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Aug 22, 2024:

8:37 PM Ticket #15815 ('AtomicStructure' object has no attribute '_alt_loc_changes_handler') created by chimerax-bug-report@…: […]
3:51 PM Ticket #15814 (ToolInstance.bundle_info is None) created by qinli.hu@…: […]
3:45 PM Ticket #15805 (ScholAR: bad function declaration) closed by prottinghuis: 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 pett: 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 Tom Goddard: nonchimerax: ChimeraX did not have permission to list the AlphaFold results …
3:12 PM Ticket #15809 (Crash repositioning window (dual display)) closed by Tom Goddard: 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 Piet Rottinghuis: […] ChimeraX_ScholAR-0.3.3-py3-none-any.whl
2:25 PM Ticket #15812 (AlphaFold Error Plot: listdir: Operation not permitted) created by chimerax-bug-report@…: […]
2:18 PM Ticket #15811 (Session save: No bundle information for chimerax.core.tasks.Tasks) created by chimerax-bug-report@…: […]
2:13 PM Ticket #15479 (Could not save clashes to non-ASCII file path) closed by pett: 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 Elaine Meng: As per chimerax-users exchange …
12:53 PM 2024-8-22 edited by Tom Goddard: (diff)
12:44 PM Ticket #15809 (Crash repositioning window (dual display)) created by alex.long@…: […]
12:34 PM Ticket #15808 (JSON from Mol 2.0 desktop version) closed by Tom Goddard: 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 Tom Goddard: nonchimerax: Apple Intel graphics driver crash.
10:12 AM Ticket #15808 (JSON from Mol 2.0 desktop version) created by nkoylas1@…: Hi Elaine, The desktop version provides an XML file. I converted …
10:08 AM Ticket #15806 (testing attachments going to email2trac) closed by pett: not a bug
8:54 AM Ticket #15807 (Graphics crash, macOS 14.5, Intel Iris Plus Graphics) created by chimerax-bug-report@…: […]
8:43 AM Ticket #15806 (testing attachments going to email2trac) created by pett: […] test_image.png
7:31 AM Ticket #15805 (ScholAR: bad function declaration) created by chimerax-bug-report@…: […]
4:09 AM Ticket #15804 (Log cannot restore session state) created by chimerax-bug-report@…: […]

Aug 21, 2024:

5:37 PM Ticket #15803 (Crash in garbage collection) closed by pett: duplicate
4:29 PM Ticket #15797 (alphafold pae file: structure is None) closed by Tom Goddard: 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 chimerax-bug-report@…: […]
1:25 PM Ticket #15802 (Crash on Mac waking from sleep) closed by Tom Goddard: 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 Tom Goddard: 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 Tom Goddard: 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 Tom Goddard: can't reproduce: Mac Qt 6.6 crash in _NSViewHierarchyDidChangeBackingProperties. …
12:20 PM DeveloperMeetings edited by Tom Goddard: (diff)
12:19 PM DeveloperMeetings edited by Tom Goddard: (diff)
12:19 PM Dev2024-8-26 created by Tom Goddard
12:18 PM 2024-8-22 created by Tom Goddard
12:16 PM DeveloperMeetings edited by Tom Goddard: (diff)
12:15 PM DeveloperMeetings edited by Tom Goddard: (diff)
12:14 PM Ticket #15782 (ChimeraX downloads all OneDrive files) closed by Tom Goddard: 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 Tom Goddard: duplicate: Mac Qt 6.6 crash in _NSViewHierarchyDidChangeBackingProperties. Was …
12:05 PM Ticket #15776 (Crash waking Mac up from sleep) closed by Tom Goddard: duplicate: Mac Qt 6.6 bug, crash in _NSViewHierarchyDidChangeBackingProperties. …
12:02 PM Ticket #15774 (MemoryError saving map in session) closed by Tom Goddard: 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 Tom Goddard: 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 pett: nonchimerax
7:35 AM Ticket #15802 (Crash on Mac waking from sleep) created by chimerax-bug-report@…: […]
5:37 AM Ticket #15801 (XMAS: KeyError uploading DisVis outputs) created by g.picco@…: […]
1:48 AM Ticket #15800 (XMAS: "Integrate" -> "create HADDOCK input" does not respond / crashes) created by g.picco@…: […]

Aug 20, 2024:

11:36 PM Ticket #15799 (Crash on Mac waking from sleep) created by kelvin.lau@…: […]
10:37 PM Ticket #15798 (Window Device Guard screws everything up) created by chimerax-bug-report@…: […]
5:22 PM Ticket #15797 (alphafold pae file: structure is None) created by pmcarlton@…: […] …
3:05 PM Ticket #15796 (CliX error when preferences file missing) created by colingauvin@…: […]
2:02 PM Ticket #15795 (Sequence characters not updated appropriately) created by pett: […]
11:34 AM Ticket #15794 (Crash in event loop) created by dothideomycetes@…: […]
11:24 AM Ticket #15793 (ViewDockX: cannot convert float infinity to integer) closed by pett: fixed: Hi Mojgan, Thanks for reporting this error. I have applied a fix …
10:55 AM Ticket #15790 (Unknown crash) closed by pett: can't reproduce
10:53 AM Ticket #15793 (ViewDockX: cannot convert float infinity to integer) created by asadi1@…: […]
10:41 AM Ticket #15792 (SEQCROW: `y` must contain only finite values) created by neryvillegas@…: […]
10:41 AM Ticket #15791 (SEQCROW: `y` must contain only finite values) created by chimerax-bug-report@…: […]
9:38 AM Ticket #15789 (MemoryError opening mmCIF file) closed by pett: duplicate
9:37 AM Ticket #15788 (pbond adding group to scene twice) closed by pett: duplicate: Duplicate of #15770
9:25 AM Ticket #15787 (All hydrogen names for taken) closed by pett: 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 pett: duplicate: Duplicate of #15775
9:10 AM Ticket #15790 (Unknown crash) created by chimerax-bug-report@…: […]
1:00 AM Ticket #15789 (MemoryError opening mmCIF file) created by chimerax-bug-report@…: […]

Aug 19, 2024:

11:52 PM Ticket #15788 (pbond adding group to scene twice) created by chimerax-bug-report@…: […]
11:52 PM Ticket #15787 (All hydrogen names for taken) created by wangyue1@…: […]
10:34 PM Ticket #15786 (KeyError (platform) checking for updates) created by chimerax-bug-report@…: […]
6:14 PM Ticket #15785 (Crash moving window between displays) created by chimerax-bug-report@…: […]
5:14 PM Ticket #15758 (IndexError showing MatchMaker alignment) closed by pett: fixed: Fix: …
4:59 PM Ticket #15784 (Unresponsive on Ubuntu 20.04) closed by Greg Couch: 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 pett: 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 Zach Pearson: fixed: Should be …
11:38 AM Ticket #15784 (Unresponsive on Ubuntu 20.04) created by Dr. Michael F. Schmid <mfschmid@…>: […]
11:31 AM Ticket #15780 (MatchMaker: circular import of _sw) closed by pett: can't reproduce
11:22 AM Ticket #15777 (UnicodeDecodeError reading JSON file) closed by pett: can't reproduce: Would need the file to make progress.
10:30 AM Ticket #15783 (Open CHARMM .crd file) created by alphataubio@…: […] charmm-gui (4).tgz
7:43 AM Ticket #15782 (ChimeraX downloads all OneDrive files) created by dmsmith@…: […]
7:09 AM Ticket #15781 (Crash moving window between displays) created by chimerax-bug-report@…: […]
5:34 AM Ticket #15780 (MatchMaker: circular import of _sw) created by chimerax-bug-report@…: […]
4:52 AM Ticket #15779 (Follow-on error to: 'ClipCap' object has no attribute 'data') created by julia.charl@…: […]
4:51 AM Ticket #15778 (Segmentations: 'ClipCap' object has no attribute 'data') created by julia.charl@…: […]
2:35 AM Ticket #15777 (UnicodeDecodeError reading JSON file) created by chimerax-bug-report@…: […]

Aug 17, 2024:

9:53 AM Ticket #15776 (Crash waking Mac up from sleep) created by chimerax-bug-report@…: […]
1:32 AM Ticket #15775 (KeyError (platform) checking for updates) created by chimerax-bug-report@…: […]

Aug 16, 2024:

11:30 PM Ticket #15774 (MemoryError saving map in session) created by chimerax-bug-report@…: […]
11:58 AM Ticket #15773 (Copick: validation_error) created by chimerax-bug-report@…: […]
9:16 AM Ticket #15771 (Crash in garbage collection) closed by pett: duplicate
9:05 AM Ticket #15772 (Missing the required parameter `arch` when calling `check_for_updates`) created by Tony Schaefer: […]

Aug 15, 2024:

4:25 PM Ticket #15770 (pbond adding group to scene twice) closed by pett: fixed: Fixed in the next daily. Note that running "pbond" twice with the …
2:58 PM Ticket #15771 (Crash in garbage collection) created by chimerax-bug-report@…: […]
2:33 PM Ticket #15768 (Crash drawing pixmap in Qt interface) closed by pett: can't reproduce
1:24 PM NIAID2024 edited by Elaine Meng: (diff)
11:50 AM 2024-8-15 edited by Zach Pearson: (diff)
11:37 AM 2024-8-15 edited by Zach Pearson: (diff)
5:51 AM Ticket #15770 (pbond adding group to scene twice) created by Tristan Croll: […]
12:17 AM Ticket #15769 (ArrayMemoryError in volume splitbyzone) created by chimerax-bug-report@…: […]
12:06 AM Ticket #15768 (Crash drawing pixmap in Qt interface) created by chimerax-bug-report@…: […]

Aug 14, 2024:

2:58 PM Ticket #5401 (Blast Protein: Ligand Formulas (chemical formulas) hard to read) closed by Zach Pearson: fixed: [https://github.com/RBVI/ChimeraX/commit/9dfee68f9f16d850b48b92219cd6e0 …
12:48 PM Ticket #15767 (Fetch IHM entries by 4 character PDB id) created by Tom Goddard: 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 Tom Goddard: duplicate: The usual crash in _NSViewHierarchyDidChangeBackingProperties either …
12:24 PM Ticket #15766 (Crash in QComboBox.findData()) created by chimerax-bug-report@…: […]
12:02 PM Ticket #15759 ('MarkedHistogram' object has no attribute '_min_val') closed by pett: fixed
10:23 AM Ticket #15764 (Crash initializing libarrow) closed by pett: 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 pett: can't reproduce
5:57 AM Ticket #15765 (Crash on Mac waking from sleep) created by chimerax-bug-report@…: […]
1:10 AM Ticket #15764 (Crash initializing libarrow) created by chimerax-bug-report@…: […]

Aug 13, 2024:

5:55 PM Ticket #15760 (Crash on Mac waking from sleep) closed by Tom Goddard: 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 Tom Goddard: 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 goddard@…: […]
1:46 PM Ticket #15762 (Graphics crash, macOS 11.6, AMD Radeon Pro 5500M) created by chimerax-bug-report@…: […]
1:40 PM Ticket #15761 (Foldseek sequences: IndexError) closed by Tom Goddard: fixed: Fixed. The code did not properly handle the case where a query …
1:37 PM Ticket #15761 (Foldseek sequences: IndexError) created by goddard@…: […]
1:08 PM Ticket #15760 (Crash on Mac waking from sleep) created by hannesludewig@…: […]
10:42 AM Dev2024-8-12 edited by Tom Goddard: (diff)
10:42 AM Dev2024-8-19 created by Tom Goddard
10:41 AM 2024-8-15 created by Tom Goddard
10:40 AM 2024-8-8 edited by Tom Goddard: (diff)
10:33 AM DeveloperMeetings edited by Tom Goddard: (diff)

Aug 12, 2024:

7:09 PM Ticket #15736 (Segger menus not working) closed by Tom Goddard: 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 chimerax-bug-report@…: […]
5:23 PM Ticket #15612 (PAE surf output problem) closed by pett: 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 Greg Couch: 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 Greg Couch: fixed: Should be fixed in next daily build.
3:59 PM Dev2024-8-12 edited by Tom Goddard: (diff)
1:42 PM Ticket #15753 (Crash in Modeller tool _update_sequence_menus in Qt call ...) closed by pett: fixed: Thanks for reporting this problem. Should be fixed in the next daily …
12:57 PM Ticket #15758 (IndexError showing MatchMaker alignment) created by chimerax-bug-report@…: […]
12:02 PM Ticket #15757 (ArrayMemoryError saving molecular surface in session) closed by Tom Goddard: 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 Tom Goddard: can't reproduce: Crash in QTimer event callback. Appears the Python callback was …
11:48 AM Ticket #15756 (glGetIntegerv: invalid value) closed by Tom Goddard: 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 Praffuls@…: […]
10:55 AM Ticket #15756 (glGetIntegerv: invalid value) created by chunxiang.wu@…: […]
10:53 AM Ticket #15755 (Crash in QTimer event callback) created by chimerax-bug-report@…: […]

Aug 9, 2024:

4:36 PM Ticket #15754 (toolshed uninstall: 'NoneType' object is not iterable) created by Tony Schaefer: […]
3:06 PM Dev2024-8-12 edited by Zach Pearson: (diff)
12:28 PM Ticket #15743 (Index out of bounds morphing morphs) closed by Tom Goddard: 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 Tom Goddard: fixed: Fixed. The morph code copied the first model and since it had …
11:49 AM ChangeLog edited by pett: (diff)
11:36 AM Ticket #15751 (Crash in Qt window toolkit, no Python traceback, no log) closed by Tom Goddard: 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 Tom Goddard: duplicate: Same as #15749, same reporter.
11:28 AM Ticket #15753 (Crash in Modeller tool _update_sequence_menus in Qt call ...) created by george.rooms@…: […]
11:26 AM Ticket #15748 (glGetFramebufferAttachmentParameteriv invalid enumerant on startup, Windows) closed by Tom Goddard: nonchimerax: Graphics driver bug with ancient 2011 graphics card: AMD RADEON HD 6350.
11:07 AM Ticket #15752 (Better reporting for webservices) created by Zach Pearson: The recent BLAST outage really illustrates the need for more …
9:31 AM ChangeLog edited by Elaine Meng: (diff)
3:29 AM Ticket #15751 (Crash in Qt window toolkit, no Python traceback, no log) created by vinod@…: \{{{ The following bug report has been submitted: Platform: …
1:42 AM Ticket #15750 (SEQCROW error: AttributeError: 'NoneType' object has no attribute 'group') created by chimerax-bug-report@…: […]
1:42 AM Ticket #15749 (SEQCROW error: AttributeError: 'NoneType' object has no attribute 'group') created by chimerax-bug-report@…: […]
12:25 AM Ticket #15748 (glGetFramebufferAttachmentParameteriv invalid enumerant on startup, Windows) created by chimerax-bug-report@…: […]

Aug 8, 2024:

7:33 PM Ticket #15747 (Morphing from an existing morph: IndexError) created by goddard@…: […]
7:15 PM Ticket #15746 (DeepSSETracer installs numpy 2 which causes pip install errors) closed by Tom Goddard: 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 Tom Goddard: duplicate: Probable Mac Qt 6.6 bug. Crash in …
7:01 PM Ticket #15742 (Crash on Mac waking from sleep) closed by Tom Goddard: duplicate: ChimeraX crashed in _NSViewHierarchyDidChangeBackingProperties. This …
6:57 PM Ticket #15740 (Crash on Mac waking from sleep) closed by Tom Goddard: 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 goddard@…: […]
3:53 PM Ticket #15745 (Crash on Mac waking from sleep) created by chimerax-bug-report@…: […]
10:12 AM Ticket #15744 (Crash running open-file dialog) closed by pett: can't reproduce
8:53 AM Ticket #15741 (QWebEngine crash) closed by pett: can't reproduce
8:07 AM Ticket #15744 (Crash running open-file dialog) created by chimerax-bug-report@…: […]
4:57 AM Ticket #15743 (Index out of bounds morphing morphs) created by gbrierley@…: […]
1:46 AM Ticket #15742 (Crash on Mac waking from sleep) created by 2300502p@…: […]

Aug 7, 2024:

1:53 PM Ticket #15741 (QWebEngine crash) created by chimerax-bug-report@…: […]
11:48 AM Ticket #15489 (Editable installs broken on latest revision) closed by Zach Pearson: 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 chimerax-bug-report@…: […]

Aug 6, 2024:

6:17 PM Ticket #15739 (Loading an ESMFold BLAST result gives error "Expected a keyword") closed by Tom Goddard: 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 goddard@…: […]
3:23 PM Ticket #7387 (BLAST of Uniref50, UniRef90, UniRef100 appears to be using old ...) reopened by Elaine Meng: 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 chimerax-bug-report@…: […] bodipy_s1_opt.gjf
12:05 PM Dev2024-8-12 created by Tom Goddard
12:03 PM 2024-8-8 created by Tom Goddard
12:02 PM DeveloperMeetings edited by Tom Goddard: (diff)
11:32 AM Ticket #15737 (AmberTools 24 breaks Mac ChimeraX verification) created by goddard@…: […]
11:13 AM ChangeLog edited by pett: (diff)
11:03 AM Ticket #15735 (Various sequence-related session problems) closed by pett: can't reproduce: version 0.91
10:27 AM Ticket #15736 (Segger menus not working) created by logicvay2010@…: […] Screenshot-1.png
3:54 AM Ticket #15735 (Various sequence-related session problems) created by chimerax-bug-report@…: […]

Aug 5, 2024:

10:17 PM Ticket #15733 (ChimeraX check for new versions returns Intel Mac even on ARM Mac computer) closed by Zach Pearson: 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 goddard@…: […]
7:23 PM Ticket #15732 (Checking to see if bug report can distinguish Intel Mac from Universal ...) closed by Tom Goddard: 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 Tom Goddard: 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 goddard@…: […]
3:53 PM Dev2024-8-5 edited by Tom Goddard: (diff)
3:43 PM Dev2024-8-5 edited by Tom Goddard: (diff)
3:02 PM Dev2024-8-5 edited by Tom Goddard: (diff)
3:01 PM Dev2024-8-5 edited by Tom Goddard: (diff)
3:01 PM Dev2024-8-5 edited by Tom Goddard: (diff)
2:53 PM Ticket #7387 (BLAST of Uniref50, UniRef90, UniRef100 appears to be using old ...) closed by pett: 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 pett: duplicate
1:19 PM Ticket #15730 (UnicodeDecodeError opening Mol2 file) closed by pett: 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 goddard@…: […]
11:55 AM Ticket #15728 (Crash in python_instances_of_class) closed by pett: can't reproduce
11:40 AM Ticket #15727 (Crash in event loop) closed by pett: can't reproduce
11:36 AM Ticket #15726 (Bad silhouette edges) closed by pett: duplicate: Asked and answered on the chimerax-users list
11:35 AM Ticket #15725 (Crash getting residue atoms while writing mmCIF) closed by pett: can't reproduce
10:58 AM Ticket #15723 (Restoring new session in old ChimeraX) closed by pett: limitation: Hi Nitesh, While you can open old sessions in new versions of …
10:50 AM Ticket #15721 (Crash in garbage collection) closed by pett: duplicate
7:44 AM Ticket #15731 (pydantic dependency not installed (on upgrade?)) created by chimerax-bug-report@…: […]
6:50 AM Ticket #15730 (UnicodeDecodeError opening Mol2 file) created by chimerax-bug-report@…: […]
6:40 AM Ticket #15729 (Crash under Rosetta emulation) created by xiang.zhang@…: […]
5:57 AM Ticket #15728 (Crash in python_instances_of_class) created by chimerax-bug-report@…: […]

Aug 3, 2024:

3:46 PM Ticket #15727 (Crash in event loop) created by chimerax-bug-report@…: […]
6:33 AM Ticket #15726 (Bad silhouette edges) created by sha4008@…: […]
5:58 AM Ticket #15725 (Crash getting residue atoms while writing mmCIF) created by chimerax-bug-report@…: […]

Aug 2, 2024:

7:00 PM Ticket #15724 (ChimeraX installed in non-ASCII path on Windows cannot execute al2co) created by chimerax-bug-report@…: […]
6:29 PM Ticket #15723 (Restoring new session in old ChimeraX) created by nkkhandelwal@…: […]
5:56 PM Ticket #15722 (Improve bundle-installation requirements message) created by pett: Installing PhenixUI into ChimeraX 1.5 produces the cryptic and …
5:15 PM 2024-8-1 edited by Tom Goddard: (diff)
4:48 PM Ticket #15721 (Crash in garbage collection) created by chimerax-bug-report@…: […]
4:05 PM Ticket #15706 (AlphaFold database missing) closed by Tom Goddard: 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 pett: fixed: Fixed. Fix will be in tomorrow's daily build.
2:26 PM Ticket #15716 (non-MOLE JSON file) closed by Tom Goddard: 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 pett: 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 pett: duplicate
12:48 PM Ticket #15697 (Updating to pyopenxr 1.1.3601 breaks ChimeraX OpenXR) closed by Tom Goddard: 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 Tom Goddard: nonchimerax: Very likely an Apple AMD graphics crash. The stack trace is missing …
12:16 PM Ticket #15715 (White pixel artifacts) closed by Zach Pearson: duplicate: Thanks for the thorough explanation! Let's call this a duplicate of …
9:48 AM Ticket #15720 (Crash in garbage collection) created by rslack@…: […]
8:27 AM Ticket #15719 (Blast failure) created by zeke_cook@…: […]
7:35 AM Ticket #15718 (Clash attribute not registered) created by smacgowan@…: […]

Aug 1, 2024:

10:30 PM Ticket #15717 (Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device ...) created by chimerax-bug-report@…: […]
8:31 PM Ticket #15716 (non-MOLE JSON file) created by zgyi@…: […]
1:54 PM NIAID2024 edited by Elaine Meng: (diff)
1:52 PM NIAID2024 edited by Elaine Meng: (diff)
1:37 PM NIAID2024 edited by Elaine Meng: (diff)
11:01 AM Ticket #15710 (ChimeraX won't start after installation) closed by Greg Couch: 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 Greg Couch: limitation: msgpack supports 64-bit integers. This is probably related to the …
10:43 AM Ticket #15715 (White pixel artifacts) created by olibclarke@…: […] 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 pett: 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 pett: 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 jnzigou@…: […]
9:48 AM Ticket #15713 (Session save: int too big to convert) created by chimerax-bug-report@…: […]
3:51 AM Ticket #15712 (UnicodeDecodeError reading PDB file) created by chimerax-bug-report@…: […]
1:54 AM Ticket #15711 (Crash in event loop, setting volume level, probable Apple AMD graphics ...) created by chimerax-bug-report@…: […]

Jul 31, 2024:

6:10 PM Ticket #15710 (ChimeraX won't start after installation) created by hshawmd95@…: […] [[Image(...)]]
3:51 PM Ticket #15709 (BLAST Protein failing: 'NoneType' object has no attribute 'keys') created by goddard@…: […]
3:38 PM Ticket #15708 (bug-reporter startup failure) closed by Greg Couch: fixed: It was a quoting issue.
2:55 PM Ticket #15708 (bug-reporter startup failure) created by pett: WARNING: Traceback (most recent call last): File …
12:37 PM Ticket #15707 (Turning on raycasting with an open segmentation results in ...) created by Zach Pearson
12:31 PM Ticket #15224 (ChimeraX tries to open debugger arguments as if they were files) closed by Zach Pearson: fixed: This is mostly a bug in the debuggers/DAP implementations, where (in …
11:44 AM Ticket #15706 (AlphaFold database missing) created by andreyf@…: […]
11:26 AM Ticket #15705 (Crash in event loop) closed by pett: can't reproduce
10:36 AM Ticket #15342 (Add dark theme support) closed by Greg Couch: fixed: Dark theme support is in daily build. Please report any bug with …
12:01 AM Ticket #15705 (Crash in event loop) created by chimerax-bug-report@…: […]

Jul 30, 2024:

11:15 PM Ticket #15704 (BLAST databases missing) created by 23036745r@…: […]
8:32 PM Dev2024-8-5 edited by Tom Goddard: (diff)
6:45 PM Ticket #15703 (Orthoplanes in the 2D view modes should react to things like "volume ...) created by Zach Pearson
5:03 PM Ticket #15695 (Close volume log equivalent command: v.session is None) closed by Zach Pearson: fixed: [https://github.com/RBVI/ChimeraX/commit/56d604bd96cb75074d54d773425824 …
4:58 PM Ticket #15702 (Crash using Rosetta emulation) created by akhtaralimuhammad@…: […]
2:53 PM Ticket #15694 (Volume-reading progress: unsupported format character) closed by Tom Goddard: fixed: Fixed. Escaped "%" characters in volume file name status messages.
2:38 PM ChangeLog edited by Elaine Meng: (diff)
12:51 PM Dev2024-8-5 created by Tom Goddard
12:49 PM 2024-8-1 created by Tom Goddard
12:47 PM DeveloperMeetings edited by Tom Goddard: (diff)
10:32 AM Ticket #15701 (Bounding box breaks regions of interest when raycasting) created by Zach Pearson: When showing a bounding box for a raycast image, whatever (texture?) …
10:28 AM Ticket #15700 (Lower resolution textures cause artifacts with raycasting) created by Zach Pearson: When using lower resolution textures (step 4 or higher), a volume …
9:45 AM Ticket #15699 (Crash in garbage collection) closed by pett: duplicate: Hi PY, Thanks for reporting this problem. It has been fixed in the …
9:36 AM Ticket #15699 (Crash in garbage collection) created by P.Yu@…: […]
1:10 AM Ticket #15698 (ISOLDE start simulation: There is no registered Platform called "HIP") created by chimerax-bug-report@…: […]

Jul 29, 2024:

8:18 PM Ticket #15697 (Updating to pyopenxr 1.1.3601 breaks ChimeraX OpenXR) created by goddard@…: […]
7:02 PM Ticket #15696 (Crash setting Update Bundles QComboBox index) created by chimerax-bug-report@…: […]
3:15 PM Ticket #15625 (Dark mode changes broke command-line error reporting) closed by pett: fixed: I guess I must not have re-installed the cmd_line bundle in that build.
1:53 PM Ticket #15678 (Missing structure labels make opening PDB 8jnb not focus view on full model) closed by pett: fixed: Adding the labels as the pseudobond group is created seems to solve …
1:46 PM Dev2024-7-29 edited by Tom Goddard: (diff)
1:44 PM Dev2024-7-29 edited by Tom Goddard: (diff)
1:43 PM Ticket #15695 (Close volume log equivalent command: v.session is None) created by chimerax-bug-report@…: […]
1:06 PM Dev2024-7-29 edited by Tom Goddard: (diff)
1:05 PM Dev2024-7-29 created by Tom Goddard
1:03 PM DeveloperMeetings edited by Tom Goddard: (diff)
11:34 AM Ticket #15694 (Volume-reading progress: unsupported format character) created by chimerax-bug-report@…: […]
10:22 AM Ticket #15691 (Crash running open-file dialog) closed by pett: can't reproduce
10:19 AM Ticket #15689 (Crash in garbage collection) closed by pett: duplicate
8:12 AM Ticket #15693 (ResidueStepper holding reference to closed structure) created by chimerax-bug-report@…: […]

Jul 28, 2024:

1:30 PM Ticket #15692 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by chimerax-bug-report@…: […]

Jul 26, 2024:

6:14 PM Ticket #15690 (Avoid red-green color scheme in Foldseek sequences plot, worst choice ...) closed by Tom Goddard: fixed: Fixed. Switched to a bluish-yellowish scheme suggested by this web …
6:12 PM Ticket #15691 (Crash running open-file dialog) created by chimerax-bug-report@…: […]
6:01 PM Ticket #15666 (Deleting chain B of 3h7s leads to a crash) closed by pett: fixed: Fixed. Fix: …
5:38 PM Ticket #15690 (Avoid red-green color scheme in Foldseek sequences plot, worst choice ...) created by goddard@…: […]
5:27 PM Ticket #15684 (foldseek ligands warns of about a dozen sequence mismatch problems) closed by Tom Goddard: fixed: Fixed. All of the sequence mismatches observed with foldseek query …
5:24 PM Ticket #15681 (Foldseek loading mmCIF files slows after hundreds already in session) closed by Tom Goddard: fixed: Fixed. The problem was in the foldseek code which was trimming the …
5:19 PM Ticket #15668 (Foldseek excludes residues missing backbone N, e.g. PDB 7w7g /B:654) closed by Tom Goddard: fixed: Fixed. I made ChimeraX foldseek code use …
3:31 PM Ticket #15688 (Improve speed of foldseek ligands command) closed by Tom Goddard: fixed: Fixed. Improved speed finding ligands of 845 hits from 500 seconds …
2:37 PM Ticket #15682 (Combine command is not copying altloc coordinates correctly) closed by pett: fixed: Fix: …
1:31 PM Ticket #15689 (Crash in garbage collection) created by chimerax-bug-report@…: […]
12:08 PM Ticket #15688 (Improve speed of foldseek ligands command) created by goddard@…: […]
11:37 AM Ticket #15687 (Crash floating window on Mac) closed by Tom Goddard: can't reproduce: Seems like a Qt bug. The last lines of the stack have lots of …
11:06 AM Ticket #15686 (Crash in event loop) closed by pett: can't reproduce
11:05 AM Ticket #15685 (Crash in event loop) closed by pett: can't reproduce
10:50 AM Ticket #15680 (Crash in chem_group.find_group) closed by pett: can't reproduce: Crashed in threaded C++ implementation of find_group. Not too much …
8:11 AM Ticket #15687 (Crash floating window on Mac) created by chimerax-bug-report@…: […]
6:51 AM Ticket #15686 (Crash in event loop) created by chimerax-bug-report@…: […]
12:57 AM Ticket #15685 (Crash in event loop) created by chimerax-bug-report@…: […]

Jul 25, 2024:

6:21 PM Ticket #15684 (foldseek ligands warns of about a dozen sequence mismatch problems) created by goddard@…: […]
5:58 PM Ticket #15683 (Foldseek ligands does not dock all altlocs to query) closed by Tom Goddard: fixed: Fixed. I made foldseek ligands keep only one altloc for each ligand …
5:47 PM Ticket #15683 (Foldseek ligands does not dock all altlocs to query) created by goddard@…: […]
5:38 PM Ticket #15682 (Combine command is not copying altloc coordinates correctly) created by goddard@…: […]
4:34 PM Ticket #15681 (Foldseek loading mmCIF files slows after hundreds already in session) created by goddard@…: […]
4:29 PM Ticket #15670 (Foldseek ligands uses illegal chain id character "_") closed by Tom Goddard: wontfix
4:21 PM Ticket #15680 (Crash in chem_group.find_group) created by chimerax-bug-report@…: […]
4:18 PM Ticket #15679 (Foldseek panel expands to full window width) closed by Tom Goddard: fixed: Fixed. Eric does not observe this problem, and I did not encounter it …
4:15 PM Ticket #15679 (Foldseek panel expands to full window width) created by goddard@…: […]
3:57 PM Ticket #15677 (Foldseek does not delete old results table when new results open) closed by Tom Goddard: fixed: Fixed. I was calling the QTableView destroy() method which is …
3:10 PM Ticket #15678 (Missing structure labels make opening PDB 8jnb not focus view on full model) created by goddard@…: […]
2:23 PM Ticket #15669 (module 'xr' has no attribute 'GraphicsBindingOpenGLWin32KHR') closed by Tom Goddard: not a bug: Hi Colin, The ChimeraX xr command uses OpenXR which in theory works …
2:09 PM Ticket #15673 (Qt fatal error: QEventDispatcherUNIXPrivate(): Cannot continue without ...) closed by Tom Goddard: can't reproduce: Qt crashed when Save dialog shown. QEventDispatcherUNIXPrivate(): …
1:51 PM Ticket #15663 (glDrawBuffer: invalid operation) closed by Tom Goddard: duplicate: Linux OpenGL invalid operation error glDrawBuffer(GL_BACK). Have seen …
1:48 PM Ticket #15671 (Crash waking Mac up from sleep) closed by Tom Goddard: duplicate: ChimeraX crashed due to a bug in the Qt window toolkit. The crash can …
1:42 PM Ticket #15677 (Foldseek does not delete old results table when new results open) created by goddard@…: […]
1:01 PM 2024-7-25 edited by Tom Goddard: (diff)
12:46 PM Ticket #15676 (Crash in garbage collection) closed by pett: duplicate
12:45 PM Ticket #15675 (Crash in garbage collection) closed by pett: duplicate
10:58 AM Ticket #15674 (Restore new session in old ChimeraX) closed by pett: limitation: Hi Christoph, The session your collaborator sent you needs to be …
10:46 AM Ticket #15672 (Crash showing/running open-file dialog) closed by pett: can't reproduce
10:08 AM Ticket #15662 (Crash in garbage collection) closed by pett: duplicate
8:22 AM Ticket #15676 (Crash in garbage collection) created by chimerax-bug-report@…: […]
7:53 AM Ticket #15675 (Crash in garbage collection) created by chimerax-bug-report@…: […]
6:28 AM Ticket #15674 (Restore new session in old ChimeraX) created by chkaiser@…: […]
2:59 AM Ticket #15673 (Qt fatal error: QEventDispatcherUNIXPrivate(): Cannot continue without ...) created by chimerax-bug-report@…: […]
2:08 AM Ticket #15672 (Crash showing/running open-file dialog) created by chimerax-bug-report@…: […]

Jul 24, 2024:

10:09 PM Ticket #15671 (Crash waking Mac up from sleep) created by shruthiv@…: […]
8:29 PM Ticket #15670 (Foldseek ligands uses illegal chain id character "_") created by goddard@…: […]
6:39 PM Ticket #15669 (module 'xr' has no attribute 'GraphicsBindingOpenGLWin32KHR') created by colingauvin@…: […]
4:45 PM Ticket #15668 (Foldseek excludes residues missing backbone N, e.g. PDB 7w7g /B:654) created by goddard@…: […]
4:14 PM Ticket #15667 (Foldseek sequence length mismatch PDB 5v5h_B) closed by Tom Goddard: fixed: Fixed. The terminal lysine residue did not have a CA. Made ChimeraX …
4:09 PM Ticket #15667 (Foldseek sequence length mismatch PDB 5v5h_B) created by goddard@…: […]
3:50 PM Ticket #15665 (Foldseek opening 3h7s crashes) closed by Tom Goddard: duplicate: Made a simpler version of this crash that does not involve Foldseek, …
3:44 PM Ticket #15666 (Deleting chain B of 3h7s leads to a crash) created by goddard@…: […]
3:25 PM Ticket #15665 (Foldseek opening 3h7s crashes) created by goddard@…: […]
2:42 PM Ticket #15664 (Foldseek fails opening 6xhb_B with query 8jnb) closed by Tom Goddard: fixed: Fixed. Turns out foldseek code has another shorter list of accepted …
2:38 PM Ticket #15664 (Foldseek fails opening 6xhb_B with query 8jnb) created by goddard@…: […]
1:40 PM Ticket #15663 (glDrawBuffer: invalid operation) created by chimerax-bug-report@…: […]
1:26 PM Ticket #15662 (Crash in garbage collection) created by chimerax-bug-report@…: […]
10:01 AM Ticket #15661 (Crash running modal dialog) closed by pett: can't reproduce
10:00 AM Ticket #15660 (Crash in garbage collection) closed by pett: can't reproduce: Hi Peter, Thanks for reporting this problem. The crash occurred in …
9:54 AM Ticket #15659 (Crash in event loop) closed by pett: can't reproduce
9:53 AM Ticket #15658 (Crash calculating contour surface) closed by pett: can't reproduce
6:59 AM Ticket #15661 (Crash running modal dialog) created by chimerax-bug-report@…: […]
1:05 AM Ticket #15660 (Crash in garbage collection) created by carlton.petermark.3v@…: […]
12:19 AM Ticket #15659 (Crash in event loop) created by chimerax-bug-report@…: […]

Jul 23, 2024:

9:57 PM Ticket #15658 (Crash calculating contour surface) created by chimerax-bug-report@…: […]
8:01 PM Ticket #15655 (Use/offer official AlphaFold color palette) closed by Tom Goddard: wontfix: This was discussed on the ChimeraX mailing list in May 2024 …
6:06 PM Ticket #15654 (Residue 1-letter code reported as X while PDB reports it as K) closed by Greg Couch: fixed: Add prefetching of all residue templates so one-letter code is known …
4:53 PM Ticket #15657 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by chimerax-bug-report@…: […]
3:48 PM ChangeLog edited by Elaine Meng: (diff)
10:03 AM 2024-7-25 created by Tom Goddard
10:02 AM DeveloperMeetings edited by Tom Goddard: (diff)
10:00 AM Ticket #15651 (Crash waking Mac from sleep) closed by Tom Goddard: duplicate: Qt 6.6 bug, crashes in _NSViewHierarchyDidChangeBackingProperties …
1:20 AM Ticket #15656 (Qt fatal error: Failed to initialize graphics backend for OpenGL) created by chimerax-bug-report@…: […]
12:49 AM Ticket #15655 (Use/offer official AlphaFold color palette) created by 419434238@…: […] 屏幕截图 2024-07-20 233927.png

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