![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Feb 10, 2023:
- 12:56 PM Dev2022-2-13 created by
- 12:54 PM DeveloperMeetings edited by
- (diff)
- 12:50 PM 2023-2-9 edited by
- (diff)
- 9:18 AM Ticket #8473 (Show chain sequence: TypeError: __init__() got an unexpected keyword ...) created by
- […]
- 8:01 AM Ticket #8472 (Various simulation errors) created by
- […]
- 4:15 AM Ticket #8471 (Crash handling pointer in numpy) created by
- […]
- 4:08 AM Ticket #8470 (KeyError formatting blast results) created by
- […]
- 3:55 AM Ticket #8464 (ISOLDE: Unparameterised residue detected) closed by
- duplicate: Updating to ISOLDE 1.5 (by first updating to ChimeraX 1.5) should take …
- 1:01 AM Ticket #8469 (Crash using File→Open dialog on Windows and/or returning from function) created by
- […]
Feb 9, 2023:
- 9:38 PM Ticket #8468 (Change Google account for AlphaFold) created by
- […]
- 7:27 PM Ticket #8465 (Marker surface does not move with marker) closed by
- worksforme: The molecular surface updates as expected for me in the current …
- 6:53 PM Ticket #8466 (Graphics crash, macOS 13.0.1, Intel Iris Plus Graphics 645) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 4:25 PM Ticket #8462 (Graphics crash, macOS 11.5.2, Intel Iris Plus Graphics 640) closed by
- can't reproduce: 1.2.5
- 4:22 PM Ticket #8467 (need to vary number of dashes in missing segments psuedobond depending ...) created by
- 6xra_rebuilt_glycan_chains_reassigned.cif in #4342 has a really long, …
- 4:18 PM Ticket #8461 (Crash in event loop) closed by
- can't reproduce
- 2:18 PM NIAID2022 edited by
- (diff)
- 2:01 PM NIAID2022 edited by
- (diff)
- 1:33 PM NIAID2022 edited by
- (diff)
- 1:25 PM NIAID2022 edited by
- (diff)
- 11:04 AM Ticket #8466 (Graphics crash, macOS 13.0.1, Intel Iris Plus Graphics 645) created by
- […]
- 10:57 AM Ticket #8465 (Marker surface does not move with marker) created by
- […] disconnect.cxs
- 10:12 AM Ticket #8308 (Crash opening mmCIF) closed by
- can't reproduce: Need the mmCIF file to reproduce the problem.
- 5:29 AM Ticket #8464 (ISOLDE: Unparameterised residue detected) created by
- […]
- 2:02 AM Ticket #8463 (XMAS: 'Tabular' object has no attribute 'peptide_pairs') created by
- […]
Feb 8, 2023:
- 6:08 PM Ticket #8459 (mmCIF "more info" shows raw HTML) closed by
- fixed: Fixed.
- 3:45 PM Ticket #8462 (Graphics crash, macOS 11.5.2, Intel Iris Plus Graphics 640) created by
- […]
- 3:30 PM Ticket #8451 (Load a default database with Download DICOM tool) closed by
- fixed: In …
- 1:52 PM Ticket #8461 (Crash in event loop) created by
- […]
- 11:21 AM Ticket #8456 (alphafold pae: 'NoneType' object has no attribute 'residues') closed by
- duplicate: This error was fixed in ChimeraX 1.5. You are opening AlphaFold PAE …
- 11:18 AM Ticket #8460 (self._current_reference is None) created by
- […]
- 9:39 AM Ticket #8458 (Save mmCIF: 'SaveOptionsWidget' object has no attribute 'compute_sheets') closed by
- duplicate: Hi Haaris, Thanks for reporting this problem. It was fixed in the …
- 8:59 AM Ticket #8459 (mmCIF "more info" shows raw HTML) created by
- […]
- 4:29 AM Ticket #8458 (Save mmCIF: 'SaveOptionsWidget' object has no attribute 'compute_sheets') created by
- […]
Feb 7, 2023:
- 11:33 PM Ticket #8457 (Crash clearing aniso_u6) created by
- […]
- 6:34 PM Ticket #8456 (alphafold pae: 'NoneType' object has no attribute 'residues') created by
- […]
- 5:56 PM Ticket #8455 (Crash in garbage collection) closed by
- duplicate: Hi Haoyang, Thanks for reporting this problem. Please upgrade to the …
- 5:02 PM Ticket #3871 (Add zone selection panel option to omit original selection) closed by
- fixed: Available in next daily build. Subject to Elaine tweaking.
- 3:01 PM Ticket #8455 (Crash in garbage collection) created by
- […]
- 2:19 PM Ticket #3387 (Render By Attribute tool) closed by
- duplicate
- 2:07 PM Ticket #4794 (Dock Prep) closed by
- fixed
- 1:22 PM Ticket #8452 (Fix labelling errors in the Download DICOM tool) closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/4bfbc63551fab092c50243a83774f5 …
- 11:43 AM Ticket #8454 (Token starts with space) created by
- […]
- 11:20 AM Ticket #8453 (Associate Download DICOM entries with corresponding TCIA webpage) created by
- (6) If possible, I would like this additional action available for …
- 11:19 AM Ticket #8452 (Fix labelling errors in the Download DICOM tool) created by
- From an email sent by Elaine: (5b) The "Back to Databases" button …
- 11:17 AM Ticket #8451 (Load a default database with Download DICOM tool) created by
- From an email from Elaine: (1) Tool starts up with Database: None. …
- 10:39 AM 2023-2-9 edited by
- (diff)
- 10:38 AM 2023-2-9 created by
- 10:37 AM DeveloperMeetings edited by
- (diff)
- 9:52 AM Ticket #8445 (Help Viewer, authorize: 'PasswordDialog' object has no attribute 'exec_') closed by
- fixed: This problem was due to a missed change from PyQt 5 to PyQt 6. It's …
- 9:37 AM Ticket #8450 (MatchMaker: 'NoneType' object has no attribute 'setChecked') closed by
- can't reproduce
- 9:25 AM Ticket #8448 ('CentroidModel' object has no attribute 'distance') closed by
- duplicate: Duplicate of #8449
- 4:45 AM Ticket #8450 (MatchMaker: 'NoneType' object has no attribute 'setChecked') created by
- […]
- 4:38 AM Ticket #8449 ('CentroidModel' object has no attribute 'distance') created by
- […]
- 4:36 AM Ticket #8448 ('CentroidModel' object has no attribute 'distance') created by
- […]
Feb 6, 2023:
- 12:47 PM Ticket #8447 (Crash closing tool window) created by
- […]
- 11:37 AM Ticket #8443 (No checkwaters command) closed by
- fixed: Removed references to non-existent "checkwaters" command
- 11:12 AM Ticket #8434 (Rainbow and color sequential) closed by
- not a bug: The rainbow chain or color sequential chain command colors only the …
- 10:55 AM Ticket #8446 (Cartoon of large 7y5e is slow, takes 30 seconds first time, 4 seconds ...) created by
- […]
- 10:48 AM Ticket #8435 (Crash computing ribbons) closed by
- can't reproduce: That 7y5e PDB model is a monster with 1.2 million atoms and 150,000 …
- 10:28 AM Ticket #8444 (invalid parameter not satisfying: !isnan(newOrigin.y)) closed by
- can't reproduce: Hi TJ, You should drag ChimeraX from the .dmg window into your …
- 10:10 AM Ticket #8440 (Clipper: crash setting aniso_u6) closed by
- can't reproduce: Right. We hope to make it more obvious that you need to drag the app …
- 9:45 AM Ticket #8445 (Help Viewer, authorize: 'PasswordDialog' object has no attribute 'exec_') created by
- […]
- 9:42 AM Ticket #8442 (Crash opening PDB) closed by
- can't reproduce
- 9:41 AM Ticket #8441 (Incorrectly installed CUDA) closed by
- fixed: Hi Saverio, Glad you were able to get it working. --Eric Eric …
- 9:37 AM Ticket #8390 (Allow opening (downloading) DICOM files from tcia) closed by
- fixed: This was implemented in a …
- 9:26 AM Ticket #8439 (Crash in event loop) closed by
- can't reproduce: Hi Cesar, I recommend upgrading to ChimeraX 1.5, which will provide …
Feb 5, 2023:
- 10:40 PM Ticket #8444 (invalid parameter not satisfying: !isnan(newOrigin.y)) created by
- […]
- 4:30 AM Ticket #8443 (No checkwaters command) created by
- […]
- 2:57 AM Ticket #8442 (Crash opening PDB) created by
- […]
- 1:15 AM Ticket #8441 (Incorrectly installed CUDA) created by
- […]
Feb 4, 2023:
- 4:36 PM Ticket #8440 (Clipper: crash setting aniso_u6) created by
- […]
- 4:31 AM Ticket #8439 (Crash in event loop) created by
- […]
Feb 3, 2023:
- 5:17 PM Ticket #8438 (AlphaFold JSON vs. MOLE JSON) closed by
- not a bug: ChimeraX does not use the open command to AlphaFold PAE error …
- 5:02 PM Ticket #8438 (AlphaFold JSON vs. MOLE JSON) created by
- […]
- 4:33 PM Ticket #8436 (VR picking distance is too large) closed by
- fixed: Fixed. I've changed the definition of the vr command clickRange value …
- 4:25 PM Ticket #8437 (QWindowsWindow::setDarkBorderToWindow: Unable to set dark window border) created by
- […]
- 4:23 PM Ticket #8436 (VR picking distance is too large) created by
- […]
- 3:25 PM Ticket #8435 (Crash computing ribbons) created by
- […]
- 1:06 PM Ticket #8394 (RFE: EMDB-SFF transform) closed by
- fixed: Fixed. In tonight's daily builds dated Feb 4. The ChimeraX EMDB SFF …
- 11:24 AM Ticket #8432 (Correctly handle 'view sel' for custom model with only some positions ...) closed by
- limitation: You came to the right conclusion. Adding a Model child using …
- 11:15 AM Ticket #8433 (PermissionError launching ffmpeg to encode movie, Windows) closed by
- nonchimerax: Unclear why Windows refuses to start ffmpeg. Maybe antivirus shut it down.
- 10:24 AM Ticket #8434 (Rainbow and color sequential) created by
- […]
- 5:31 AM Ticket #8433 (PermissionError launching ffmpeg to encode movie, Windows) created by
- […]
- 5:26 AM Ticket #8432 (Correctly handle 'view sel' for custom model with only some positions ...) created by
- […]
Feb 2, 2023:
- 6:22 PM 2023-2-2 edited by
- (diff)
- 6:10 PM ChangeLog edited by
- (diff)
- 6:08 PM Ticket #8431 (Make VR picking use proximity to cone tip) created by
- Currently VR hand controller modes pick objects by looking at the …
- 6:05 PM Ticket #4232 (RFE: make ViewDockX understand SwissDock output) closed by
- fixed: Will be available in the next daily build. You will have to open both …
- 2:52 PM Ticket #8430 (Make SDF markups available as attributes) created by
- ... and present them in log as table. Only single-value attributes …
- 2:25 PM NIAID2022 edited by
- (diff)
- 2:23 PM NIAID2022 edited by
- (diff)
- 2:08 PM NIAID2022 edited by
- (diff)
- 1:07 PM NIAID2022 edited by
- (diff)
- 12:24 PM Ticket #8429 (Allow GLTF export to divide objects so each can be a single color for ...) created by
- The Enduvo VR presentation software does not appear to handle texture …
- 10:59 AM Ticket #8428 (Include electrostatic coloring in GLTF exported models using textures) created by
- It would be worth trying exporting texture colors for surfaces colored …
- 10:52 AM GrantAims2 edited by
- (diff)
- 10:51 AM GrantAims2 edited by
- (diff)
- 10:24 AM Ticket #8427 (Unsupported scale factor (0.000000) detected on Display0) closed by
- can't reproduce: *Possibly* the same as #8226. The user does have two displays.
- 10:18 AM Ticket #8392 (Crash calculating step 1 contour surface) closed by
- can't reproduce: Crash trying to compute the contour surface of a large map 1100 by …
- 10:09 AM Ticket #8426 (Crash using File→Open dialog on Windows and/or returning from function) closed by
- can't reproduce: 1.3
- 10:05 AM Ticket #8423 (Graphics crash, macOS 11.7.2, Intel Iris Plus Graphics) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 7:50 AM Ticket #8427 (Unsupported scale factor (0.000000) detected on Display0) created by
- […]
- 7:18 AM Ticket #8426 (Crash using File→Open dialog on Windows and/or returning from function) created by
- […]
- 6:50 AM Ticket #8425 (Reload non-bundle) created by
- […]
- 6:46 AM Ticket #8424 (devel bundle reloadModule) created by
- […]
Feb 1, 2023:
- 5:48 PM 2023-2-2 edited by
- (diff)
- 2:37 PM Ticket #8423 (Graphics crash, macOS 11.7.2, Intel Iris Plus Graphics) created by
- […]
- 2:29 PM Ticket #8422 (Testing bug reporter to see if submit button goes away. It does.) closed by
- not a bug
- 2:25 PM Ticket #8422 (Testing bug reporter to see if submit button goes away. It does.) created by
- […]
- 1:58 PM Ticket #8420 (Crash showing Rapid Access at startup: Qt fatal error: Failed to ...) closed by
- can't reproduce: Linux
- 1:56 PM Ticket #8404 (glClear: out of memory) closed by
- nonchimerax: The glClear() out of memory error seems unexpected given that only a …
- 1:23 PM Ticket #8418 (glClear: out of memory) closed by
- duplicate
- 1:22 PM Ticket #8417 (glClear: out of memory) closed by
- duplicate
- 1:21 PM Ticket #8416 (glClear: out of memory) closed by
- duplicate
- 1:21 PM Ticket #8415 (glClear: out of memory) closed by
- duplicate
- 1:20 PM Ticket #8414 (glClear: out of memory) closed by
- duplicate
- 1:19 PM Ticket #8413 (glClear: out of memory) closed by
- duplicate
- 1:18 PM Ticket #8421 (DevelExtras: opanel.bundle_info.value is None) created by
- […]
- 1:18 PM Ticket #8412 (glClear: out of memory) closed by
- duplicate
- 1:17 PM Ticket #8411 (glClear: out of memory) closed by
- duplicate
- 1:17 PM Ticket #8420 (Crash showing Rapid Access at startup: Qt fatal error: Failed to ...) created by
- […]
- 1:16 PM Ticket #8410 (glClear: out of memory) closed by
- duplicate
- 1:15 PM Ticket #8409 (glClear: out of memory) closed by
- duplicate
- 1:14 PM Ticket #8408 (glClear: out of memory) closed by
- duplicate
- 1:13 PM Ticket #8407 (glClear: out of memory) closed by
- duplicate
- 1:12 PM Ticket #8406 (glClear: out of memory) closed by
- duplicate
- 1:11 PM Ticket #8405 (glClear: out of memory) closed by
- duplicate
- 12:59 PM Ticket #8419 (XMAS: pandas.errors.ParserError: Too many columns specified) created by
- […]
- 12:52 PM Ticket #8397 (Read PDB: UnicodeDecodeError: 'utf-8' codec can't decode byte) closed by
- can't reproduce: Can't reproduce it on Windows either
- 12:45 PM Ticket #8418 (glClear: out of memory) created by
- […]
- 12:45 PM Ticket #8417 (glClear: out of memory) created by
- […]
- 12:45 PM Ticket #8416 (glClear: out of memory) created by
- […]
- 12:45 PM Ticket #8415 (glClear: out of memory) created by
- […]
- 12:45 PM Ticket #8414 (glClear: out of memory) created by
- […]
- 12:45 PM Ticket #8413 (glClear: out of memory) created by
- […]
- 12:45 PM Ticket #8412 (glClear: out of memory) created by
- […]
- 12:45 PM Ticket #8411 (glClear: out of memory) created by
- […]
- 12:45 PM Ticket #8410 (glClear: out of memory) created by
- […]
- 12:45 PM Ticket #8409 (glClear: out of memory) created by
- […]
- 12:45 PM Ticket #8408 (glClear: out of memory) created by
- […]
- 12:45 PM Ticket #8407 (glClear: out of memory) created by
- […]
- 12:45 PM Ticket #8406 (glClear: out of memory) created by
- […]
- 12:45 PM Ticket #8405 (glClear: out of memory) created by
- […]
- 12:45 PM Ticket #8404 (glClear: out of memory) created by
- […]
- 12:17 PM Ticket #8403 (Delete status bar: wrapped C/C++ object of type QScreen has been deleted) created by
- […]
- 12:06 PM Ticket #8402 (Crash in ffmpeg fork under Rosetta emulation) closed by
- nonchimerax: The problem seems to be that ChimeraX is trying to run ffmpeg to …
- 11:31 AM Ticket #8398 (ISOLDE: crash in populate_clash_table) closed by
- fixed: Fixed since ISOLDE 1.4.
- 11:09 AM Ticket #8401 (Read .gro: name 'UserError' is not defined) closed by
- duplicate
- 11:09 AM Ticket #8402 (Crash in ffmpeg fork under Rosetta emulation) created by
- […]
- 11:00 AM Ticket #8399 (Crash in fork() under Rosetta emulation) closed by
- duplicate: Looks like it was forking off ffmpeg
- 7:42 AM Ticket #8401 (Read .gro: name 'UserError' is not defined) created by
- […]
- 2:58 AM Ticket #8400 (ISOLDE cursor freeze) created by
- […]
- 2:09 AM Ticket #8399 (Crash in fork() under Rosetta emulation) created by
- […]
- 1:57 AM Ticket #8398 (ISOLDE: crash in populate_clash_table) created by
- […]
Jan 31, 2023:
- 5:47 PM Ticket #8396 (Crash saving image) closed by
- can't reproduce: Linux
- 3:29 PM Ticket #8397 (Read PDB: UnicodeDecodeError: 'utf-8' codec can't decode byte) created by
- […]
- 1:23 PM Ticket #8364 (MatchMaker: 'NoneType' object has no attribute 'setChecked') closed by
- can't reproduce: Not Linux-only (see #8393)
- 1:00 PM Ticket #8396 (Crash saving image) created by
- […]
- 11:58 AM Ticket #8395 (Restore new session in old ChimeraX) closed by
- limitation: Hi Rishi, While ChimeraX is guaranteed to restore old session files …
- 11:52 AM Ticket #8393 (Matchmaker: 'NoneType' object has no attribute 'setChecked') closed by
- can't reproduce: Tried various things -- couldn't reproduce
- 9:36 AM 2023-2-2 created by
- 9:34 AM DeveloperMeetings edited by
- (diff)
- 9:17 AM Ticket #8395 (Restore new session in old ChimeraX) created by
- […]
- 8:58 AM Ticket #8394 (RFE: EMDB-SFF transform) created by
- […]
- 2:35 AM Ticket #8393 (Matchmaker: 'NoneType' object has no attribute 'setChecked') created by
- […]
Jan 30, 2023:
- 5:42 PM Dev2022-1-30 edited by
- (diff)
- 5:19 PM Ticket #8392 (Crash calculating step 1 contour surface) created by
- […]
- 1:33 PM Ticket #8345 (Crash clearing aniso_u6) closed by
- can't reproduce: Instead of detecting whether it's running directly from the .dmg, I …
- 12:24 PM Ticket #8386 (glClear: invalid framebuffer operation) closed by
- nonchimerax: OpenGL error on Mac with two displays and AMD Radeon Pro Vega 20. …
- 12:21 PM Ticket #8385 (Graphics crash, macOS 11.7, NVIDIA GeForce GT 750M) closed by
- nonchimerax: Apple Nvidia graphics driver crash.
- 12:14 PM Ticket #8383 (cannot import name '_log_alphafold_chain_table') closed by
- fixed: This is a bug in your ChimeraX daily build from November 19, 2022. …
- 11:32 AM Ticket #8377 (Zone selection: NumPy array is not contiguous) closed by
- fixed: Fixed. There are no C3 atoms in the structure where "select zone C 2 …
- 11:08 AM Ticket #8391 (Make AlphaFold Coloring CA-distance coloring work for any two aligned ...) created by
- Two comments on a YouTube ChimeraX video that shows AlphaFold …
- 10:12 AM Ticket #8390 (Allow opening (downloading) DICOM files from tcia) created by
- In the latest NIAID statement of work, we write that we want to be …
- 10:10 AM Ticket #8389 (Implement a NifTI File Reader) created by
- NifTI is increasingly popular as a medical imaging format. TCIA, a …
- 9:22 AM Ticket #8387 (Unknown crash) closed by
- can't reproduce
- 9:05 AM Ticket #8382 (Crash processing timer event) closed by
- can't reproduce: This is kind of weird: ChimeraX Version: 1.5 (2022-11-24 00:03:27 …
- 8:57 AM Ticket #8388 (gaps between pseudobonds and ribbons in printable representations) created by
- […] [[Image(...)]] [[Image(...)]] …
- 8:57 AM Ticket #8381 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 8:54 AM Ticket #8380 (Crash reading PDB file) closed by
- can't reproduce: 1.2.5
- 8:52 AM Ticket #8379 (Dead Structure Measurement tool trying to show status) closed by
- duplicate: duplicate of #8148
- 8:47 AM Ticket #8378 (Unknown crash at startup) closed by
- can't reproduce
- 8:44 AM Ticket #8387 (Unknown crash) created by
- […]
- 7:37 AM Ticket #8386 (glClear: invalid framebuffer operation) created by
- […]
- 12:21 AM Ticket #8385 (Graphics crash, macOS 11.7, NVIDIA GeForce GT 750M) created by
- […]
- 12:14 AM Ticket #8384 (sm.start_sim: _openmm.new_Context: bad allocation) created by
- […]
Jan 29, 2023:
Jan 28, 2023:
Jan 27, 2023:
- 4:48 PM Ticket #8381 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 4:20 PM Ticket #8380 (Crash reading PDB file) created by
- […]
- 3:05 PM Ticket #8379 (Dead Structure Measurement tool trying to show status) created by
- […]
- 2:08 PM Ticket #8378 (Unknown crash at startup) created by
- […]
Jan 26, 2023:
- 6:33 PM Ticket #8377 (Zone selection: NumPy array is not contiguous) created by
- […]
- 6:03 PM Ticket #8376 ("measure sasa" does not return value) closed by
- fixed: Fixed. The measure sasa command now returns the total area, and if …
- 5:42 PM Ticket #8376 ("measure sasa" does not return value) created by
- The "measure sasa" command does not return the value, making it pretty …
- 5:12 PM Ticket #8375 (Quest 2 VR viewer of ChimeraX GLTF scenes) created by
- Allow viewing ChimeraX exported scenes in GLTF format on standalone VR …
- 5:05 PM Ticket #8373 (swapna: 'NoneType' object has no attribute 'coord') closed by
- fixed: Structure O1P/O2P needs to be looked up as OP1/OP2 in template. Fix: …
- 5:02 PM 2023-1-26 edited by
- (diff)
- 4:37 PM Ticket #8374 (crash while saving a PDB file) closed by
- fixed: Fix: …
- 4:12 PM 2023-1-26 edited by
- (diff)
- 3:07 PM NIAID2022 edited by
- (diff)
- 2:16 PM NIAID2022 edited by
- (diff)
- 2:13 PM NIAID2022 edited by
- (diff)
- 2:03 PM NIAID2022 edited by
- (diff)
- 2:02 PM Ticket #8218 (Bio assembly of 2JTN missing many atoms) closed by
- duplicate: Duplicate of #8153
- 1:40 PM NIAID2022 edited by
- (diff)
- 10:53 AM Ticket #8372 (isolde sim stop discardTo start: 'NoneType' object has no attribute 'atoms') closed by
- duplicate: Stopping a simulation with the rotamer preview visible. Fixed a while back.
- 10:45 AM Ticket #8374 (crash while saving a PDB file) created by
- Open 2-compound.cif from #4479 and then try to save it as a PDB file. …
- 9:06 AM Ticket #8373 (swapna: 'NoneType' object has no attribute 'coord') created by
- […]
- 9:02 AM Ticket #8372 (isolde sim stop discardTo start: 'NoneType' object has no attribute 'atoms') created by
- […]
- 8:54 AM Ticket #8371 (KeyError in floating-tool dict after de-iconfiy) closed by
- duplicate: Duplicate of #7743
- 3:54 AM Ticket #8371 (KeyError in floating-tool dict after de-iconfiy) created by
- […]
Jan 25, 2023:
- 4:40 PM Ticket #8263 (Problems with combine command) closed by
- fixed: Structure::_copy(), which combine uses, transforms coordinates *in …
- 10:37 AM Ticket #8370 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 10:32 AM Ticket #8370 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 9:26 AM Ticket #8369 (Crash showing Rapid Access at startup) closed by
- can't reproduce: Linux
- 9:24 AM Ticket #8368 (Crash saving image) closed by
- can't reproduce: Linux, 1.3
- 8:47 AM Ticket #8369 (Crash showing Rapid Access at startup) created by
- […]
- 8:25 AM Ticket #8368 (Crash saving image) created by
- […]
Jan 24, 2023:
- 7:01 PM Ticket #4558 (Saved mmCIF files of edited structures sometime problematic) closed by
- fixed: Fingers still crossed.
- 11:14 AM Ticket #8362 (Immortal context menus) closed by
- fixed: Fixed. Posting a context menu calls QMenu.exec() which starts an …
- 10:44 AM Dev2022-1-30 created by
- 10:43 AM 2023-1-26 created by
- 10:42 AM DeveloperMeetings edited by
- (diff)
- 10:32 AM Ticket #8367 (Crash destroying atomic structure) closed by
- can't reproduce
- 10:30 AM Ticket #8366 (Crash in event loop) closed by
- can't reproduce
- 10:28 AM Ticket #8365 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 10:10 AM Ticket #8363 (Crash saving image) closed by
- can't reproduce: Linux
- 3:41 AM Ticket #8367 (Crash destroying atomic structure) created by
- […]
- 2:39 AM Ticket #8366 (Crash in event loop) created by
- […]
- 12:49 AM Ticket #8365 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 12:43 AM Ticket #8364 (MatchMaker: 'NoneType' object has no attribute 'setChecked') created by
- […]
Jan 23, 2023:
- 10:21 PM Ticket #8363 (Crash saving image) created by
- […]
- 5:18 PM GrantAims2 edited by
- (diff)
- 5:15 PM GrantAims2 edited by
- (diff)
- 4:48 PM Dev2022-1-23 edited by
- (diff)
- 3:22 PM GrantAims2 edited by
- (diff)
- 2:11 PM Ticket #8360 (Volume Viewer: wrapped C/C++ object of type QScrollArea has been deleted) closed by
- duplicate: This was fixed 7 months ago. The fix is in the current ChimeraX 1.5. …
- 1:54 PM Ticket #8361 (QOpenGLFramebufferObject: Framebuffer incomplete attachment) closed by
- can't reproduce
- 1:45 PM Ticket #8355 (alphafold pae: No module named 'jax') closed by
- duplicate: Duplicate of #8032. Fixed in ChimeraX 1.5
- 1:45 PM Ticket #8359 (Crash in garbage collection) closed by
- duplicate
- 1:41 PM Ticket #8357 (Restore new session in old ChimeraX) closed by
- limitation
- 1:39 PM Ticket #8356 (Crash in event loop) closed by
- can't reproduce
- 1:32 PM Ticket #8354 (Crash destroying tool) closed by
- can't reproduce
- 1:28 PM Ticket #8353 (Restore new session in old ChimeraX) closed by
- limitation
- 1:25 PM Ticket #8352 (QPaintDevice: Cannot destroy paint device that is being painted) closed by
- can't reproduce
- 1:22 PM Ticket #8351 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: 1.3
- 1:19 PM Ticket #8350 (MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted) closed by
- duplicate: Hi Disha, Thanks for reporting this problem. It has been fixed for …
- 1:14 PM Ticket #8349 (Crash showing Rapid Access at startup) closed by
- can't reproduce: Linux
- 1:12 PM Ticket #8348 (Crash showing Rapid Access at startup: Qt fatal error: Failed to ...) closed by
- can't reproduce: Linux
- 1:09 PM Ticket #8347 (Crash clearing aniso_u6) closed by
- duplicate: Duplicate of #8345
- 1:07 PM Ticket #8346 (Crash clearing aniso_u6) closed by
- duplicate: Duplicate of #8345
- 1:01 PM Ticket #8362 (Immortal context menus) created by
- […] Screen Shot 2023-01-23 at 12.58.13 PM.png
- 12:58 PM Ticket #8341 (rainbow command ignores palette alpha values) closed by
- fixed: Fixed. The rainbow command is the same as "color sequential". In …
- 12:07 PM Ticket #8361 (QOpenGLFramebufferObject: Framebuffer incomplete attachment) created by
- […]
- 12:00 PM Ticket #8342 (Bad set of Atoms.aniso_u6 from remove_invalid_anisou?) closed by
- duplicate: Using #8345 now, since that had an actual reporter
- 11:30 AM Ticket #8344 (Bad set of Atoms.aniso_u6 from remove_invalid_anisou?) closed by
- duplicate: Duplicate of #8342
- 11:23 AM Ticket #8343 (Bad set of Atoms.aniso_u6 from remove_invalid_anisou?) closed by
- duplicate: Duplicate of #8342
- 11:20 AM Ticket #8358 (EMDB SFF segmentation file: AttributeError: 'SFFMesh' object has no ...) closed by
- fixed: Fixed. The ChimeraX EMDB SFF file reader was based on the sfftkrw API …
- 11:17 AM Ticket #8360 (Volume Viewer: wrapped C/C++ object of type QScrollArea has been deleted) created by
- […]
- 11:15 AM Ticket #8359 (Crash in garbage collection) created by
- […]
- 10:57 AM Ticket #8358 (EMDB SFF segmentation file: AttributeError: 'SFFMesh' object has no ...) created by
- […] […]
- 9:44 AM Ticket #6716 (Blast protein duplicate result-window identifiers (more than one bp1)) closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/9d06f2049ded7c8d0128bb85a0c24f …
- 9:43 AM Ticket #7373 (Make segmentations overlap DICOM volumes properly) reopened by
- Closed the wrong ticket, agh…
- 9:42 AM Ticket #7373 (Make segmentations overlap DICOM volumes properly) closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/9d06f2049ded7c8d0128bb85a0c24f …
- 9:17 AM Ticket #8190 (Have web services use HTTPS proxy if set) closed by
- fixed: [https://github.com/RBVI/ChimeraX/commit/0b036ebf550101e787ef2459b73738 …
- 7:06 AM Ticket #8357 (Restore new session in old ChimeraX) created by
- […]
- 3:58 AM Ticket #8356 (Crash in event loop) created by
- […]
- 2:05 AM Ticket #8355 (alphafold pae: No module named 'jax') created by
- […]
Jan 22, 2023:
- 11:20 PM Ticket #8354 (Crash destroying tool) created by
- […]
- 11:31 AM Ticket #8353 (Restore new session in old ChimeraX) created by
- […]
- 7:32 AM Ticket #8352 (QPaintDevice: Cannot destroy paint device that is being painted) created by
- […]
- 6:55 AM Ticket #8351 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 3:45 AM Ticket #8350 (MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted) created by
- […]
Jan 21, 2023:
- 2:02 PM Ticket #8349 (Crash showing Rapid Access at startup) created by
- […]
- 4:11 AM Ticket #8348 (Crash showing Rapid Access at startup: Qt fatal error: Failed to ...) created by
- […]
Jan 20, 2023:
- 7:10 PM Ticket #8347 (Crash clearing aniso_u6) created by
- […]
- 6:58 PM Ticket #8346 (Crash clearing aniso_u6) created by
- […]
- 6:57 PM Ticket #8345 (Crash clearing aniso_u6) created by
- […]
- 6:31 PM Ticket #8344 (Bad set of Atoms.aniso_u6 from remove_invalid_anisou?) created by
- […]
- 6:29 PM Ticket #8343 (Bad set of Atoms.aniso_u6 from remove_invalid_anisou?) created by
- […]
- 6:28 PM Ticket #8342 (Bad set of Atoms.aniso_u6 from remove_invalid_anisou?) created by
- […]
- 1:26 PM Ticket #8340 (Crash in getTrackedDeviceIndexForControllerRole) closed by
- can't reproduce: They are trying to start VR on a Mac and it crashed in the openvr PyPi …
- 1:10 PM Ticket #8341 (rainbow command ignores palette alpha values) created by
- […]
- 12:56 PM Ticket #8339 (Crash in color chooser) closed by
- duplicate: duplicate of #7995
- 12:44 PM Ticket #8340 (Crash in getTrackedDeviceIndexForControllerRole) created by
- […]
- 11:21 AM Ticket #8329 (Ring mis-typed as aromatic) closed by
- fixed: Aromaticity isn't judged from ring planarity. There are plenty of …
- 9:31 AM Ticket #8339 (Crash in color chooser) created by
- […]
- 9:11 AM Ticket #8338 (Crash in event loop) closed by
- can't reproduce
- 9:04 AM Ticket #8337 (Crash handling event) closed by
- can't reproduce: "memory shortage"? Was only using 4GB
- 6:11 AM Ticket #8338 (Crash in event loop) created by
- […]
Jan 19, 2023:
- 6:35 PM Ticket #8337 (Crash handling event) created by
- […]
- 5:08 PM Ticket #7561 (Make ChimeraX fetch 8 character PDB identifiers) closed by
- fixed: There is already another ticket for lost styling I think. Can't do …
- 4:45 PM DeveloperMeetings edited by
- (diff)
- 4:44 PM Dev2022-1-16 edited by
- (diff)
- 4:44 PM Dev2022-1-23 edited by
- (diff)
- 4:44 PM Dev2022-1-23 created by
- 4:31 PM Ticket #8284 (Show fusion protein regions in sequence viewer) closed by
- not a bug: I thought what Tom had implemented *might* already be sufficient. Good!
- 4:27 PM Ticket #8336 (Port RR Distance Maps) created by
- ...from Chimera
- 4:00 PM Ticket #8335 (Compute surface normals for binary STL files if the file normals are zero) closed by
- fixed: Done. To avoid slowing down the reading of STL files that have …
- 3:56 PM Ticket #8335 (Compute surface normals for binary STL files if the file normals are zero) created by
- […]
- 3:12 PM Ticket #8330 (AlphaFold vs. UNK: negative dimensions are not allowed) closed by
- fixed: Fixed. The match search will now just give no results for sequences …
- 2:41 PM 2023-1-19 edited by
- (diff)
- 2:34 PM Ticket #8333 (Phenix bundle: module 'chimerax.phenix' has no attribute 'bundle_api') closed by
- wontfix: Okay, I have nuked the Phenix bundle.
- 2:13 PM Ticket #8334 (SEQCROW: circle_current_cs: list index out of range) created by
- […]
- 1:51 PM Ticket #8327 (Crash saving image) closed by
- duplicate: Duplicate. Always Linux 1.3 in Pillow.
- 1:21 PM Ticket #8331 (Crash showing Rapid Access at startup: "Qt fatal error: Failed to ...) closed by
- can't reproduce
- 1:17 PM NIAID2022 edited by
- (diff)
- 1:16 PM NIAID2022 edited by
- (diff)
- 1:02 PM Ticket #8333 (Phenix bundle: module 'chimerax.phenix' has no attribute 'bundle_api') created by
- […]
- 12:52 PM Ticket #8332 (Crash starting simulation) created by
- […]
- 11:00 AM Ticket #8256 (Documentation links missing) closed by
- fixed: Documentation links are working again as of today's daily build.
- 10:59 AM Ticket #8266 (Mac compiler error) closed by
- fixed: OK, I didn't check the header before I modified the .c file -- I'm …
- 10:46 AM phenix-1-12-23 edited by
- (diff)
- 9:20 AM Ticket #8331 (Crash showing Rapid Access at startup: "Qt fatal error: Failed to ...) created by
- […]
- 6:14 AM Ticket #8330 (AlphaFold vs. UNK: negative dimensions are not allowed) created by
- […]
- 5:35 AM Ticket #8329 (Ring mis-typed as aromatic) created by
- […]
- 12:32 AM Ticket #8328 (SEQCROW: no finder named AtomSpec in AaronTools.finders) created by
- […]
Jan 18, 2023:
- 4:59 PM Ticket #8318 (Looking Glass: libHoloPlayCore.dylib is an incompatible architecture) closed by
- limitation: I'm not going to fix this unless some user tests the ARM library and …
- 4:56 PM Ticket #8313 (AlphaFold: A UTF-8 locale is required. Got ANSI_X3.4-1968) closed by
- fixed: Fixed. I monkeypatched Python _locale.nl_langinfo(CODESET) to force …
- 1:00 PM Ticket #8275 (Provide user agent information) closed by
- fixed: [https://github.com/RBVI/cxwebservices/commit/ec56094df96fd3e647e7b4d50 …
- 11:55 AM Ticket #8327 (Crash saving image) created by
- […]
- 11:15 AM phenix-1-12-23 edited by
- (diff)
- 9:29 AM Ticket #8326 (Crash showing Rapid Access at startup) closed by
- can't reproduce
- 8:07 AM Ticket #8326 (Crash showing Rapid Access at startup) created by
- […]
- 6:52 AM Ticket #7996 (Rebuild residue to template: template problem) closed by
- fixed
- 6:51 AM Ticket #8083 (ISOLDE session restore: 'AtomicStructure' object has no attribute 'session') closed by
- fixed: Loading the new session deleted the existing model while a simulation …
- 6:41 AM Ticket #7766 (OpenMMException: Error initializing context: clCreateCommandQueue) closed by
- limitation: Error is CL_OUT_OF_HOST_MEMORY.
- 6:39 AM Ticket #7594 (Various Clipper problems) closed by
- fixed: Handling of map_to_structure_factors MTZ files should be greatly …
- 6:37 AM Ticket #7470 (Start simulation: openmm.OpenMMException: Error compiling kernel: ...) closed by
- duplicate: Sorry about not responding to this at the time... there was a spate of …
- 6:33 AM Ticket #6626 (Backrub requires N- and C-terminal flanking residues to be present) closed by
- limitation: I've removed the auto-fit rotamer option (which used this code) from …
- 6:32 AM Ticket #6540 (OpenMM crash) closed by
- can't reproduce
- 6:31 AM Ticket #6445 (ISOLDE/OpenMM: Error initializing context: clCreateContext) closed by
- limitation
- 6:28 AM Ticket #6083 (CUDA/OpenCL errors: CUDA_ERROR_OUT_OF_MEMORY) closed by
- limitation: Sorry I never responded at the time - seems there's a handful of …
- 6:24 AM Ticket #6081 (Symmetry handler using dead structure) closed by
- fixed
- 6:21 AM Ticket #6017 (openmm.OpenMMException: Error initializing context: clCreateContext) closed by
- can't reproduce
- 6:20 AM Ticket #5631 (ISOLDE: fix unparameterized residues: Residue already deleted) closed by
- fixed: Fixed in the new GUI.
- 6:20 AM Ticket #4989 (OpenMM simulation: Graphics kernel error) closed by
- can't reproduce: Not sure why I never responded to this at the time - sorry about that. …
- 6:17 AM Ticket #4942 (phenix connect command traceback when wrong Phenix directory given) closed by
- wontfix: Obsolete now, due to the R24 ChimeraX-Phenix interface.
- 6:16 AM Ticket #4896 (OpenMMException: No compatible OpenCL platform is available) closed by
- can't reproduce
- 6:15 AM Ticket #4888 (OpenMMException: invalid value for --gpu-architecture) closed by
- fixed
- 6:14 AM Ticket #4805 (ISOLDE: crash in find_clashing_atoms) closed by
- fixed
- 6:14 AM Ticket #4800 (ISOLDE: item.data is a method/function, not tuple) closed by
- fixed: Zombie ticket, long since fixed.
- 6:13 AM Ticket #4774 (Crash hitting "play" button) closed by
- can't reproduce: Never was able to reproduce this - and given that I've since redone …
- 6:11 AM Ticket #4740 (ISOLDE: wrapped C/C++ object of type QTableWidget has been deleted) closed by
- fixed: Fixed by new GUI.
- 6:10 AM Ticket #4738 (OpenMMException: /usr/local/cuda/bin/nvcc: not found) closed by
- fixed: These days, if the CUDA platform exists but encounters an error on …
- 6:09 AM Ticket #4721 (tilted slab: 'numpy.ndarray' object is not callable) closed by
- fixed: Closing this, since the headline errors are fixed. I'd still like to …
- 6:05 AM Ticket #4706 (Peptide flip: Simulation must be running!) closed by
- fixed: This was effectively fixed by ISOLDE's new GUI, which replaces …
- 6:03 AM Ticket #4702 (OpenMMException: Error compiling kernel: Compile Server Error) closed by
- can't reproduce: Just doing some spring cleaning and closing out old tickets. Hopefully …
- 6:01 AM Ticket #4658 (OpenMMException: Error compiling kernel: Compile Server Error) closed by
- can't reproduce
- 6:00 AM Ticket #4654 (ISOLDE: volumecommand.volume being passed session of None) closed by
- fixed
- 5:59 AM Ticket #4623 (ISOLDE: wrapped C/C++ object of type QLabel has been deleted) closed by
- fixed: Long since fixed, but I forgot to close this ticket. Sorry!
- 5:57 AM Ticket #4507 (ISOLDE: wrapped C/C++ object of type QTableWidget has been deleted) closed by
- fixed: Fixed by new GUI.
- 5:47 AM Ticket #4305 (ISOLDE residue validation: cannot unpack non-iterable ...) closed by
- fixed: Long since fixed, but forgot to close the ticket. Sorry!
- 5:47 AM Ticket #4267 (Problem docking ISOLDE widget) closed by
- fixed: This should be mostly fixed by the new ISOLDE GUI - its minimum height …
- 5:44 AM Ticket #4166 (ISOLDE/ParmEd: UnboundLocalError: local variable 'compiler_package' ...) closed by
- fixed
- 5:43 AM Ticket #4122 (End of simulation: 'PositionRestraintMgr' object has no attribute ...) closed by
- fixed: Finally got around to making sure ISOLDE (as of the next release) can …
- 5:41 AM Ticket #4093 (OpenMM crash uploading OpenCL array) closed by
- can't reproduce
- 5:40 AM Ticket #4018 (ISOLDE: OpenMM: find_glycan_template_name_and_link: multiple bonds ...) closed by
- fixed
- 5:39 AM Ticket #4003 (OpenMM OpenCL crash on Mac in Intel graphics driver) closed by
- can't reproduce
- 5:38 AM Ticket #3966 (Clipper: Failure to read BUSTER MTZ file) closed by
- fixed: Seems I never closed this. Doing so now.
- 5:37 AM Ticket #3917 (ISOLDE: get_symmetry_handler: structure is None) closed by
- fixed: Clearing out the backlog of fixed-but-unclosed tickets.
- 5:36 AM Ticket #3807 (OpenMM crash with 0.91 run directly from .dmg) closed by
- can't reproduce
- 5:36 AM Ticket #3805 (Flip peptide bond: Simulation must be running) closed by
- fixed
- 5:35 AM Ticket #3774 ('ProperDihedral' object has no attribute '_c_pointer_ref') closed by
- fixed: Most likely a GUI table failing to refresh itself when the selected …
- 5:34 AM Ticket #3768 (OpenMM/OpenCL crash) closed by
- can't reproduce
- 5:33 AM Ticket #3752 (ISOLDE validation: not enough values to unpack) closed by
- fixed
- 5:32 AM Ticket #3747 (Register shift: m > k must hold) closed by
- fixed: Sorry... forgot to close this ticket at the time.
- 5:31 AM Ticket #3743 (ISOLDE crash on startup (divide by zero; structure-prediction program ...) closed by
- fixed: Sorry... found and fixed the bug back then, but failed to close the …
- 5:29 AM Ticket #3712 (Clipper map roaming overflow in computing bounds) closed by
- can't reproduce
- 5:27 AM Ticket #3699 (Starting simulation: clEnqueueNDRangeKernel (-4)) closed by
- can't reproduce
- 5:27 AM Ticket #3696 (ISOLDE color-picker problem) closed by
- fixed: Turns out I have a really bad habit of not closing out old tickets... …
- 5:25 AM Ticket #3616 (cartoon() 'atoms' parameter type changed) closed by
- fixed
- 5:24 AM Ticket #3613 (ISOLDE: cannot import name 'save' from 'chimerax.core.commands') closed by
- fixed
- 5:23 AM Ticket #3601 (_show_selected_unparameterised_residue: not enough values to unpack) closed by
- fixed: Sorry for not closing this back then... better late than never!
- 5:21 AM Ticket #3593 (stepper.step_forward: index is out of bounds) closed by
- fixed: The offending code was retired some time ago. :)
- 5:20 AM Ticket #3569 (Problem reading MTZ data: list index out of range) closed by
- fixed: Clearing out old tickets - this was fixed quite some time ago.
- 5:18 AM Ticket #3566 (OpenMM: No template found for residue) closed by
- fixed: Clearing out the backlog of old tickets which (for various reasons) I …
- 5:16 AM Ticket #3538 (Problem matching GLYCAM templates) closed by
- can't reproduce
- 5:16 AM Ticket #3535 (Nucleotides: asking for distance from None) closed by
- fixed: Sorry for the necropost - just closing out old tickets. :)
- 5:14 AM Ticket #3508 (ISOLDE's self.selected_model is dead) closed by
- fixed: Well, I've *finally* gotten around to making ISOLDE gracefully recover …
- 5:12 AM Ticket #3407 (Maximum common substructure) closed by
- worksforme: I still need to revisit this at some time in the future to make it …
- 5:10 AM Ticket #3377 (Template mismatch errors) closed by
- fixed: Closing out old tickets - ISOLDE's had functionality to help with …
- 5:09 AM Ticket #3298 (Crash getting global interpreter lock) closed by
- fixed
- 5:08 AM Ticket #3221 (Chain mix up using ISOLDE) closed by
- can't reproduce
- 5:07 AM Ticket #3156 (Error initializing context: clGetPlatformIDs) closed by
- can't reproduce: Hmm... looks like I forgot to close out this ticket. I trust …
- 5:02 AM Ticket #3143 (Starting simulation: Error initializing context: clGetDeviceIDs) closed by
- fixed
- 5:01 AM Ticket #3068 (Crash starting ISOLDE) closed by
- can't reproduce
- 5:01 AM Ticket #3049 (OpenMM coordinate update: RuntimeError: Release Object) closed by
- can't reproduce
- 5:00 AM Ticket #3034 (Infrequent ISOLDE crash) closed by
- fixed: Fixed, I guess... (problem hasn't cropped up in a long long time).
- 3:56 AM Ticket #3021 (ISOLDE: various errors) closed by
- can't reproduce
- 3:55 AM Ticket #2992 (ISOLDE referencing a Structure that's been deleted) closed by
- fixed: All the scenarios I know of that could potentially lead to this error …
- 3:54 AM Ticket #2905 (OpenMM: Multiple matching templates found for residue) closed by
- fixed: While I do occasionally see cases where a tightly-constrained …
- 3:50 AM Ticket #2798 (Arcane version-conflict reporting) closed by
- fixed
- 3:50 AM Ticket #2796 (Crash opening structure in conjunction with ISOLDE) closed by
- can't reproduce
- 3:48 AM Ticket #2773 (Crash installing ISOLDE(?)) closed by
- can't reproduce: Just going through and closing out old tickets.
- 3:47 AM Ticket #2764 (ISOLDE not longer compatible with 0.9) closed by
- fixed: Doing some spring cleaning, closing out obsolete old tickets.
- 3:46 AM Ticket #2735 (OpenMM crash running simulation) closed by
- can't reproduce
- 3:44 AM Ticket #2652 (ISOLDE: using deleted 'session' attribute of dead Structure) closed by
- fixed: From the next ISOLDE release onwards, closing the working model with a …
- 3:42 AM Ticket #2531 ("spotlight moved" trigger handler using dead Structure) closed by
- fixed
- 3:42 AM Ticket #2424 (Array of coordinates is None) closed by
- fixed
- 3:41 AM Ticket #2374 (ISOLDE: multiple different errors) closed by
- fixed
- 3:39 AM Ticket #2336 (ChimeraX bug report submission) closed by
- fixed: Clearing out old tickets (this was fixed long ago, but I forgot to …
- 3:38 AM Ticket #2204 (ISOLDE: ramaplot: wrapped C/C++ object of type QVBoxLayout has been deleted) closed by
- fixed
- 3:37 AM Ticket #1856 (OpenGL error, glClear: invalid framebuffer operation) closed by
- can't reproduce: Doing some spring-cleaning, clearing away old tickets. Haven't seen …
- 2:46 AM Ticket #5746 (OpenMMException: Error compiling program: nvrtc: error: failed to open ...) closed by
- can't reproduce
- 2:45 AM Ticket #5745 (OpenMM: Error compiling program: nvrtc: error: failed to open ...) closed by
- fixed: Long since fixed - ISOLDE now automatically falls back to using OpenCL …
- 2:43 AM Ticket #5670 (OpenMM: Error uploading array TabulatedFunction) closed by
- can't reproduce
- 2:42 AM Ticket #3269 (Custom multitouch trackpad bindings) closed by
- fixed: Sorry for not closing this at the time…
- 2:41 AM Ticket #2906 (Building OpenMM installer in devtoolset-7) closed by
- wontfix: Closing out this ancient ticket, since things have well and truly moved on.
Jan 17, 2023:
- 7:32 PM Ticket #8320 (volume multiply: local variable 'v0' referenced before assignment) closed by
- fixed: Fixed "volume multiply" with one map and inPlace true. Made a new …
- 7:32 PM Ticket #8325 (Add an inPlace option to the "volume scale" command) created by
- In ticket #8320 Tristan was trying to invert an map in place using the …
- 5:25 PM 2023-1-19 edited by
- (diff)
- 5:25 PM 2023-1-19 edited by
- (diff)
- 5:24 PM 2023-1-19 created by
- 5:22 PM DeveloperMeetings edited by
- (diff)
- 5:08 PM Training edited by
- (diff)
- 2:49 PM Ticket #8324 (Crash in removeDockWidget from clicking on a half-docked panel) created by
- […]
- 1:37 PM Ticket #8323 (Coot-like "replace fragment") created by
- As per this thread: …
- 12:54 PM Ticket #8319 (Looking Glass: libHoloPlayCore.dylib is an incompatible architecture) closed by
- duplicate: Duplicate of #8318.
- 11:48 AM Ticket #8306 (Crash in Qt event loop after showing Volume Viewer, lots of clipper use) closed by
- can't reproduce
- 11:43 AM Ticket #8305 (AlphaFold prediction failure) closed by
- not a bug: From the files you attached, your prediction sequence is DNA …
- 10:10 AM Ticket #8322 (Unsupported scale factor (0.000000) detected on Display0) closed by
- limitation: Looks the same as #8226
- 10:04 AM Ticket #8321 (Crash QGridLayout destructor) closed by
- can't reproduce: My best guess is that it's XMAS gui code from the session.
- 9:43 AM Ticket #8317 (Crash in event loop) closed by
- can't reproduce
- 9:40 AM Ticket #8316 (Crash in Qt event loop after showing cartoons) closed by
- can't reproduce
- 9:36 AM Ticket #8315 (Crash in event loop) closed by
- can't reproduce
- 9:32 AM Ticket #8314 (AlphaFold: NotImplementedError: A UTF-8 locale is required) closed by
- duplicate: duplicate of #8313
- 9:18 AM Ticket #8311 (MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted) closed by
- duplicate
- 9:14 AM Ticket #8310 (MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted) closed by
- duplicate: long ago fixed
- 9:10 AM Ticket #8309 (Crash in event loop) closed by
- can't reproduce
- 9:00 AM Ticket #8307 (Dead Structure Measurement tool trying to show status) closed by
- duplicate: duplicate of #8148
- 8:57 AM Ticket #4917 (Keyboard interrupt while finding possible templates) closed by
- fixed: Took your advice on that... but forgot to actually close the ticket at …
- 8:56 AM Ticket #4920 (Crash in matplotlib updating Ramachandran plot) closed by
- can't reproduce
- 8:55 AM Ticket #4958 (peptide flip: Simulation must be running!) closed by
- fixed
- 8:54 AM Ticket #5576 (Update coordinates: OpenMM: RuntimeError: Release Object) closed by
- can't reproduce
- 8:53 AM Ticket #5783 (Problem swapping pseudo symmetric side chains) closed by
- can't reproduce
- 8:51 AM Ticket #5799 (ISOLDE crash in get_shell_of_residues: extremely deep recursion in ...) closed by
- fixed: Resolving this as "effectively" fixed, since the new soft-core …
- 8:49 AM Ticket #5813 (Version conflict during ISOLDE initialization?!?) closed by
- can't reproduce
- 8:48 AM Ticket #5822 (ISOLDE: .cif does not appear to contain any valid residue templates) closed by
- fixed: Never did hear back about those templates, I'm afraid. Anyway, as of …
- 8:45 AM Ticket #5899 (ISOLDE: swap equivalent atoms: Values array length 3 does not match ...) closed by
- fixed
- 8:44 AM Ticket #5900 (ISOLDE: add real-space map: structure is None) closed by
- fixed: Very sorry about the super-slow response, but this is now fixed.
- 8:42 AM Ticket #5957 (Ramachandran plot accessing deleted widgets) closed by
- fixed: Ramachandran plot was completely reworked in the ISOLDE 1.4 release.
- 8:41 AM Ticket #5961 (Crash in OpenMM getState) closed by
- fixed
- 8:41 AM Ticket #6050 (ISOLDE vs. submodels) closed by
- can't reproduce
- 8:38 AM Ticket #8322 (Unsupported scale factor (0.000000) detected on Display0) created by
- […]
- 8:35 AM Ticket #6087 (ISOLDE: swap equivalent atoms: Values array length 3 does not match ...) closed by
- fixed
- 8:35 AM Ticket #6088 (ISOLDE: add real-space map: structure is None) closed by
- fixed: This should all be fixed now.
- 8:34 AM Ticket #6095 ((ISOLDE?) segmentation fault) closed by
- can't reproduce
- 8:33 AM Ticket #6128 (Failure opening .mtz file: Spgr_cacheobj: symops fail) closed by
- can't reproduce
- 8:28 AM Ticket #6142 (ISOLDE: various errors) closed by
- fixed: Going to tentatively close this as fixed - haven't seen another …
- 8:25 AM Ticket #6245 (ISOLDE _show_selected_clash: 'residues' is empty) closed by
- fixed: If I recall correctly, the clashes table wasn't clearing itself when …
- 8:23 AM Ticket #6283 (phi-psi in isolde does not show current selection.) closed by
- not a bug: Sorry about the ridiculously slow response - seems this one fell off …
- 8:19 AM Ticket #6304 (Various errors) closed by
- fixed: Everything now seems to be working OK for both ortho and mono camera modes.
- 8:16 AM Ticket #6306 (Crash finding clashing atoms) closed by
- fixed: This was able to happen if the user hit the sim stop button while the …
- 8:15 AM Ticket #6455 (ISOLDE: crash in find_clashing_atoms) closed by
- fixed: This was able to happen if the user hit the sim stop button while the …
- 8:11 AM Ticket #6510 (Zoom/recenter with mouse) closed by
- fixed: This is now all working quite nicely - with Clipper active, …
- 8:06 AM Ticket #6783 (ISOLDE not listing clashes) closed by
- fixed: Abandoned the use of forces as a proxy for clashes - the Clashes table …
- 8:04 AM Ticket #7691 (Clipper closing possible already-closed model during session reset) closed by
- fixed: Going to close this as *probably* fixed - will revisit if it crops up …
- 8:03 AM Ticket #7709 (Simulation stop: 'NoneType' object has no attribute 'atoms') closed by
- fixed: Another instance of the rotamer preview bug.
- 8:01 AM Ticket #6844 (Flip peptide bond: wrapped C/C++ object of type QTableWidget has been ...) closed by
- fixed: Totally rebuilt GUI as of 1.4, taking care of this bug amongst others.
- 8:00 AM Ticket #8321 (Crash QGridLayout destructor) created by
- […]
- 7:59 AM Ticket #7168 (ISOLDE/OpenMM: fitting Ramachandran outliers: Particle coordinate is nan) closed by
- fixed: This should become *almost* impossible in ISOLDE 1.6 (when it comes …
- 7:51 AM Ticket #7270 (ISOLDE: sim_manager is None) closed by
- fixed: This should be fixed in the latest versions. Please let me know if it …
- 7:49 AM Ticket #7394 (Stop simulation: model is None) closed by
- fixed: This was happening if the simulation was stopped with the rotamer …
- 7:42 AM Ticket #7504 (ISOLDE Deleting symmetry model: 'AtomicStructure' object has no ...) closed by
- fixed: As of the next release, ISOLDE will now recover gracefully when the …
- 7:39 AM Ticket #7636 (ISOLDE holding ref to deleted structure) closed by
- fixed
- 7:39 AM Ticket #7638 (ISOLDE holding ref to deleted structure) closed by
- fixed
- 7:38 AM Ticket #7639 (Models closed while simulation running) closed by
- fixed
- 7:37 AM Ticket #7647 (Second sim stop: 'NoneType' object has no attribute 'atoms') closed by
- fixed
- 7:37 AM Ticket #7649 (Second sim stop: 'NoneType' object has no attribute 'atoms') closed by
- fixed
- 7:36 AM Ticket #7658 (Model is None after sim stop, and then things go pear-shaped) closed by
- fixed
- 7:35 AM Ticket #7756 (Stopping simulation: 'NoneType' object has no attribute 'atoms') closed by
- fixed: This was happening if a simulation was stopped with the rotamer …
- 7:34 AM Ticket #7873 (ISOLDE: wrapped C/C++ object of type WinAutoResizeQComboBox has been ...) closed by
- fixed
- 7:32 AM Ticket #8089 (Clipper: AttributeError: 'NoneType' object has no attribute ...) closed by
- fixed
- 7:31 AM Ticket #8098 (ISOLDE: 'AtomicStructure' object has no attribute 'session') closed by
- fixed
- 7:30 AM Ticket #8099 (ISOLDE: close session: 'AtomicStructure' object has no attribute ...) closed by
- fixed: As of the next release, ISOLDE will now recover gracefully if the …
- 7:12 AM Ticket #8320 (volume multiply: local variable 'v0' referenced before assignment) created by
- […]
- 7:01 AM Ticket #8204 ('close' after paused simulation: 'AtomicStructure' object has no ...) closed by
- fixed
- 7:00 AM Ticket #8269 (ISOLDE: closing structure after paused sim: 'AtomicStructure' object ...) closed by
- fixed
- 7:00 AM Ticket #8319 (Looking Glass: libHoloPlayCore.dylib is an incompatible architecture) created by
- […] env&log.txt
- 6:56 AM Ticket #8318 (Looking Glass: libHoloPlayCore.dylib is an incompatible architecture) created by
- […]
- 4:08 AM Ticket #8317 (Crash in event loop) created by
- […]
- 3:52 AM Ticket #8316 (Crash in Qt event loop after showing cartoons) created by
- […]
- 3:48 AM Ticket #8315 (Crash in event loop) created by
- […]
Jan 16, 2023:
- 5:42 AM Ticket #8314 (AlphaFold: NotImplementedError: A UTF-8 locale is required) created by
- […]
- 5:39 AM Ticket #8313 (AlphaFold: A UTF-8 locale is required. Got ANSI_X3.4-1968) created by
- […]
- 2:40 AM Ticket #8312 (ISOLDE: "start sim": No compatible OpenCL platform is available) created by
- […]
Jan 15, 2023:
- 5:29 PM Ticket #8311 (MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted) created by
- […]
- 5:19 PM Ticket #8310 (MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted) created by
- […]
- 2:56 PM Ticket #8309 (Crash in event loop) created by
- […]
- 1:33 PM Ticket #8308 (Crash opening mmCIF) created by
- […]
Jan 14, 2023:
- 2:22 PM Ticket #8307 (Dead Structure Measurement tool trying to show status) created by
- […]
- 1:10 PM Ticket #8306 (Crash in Qt event loop after showing Volume Viewer, lots of clipper use) created by
- […]
- 7:58 AM Ticket #8305 (AlphaFold prediction failure) created by
- […] results.zip
Jan 13, 2023:
- 2:18 PM Ticket #8304 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce: Hi Andrew, Thanks for reporting this problem. We believe it is fixed …
- 2:15 PM Ticket #8303 (Crash saving image) closed by
- can't reproduce
- 2:12 PM Ticket #8304 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 2:08 PM Ticket #8303 (Crash saving image) created by
- […]
- 1:55 PM phenix-1-12-23 edited by
- (diff)
- 1:54 PM Features edited by
- (diff)
- 1:54 PM Features edited by
- (diff)
- 12:02 PM Ticket #8299 (Graphics crash, macOS 13.1, M1 Pro graphics) closed by
- nonchimerax: Apple M1 graphics driver crash. This is the first one I have ever …
- 11:51 AM Ticket #8301 (New AlphaFold errors) closed by
- nonchimerax: I worked on this error 8 months ago, ticket #6961 …
- 11:38 AM Ticket #8302 (Log panel is blank, Windows) closed by
- nonchimerax: […]
- 11:37 AM Ticket #8302 (Log panel is blank, Windows) created by
- Log panel is blank. Also Help Viewer shows nothing. Apparently Qt …
- 11:10 AM Ticket #8301 (New AlphaFold errors) created by
- […]
- 10:46 AM Ticket #8300 (Didn't find section 'Peptide bond' in tab 'ISOLDE') closed by
- limitation: Currently you need to restart ChimeraX after installing ISOLDE for the …
- 9:48 AM Ticket #8298 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce
- 9:46 AM Ticket #8297 (Crash using File→Open on Windows and/or in return statement) closed by
- can't reproduce
- 6:31 AM Ticket #8300 (Didn't find section 'Peptide bond' in tab 'ISOLDE') created by
- […]
- 1:34 AM Ticket #8299 (Graphics crash, macOS 13.1, M1 Pro graphics) created by
- […]
Jan 12, 2023:
- 6:30 PM Ticket #8298 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 4:39 PM Ticket #8297 (Crash using File→Open on Windows and/or in return statement) created by
- […]
- 4:06 PM 2023-1-12 edited by
- (diff)
- 4:05 PM 2023-1-12 edited by
- (diff)
- 4:05 PM 2023-1-12 edited by
- (diff)
- 2:59 PM Ticket #8295 (Allow different case for fetch database name) closed by
- fixed
- 1:14 PM Ticket #8294 (Code signature problem?) closed by
- nonchimerax: The code signature for ChimeraX 1.5 is of course fine, since it works …
- 1:08 PM Ticket #8293 (Graphics crash, macOS 10.15.4, Intel Iris Plus Graphics) closed by
- nonchimerax: Apple Intel graphics driver crash.
- 12:59 PM Ticket #8296 (Add movieFramerate option to "coordset slider" command) closed by
- fixed: Done. The default recorded movie playback speed is 25 frames per …
- 12:54 PM Ticket #8296 (Add movieFramerate option to "coordset slider" command) created by
- […]
- 9:00 AM Ticket #8295 (Allow different case for fetch database name) created by
- […]
- 8:48 AM Ticket #8280 (ISOLDE: 'close' after 'sim pause': 'AtomicStructure' object has no ...) closed by
- fixed: OK, ISOLDE now recovers gracefully if the working model is deleted …
- 8:06 AM Ticket #8294 (Code signature problem?) created by
- […]
Jan 11, 2023:
- 11:04 PM Ticket #8293 (Graphics crash, macOS 10.15.4, Intel Iris Plus Graphics) created by
- […]
- 6:12 PM Ticket #8292 (Adding DisplayVersion to registry for WIndows installation) closed by
- fixed: ChimeraX uses innosetup to build the installer. I've added the …
- 3:49 PM Training edited by
- (diff)
- 3:44 PM Training edited by
- (diff)
- 1:23 PM Ticket #8288 (List index out of range for UniProt DGAL_ECOLI) closed by
- fixed: If the accession code (P02927) maps to a different entry (P0AEE6), the …
- 11:20 AM Ticket #8291 (Crash in event loop after using XMAS) closed by
- can't reproduce
- 11:09 AM Ticket #8289 (Long atom spec crashes ChimeraX) closed by
- duplicate
- 5:07 AM Ticket #8292 (Adding DisplayVersion to registry for WIndows installation) created by
- […]
- 5:05 AM Ticket #8291 (Crash in event loop after using XMAS) created by
- […]
- 12:03 AM Ticket #8290 (Mol2 not creating metal-coordination pseudobonds) created by
- […]
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