (Updating to pyopenxr 1.1.3601 breaks ChimeraX OpenXR) closed by
- limitation: For now documented why pyopenxr is pinned to older 1.0.3401. Can …
- 12:17 PM Ticket #15711 (Crash in event loop, setting volume level, probable Apple AMD graphics ...) closed by
- nonchimerax: Very likely an Apple AMD graphics crash. The stack trace is missing …
- 12:16 PM Ticket #15715 (White pixel artifacts) closed by
- duplicate: Thanks for the thorough explanation! Let's call this a duplicate of …
- 9:48 AM Ticket #15720 (Crash in garbage collection) created by
- […]
- 8:27 AM Ticket #15719 (Blast failure) created by
- […]
- 7:35 AM Ticket #15718 (Clash attribute not registered) created by
- […]
Aug 1, 2024:
- 10:30 PM Ticket #15717 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by
- […]
- 8:31 PM Ticket #15716 (non-MOLE JSON file) created by
- […]
- 1:54 PM NIAID2024 edited by
- (diff)
- 1:52 PM NIAID2024 edited by
- (diff)
- 1:37 PM NIAID2024 edited by
- (diff)
- 11:01 AM Ticket #15710 (ChimeraX won't start after installation) closed by
- nonchimerax: From googling "fatal credentials.cc check failed", it appears to be an …
- 10:53 AM Ticket #15713 (Session save: int too big to convert) closed by
- limitation: msgpack supports 64-bit integers. This is probably related to the …
- 10:43 AM Ticket #15715 (White pixel artifacts) created by
- […] Screenshot 2024-08-01 at 1.40.25 PM.png
- 10:29 AM Ticket #15714 (Crash using File→Open dialog on Windows and/or returning from function) closed by
- can't reproduce: Hi Jean, Thanks for reporting this problem. It is fixed in later …
- 10:18 AM Ticket #15712 (UnicodeDecodeError reading PDB file) closed by
- can't reproduce: Another anonymous Windows report of this problem. If anyone ever …
- 9:52 AM Ticket #15714 (Crash using File→Open dialog on Windows and/or returning from function) created by
- […]
- 9:48 AM Ticket #15713 (Session save: int too big to convert) created by
- […]
- 3:51 AM Ticket #15712 (UnicodeDecodeError reading PDB file) created by
- […]
- 1:54 AM Ticket #15711 (Crash in event loop, setting volume level, probable Apple AMD graphics ...) created by
- […]
Jul 31, 2024:
- 6:10 PM Ticket #15710 (ChimeraX won't start after installation) created by
- […] [[Image(...)]]
- 3:51 PM Ticket #15709 (BLAST Protein failing: 'NoneType' object has no attribute 'keys') created by
- […]
- 3:38 PM Ticket #15708 (bug-reporter startup failure) closed by
- fixed: It was a quoting issue.
- 2:55 PM Ticket #15708 (bug-reporter startup failure) created by
- WARNING: Traceback (most recent call last): File …
- 12:37 PM Ticket #15707 (Turning on raycasting with an open segmentation results in ...) created by
- 12:31 PM Ticket #15224 (ChimeraX tries to open debugger arguments as if they were files) closed by
- fixed: This is mostly a bug in the debuggers/DAP implementations, where (in …
- 11:44 AM Ticket #15706 (AlphaFold database missing) created by
- […]
- 11:26 AM Ticket #15705 (Crash in event loop) closed by
- can't reproduce
- 10:36 AM Ticket #15342 (Add dark theme support) closed by
- fixed: Dark theme support is in daily build. Please report any bug with …
- 12:01 AM Ticket #15705 (Crash in event loop) created by
- […]
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