![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Nov 8, 2019:
- 3:42 PM Ticket #2556 (DICOM reader: broken data stream when reading image file) closed by
- nonchimerax: The error message "OSError: broken data stream when reading image …
- 3:35 PM Ticket #2557 (Graphics hardware error) closed by
- nonchimerax: Crash in Apple graphics driver. Unfortunately macOS graphics drivers …
- 3:24 PM Ticket #2555 (Memory leak fitting volume in volume) closed by
- fixed: Fixed in tonight's ChimeraX builds. There were two memory leaks. …
- 2:16 PM Ticket #2557 (Graphics hardware error) created by
- […]
- 1:02 PM Ticket #2556 (DICOM reader: broken data stream when reading image file) created by
- […]
- 12:29 PM Ticket #2555 (Memory leak fitting volume in volume) created by
- Begin forwarded message: From: Andrei Istrate Subject: ChimeraX …
- 12:00 PM Ticket #2554 (Command History window appears randomly) created by
- […] test3.py
- 3:48 AM Ticket #2553 (Spurious dependencies with "reinstall true") created by
- […]
- 2:02 AM Ticket #2552 (Enhancement: mousemode to Z-shift CofR) created by
- I've just added this to Clipper, but it might make sense as part of …
Nov 7, 2019:
- 2:44 PM Ticket #2551 (camera sbs opengl errors) closed by
- fixed: Fixed bug using camera option pixelEyeSeparation. That option only …
- 2:25 PM Ticket #2551 (camera sbs opengl errors) created by
- […]
- 1:06 PM Ticket #2549 (Inadequate OpenGL) closed by
- not a bug: ChimeraX could not get OpenGL context. Save image error reporting was …
- 12:53 PM Ticket #2550 ('OptionalRGBAOption' object has no attribute 'get') closed by
- duplicate: Hi, Thanks for reporting this problem. It has been fixed for a few …
- 12:43 PM Ticket #2550 ('OptionalRGBAOption' object has no attribute 'get') created by
- […]
- 12:09 PM Ticket #2549 (Inadequate OpenGL) created by
- […]
- 10:55 AM Ticket #1990 (model-list widgets need to respond to name changes) closed by
- fixed: Update menu button if model name (only) changes
Nov 6, 2019:
- 5:11 PM Ticket #2492 (Error closing RealSense camera) closed by
- fixed: Fixed. RealSense Model had two delete() methods defined.
- 12:58 PM Ticket #2545 (Bad HTML anchors in help for multi-word commands) closed by
- fixed: If Sphinx doesn't use anchors with spaces and uses hyphens, then …
- 12:51 PM Ticket #2548 (surface dust command hides clip caps) closed by
- fixed: Fixed. Now surface dust does not apply to clip caps.
- 12:45 PM Ticket #2548 (surface dust command hides clip caps) created by
- […]
- 10:57 AM Ticket #2547 (Have toolshed say "reinstall" for already installed bundles) created by
- It would be great if the toolshed knew which bundles were already …
- 10:46 AM Ticket #2546 (Wrong OpenCL driver used on machine with Nvidia and Intel GPUs) created by
- Bug report from Joel Mackay in Sydney. On his Windows machine …
- 5:29 AM Ticket #2545 (Bad HTML anchors in help for multi-word commands) created by
- Adding command documentation for ISOLDE to work with the new …
- 2:16 AM Ticket #2543 (Clipper: No module named 'chimerax.core.graphics.clipping') closed by
- duplicate: Discussed with Joel off-list.
- 2:15 AM Ticket #2544 (Wrong version of Clipper installed) closed by
- duplicate
Nov 5, 2019:
- 7:19 PM Ticket #2544 (Wrong version of Clipper installed) created by
- […]
- 6:25 PM Ticket #2537 (User interface blank Windows 10 with new Intel driver 26.x.x.x) closed by
- fixed: Worked around bug as described in previous comment. Some black …
- 5:17 PM Ticket #2542 (Re: [chimerax-users] Catalina woes) closed by
- not a bug
- 5:16 PM Ticket #2543 (Clipper: No module named 'chimerax.core.graphics.clipping') created by
- […]
- 3:16 PM Ticket #2542 (Re: [chimerax-users] Catalina woes) created by
- […]
- 11:01 AM Ticket #2541 (Catalina woes) closed by
- not a bug
- 10:47 AM Ticket #2541 (Catalina woes) created by
- […] [[Image(...)]]
Nov 4, 2019:
- 11:26 AM Ticket #2368 (Handling missing structure pseudobonds when editing chains) closed by
- fixed: No problem -- we all have things to do. Committed a fix for the …
- 1:09 AM Ticket #2540 (chimerax don't start on windows 10) created by
- […]
Nov 3, 2019:
- 12:02 PM Ticket #2539 (Clipper prevents session saving) created by
- […]
- 11:59 AM Ticket #2538 (Clipper not saving in sessions) created by
- […]
Oct 31, 2019:
- 12:52 PM Ticket #2535 (Crash on structure with non-unique atom names) closed by
- fixed: The non-unique naming of the atoms in this large residue caused addh …
- 12:31 PM Ticket #2537 (User interface blank Windows 10 with new Intel driver 26.x.x.x) created by
- […]
Oct 30, 2019:
- 7:59 PM Ticket #2536 (Tug mouse mode bad allocation error) created by
- […]
- 4:29 PM Ticket #2535 (Crash on structure with non-unique atom names) created by
- […] DB13038_triolein.pdb
- 1:27 PM Ticket #2534 (Inconsistent ribbon selection behavior) created by
- If I control-click on a ribbon section, it selects the corresponding …
Oct 29, 2019:
- 10:54 PM Ticket #2523 (Better session debugging info) closed by
- fixed: I think it must, or else the "RuntimeError: Residue already deleted" …
- 10:10 PM Ticket #2526 (help links in Log for internal aliases (e.g. ribbon, blastpdb, mm, ...) closed by
- fixed: Help links for aliases need to be done by hand. I've added links for: …
- 2:37 PM Ticket #2533 ("tape measure" mouse mode: cannot unpack non-iterable NoneType object) closed by
- fixed: Fixed. Yes tape measure does support DICOM and all volume formats. …
- 2:23 PM Ticket #2533 ("tape measure" mouse mode: cannot unpack non-iterable NoneType object) created by
- […]
- 10:37 AM Ticket #2532 (SwissDock .chimerax file) closed by
- nonchimerax: Hi Angelo, I know it's confusing, but .chimerax files are used in …
Oct 28, 2019:
- 9:00 PM Ticket #2532 (SwissDock .chimerax file) created by
- […] open.chimerax
- 1:54 PM Ticket #2531 ("spotlight moved" trigger handler using dead Structure) created by
- […]
- 11:37 AM Ticket #2368 (Handling missing structure pseudobonds when editing chains) reopened by
- Needs to be smarter about more than a single atom/bond being added in …
- 10:29 AM Ticket #2530 (Crash in free_keys_object/subtype_dealloc) closed by
- can't reproduce
- 9:24 AM Ticket #2530 (Crash in free_keys_object/subtype_dealloc) created by
- […]
Oct 25, 2019:
- 3:30 PM MSC2019Deliverables edited by
- (diff)
- 3:25 PM MSC2019Deliverables edited by
- (diff)
- 3:16 PM MSC2019Deliverables edited by
- (diff)
- 3:15 PM Ticket #2527 (Deleting backbone bond should create "missing structure" pseudobond) closed by
- fixed: Okay, will be in next successful build.
- 2:57 PM MSC2019Deliverables edited by
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- 2:04 PM MSC2019Deliverables edited by
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- 2:02 PM MSC2019Deliverables edited by
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- 1:59 PM MSC2019Deliverables edited by
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- 1:53 PM MSC2019Deliverables edited by
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- 1:52 PM MSC2019Deliverables edited by
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- 1:44 PM MSC2019Deliverables edited by
- (diff)
- 2:45 AM Ticket #2529 (chimerax don't start on windows 10) created by
- […]
- 1:49 AM Ticket #2528 (Renumbering residues) created by
- (Vaguely recall asking this once before, but can't find the ticket) …
- 1:23 AM Ticket #2527 (Deleting backbone bond should create "missing structure" pseudobond) created by
- If I delete an N-C bond without deleting any atoms, then no "missing …
Oct 24, 2019:
- 4:53 PM MSC2019Deliverables edited by
- (diff)
- 4:51 PM MSC2019Deliverables edited by
- (diff)
- 4:33 PM MSC2019Deliverables edited by
- (diff)
- 4:32 PM MSC2019Deliverables edited by
- (diff)
- 2:57 PM MSC2019Deliverables edited by
- (diff)
- 2:55 PM Ticket #1658 (Structure sequence returns NULL structure pointer) closed by
- can't reproduce: No feedback from user
- 2:54 PM Ticket #1970 (C++ component of Ring gone) closed by
- duplicate: This is probably a duplicate of #2240 which was just fixed.
- 2:52 PM Ticket #2281 (C++ Ring object gone) closed by
- duplicate: This is probably a duplicate of #2240 which has been fixed.
- 2:50 PM Ticket #2420 (Error with nucleotide/ring graphics after session restore) closed by
- fixed: Ring-list info can change "spontaneously" if anything else cause a …
- 2:09 PM MSC2019Deliverables edited by
- (diff)
- 1:57 PM MSC2019Deliverables edited by
- (diff)
- 1:54 PM MSC2019Deliverables edited by
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- 1:52 PM MSC2019Deliverables edited by
- (diff)
- 1:40 PM MSC2019Deliverables edited by
- (diff)
- 1:14 PM MSC2019Deliverables edited by
- (diff)
- 12:08 PM DeveloperMeetings edited by
- (diff)
Oct 23, 2019:
- 9:43 PM MSC2019Deliverables edited by
- (diff)
- 9:37 PM WikiStart edited by
- (diff)
- 9:36 PM MSC2019Deliverables created by
- 10:51 AM ChangeLog edited by
- (diff)
- 10:35 AM Ticket #2525 (Crash drawing window) closed by
- can't reproduce: Thanks for the info! Though it doesn't help immediately, the more …
- 10:27 AM Ticket #2526 (help links in Log for internal aliases (e.g. ribbon, blastpdb, mm, ...) created by
- If somebody uses an internal alias command like "ribbon" or "colordef" …
Oct 22, 2019:
- 2:23 PM Ticket #2525 (Crash drawing window) created by
- […]
- 11:54 AM Ticket #2507 (MultColorButton stylesheet errors) closed by
- fixed: Use urllib.request.unquote to convert the escape sequences back into …
- 11:41 AM Ticket #2524 (Clipper: No module named 'chimerax.core.graphics.clipping') closed by
- duplicate
- 10:55 AM Ticket #2524 (Clipper: No module named 'chimerax.core.graphics.clipping') created by
- […]
- 10:43 AM Ticket #2517 (Start chimeraX (daily version)) reopened by
- Sorry, this might be a different bug. To see, please run the dxdiag …
- 10:38 AM Ticket #2513 (Blank main window on Windows 10) closed by
- duplicate: This is probably a duplicate of #2440. The solution was to install an …
- 10:31 AM Ticket #2518 (Invisible menus) closed by
- duplicate: This is a duplicate of #2440. The solution was to install an earlier …
- 10:30 AM Ticket #2517 (Start chimeraX (daily version)) closed by
- duplicate: This is a duplicate of #2440. The solution was to install an earlier …
- 10:23 AM ChangeLog edited by
- (diff)
- 10:21 AM ChangeLog edited by
- (diff)
- 10:15 AM Ticket #2519 (User Guide index added tools not in alphabetical order) closed by
- fixed
- 7:23 AM Ticket #2523 (Better session debugging info) created by
- […]
Oct 21, 2019:
- 4:46 PM Ticket #2497 (Session restore with BILD model fails) closed by
- fixed: Looks good.
- 3:11 PM Ticket #2522 (H-bonds tool's model-restriction option error) closed by
- fixed
- 2:17 PM Ticket #2522 (H-bonds tool's model-restriction option error) created by
- […]
- 1:13 PM Ticket #2521 (Crash in free_keys_object/subtype_dealloc) closed by
- can't reproduce
- 1:11 PM Ticket #2521 (Crash in free_keys_object/subtype_dealloc) created by
- […]
- 10:47 AM Ticket #2516 (ISOLDE error) closed by
- duplicate
- 10:46 AM Ticket #2516 (ISOLDE error) reopened by
- 10:00 AM Ticket #2520 (ISOLDE synopsis in User Guide Index should link to ISOLDE website) created by
- Hi Tristan, ChimeraX tools automatically (through some magic from Greg …
- 9:42 AM Ticket #2519 (User Guide index added tools not in alphabetical order) created by
- Minor issue. In the auto-assembled User Guide Index included in the …
- 6:52 AM Ticket #2516 (ISOLDE error) closed by
- duplicate: Duplicate of #2515.
- 6:52 AM Ticket #2515 (ISOLDE error when attempting to restrain hydrogens) closed by
- fixed: Selecting a hydrogen atom will no longer cause the position restraints …
- 6:28 AM Ticket #2518 (Invisible menus) created by
- […]
- 6:13 AM Ticket #2517 (Start chimeraX (daily version)) created by
- […]
Oct 19, 2019:
- 9:00 AM Ticket #2516 (ISOLDE error) created by
- […]
- 9:00 AM Ticket #2515 (ISOLDE error when attempting to restrain hydrogens) created by
- […]
Oct 18, 2019:
- 5:34 PM Ticket #2368 (Handling missing structure pseudobonds when editing chains) closed by
- fixed: I believe missing-structure pseudo bonds adjust accordingly now.
- 5:01 PM Ticket #2513 (Blank main window on Windows 10) created by
- […] problem.PNG
- 3:51 PM Ticket #2512 (bundle "ChimeraX-Map"'s API forgot to override open_file()) closed by
- fixed
- 3:43 PM Ticket #2512 (bundle "ChimeraX-Map"'s API forgot to override open_file()) created by
- […]
- 2:06 PM Ticket #2511 (Can't open files due to cache problem) closed by
- not a bug: Could catch this error from os.makedirs() trying to create …
- 1:55 PM Ticket #2505 (Session save failed: AttributeError: 'Sequence' object has no ...) closed by
- fixed: Sequence-to-chain information wasn't being saved in the session. Now …
- 1:52 PM Ticket #2451 (Tiling not working for volumes) closed by
- duplicate: This was fixed as part of #2484.
- 1:38 PM Ticket #2511 (Can't open files due to cache problem) created by
- […]
- 12:15 PM Ticket #2510 (Toolshed startup code not guarding against 'cache_dir' being None) closed by
- fixed: Fixed in 36553cd0e. Check whether the cache directory is …
- 11:42 AM Ticket #2510 (Toolshed startup code not guarding against 'cache_dir' being None) created by
- Hello and good morning, I have always had a great experience using …
- 10:55 AM Ticket #2509 (Volume Viewer hanging redraw?) closed by
- can't reproduce: Don't know what problem the user is reporting. They opened and mmCIF …
- 8:20 AM Ticket #2509 (Volume Viewer hanging redraw?) created by
- […]
- 6:24 AM Ticket #2508 (atomic structure session save: 'utf-8' codec can't decode byte: ...) created by
- […]
Oct 17, 2019:
- 3:30 PM Ticket #2507 (MultColorButton stylesheet errors) created by
- […] test1.cmap
- 10:34 AM Ticket #2506 (Crash closing a window) closed by
- can't reproduce
- 8:30 AM Ticket #2506 (Crash closing a window) created by
- […]
Oct 16, 2019:
- 4:45 PM Ticket #1254 (Too many bundle cache startup messages) closed by
- fixed: done.
- 4:01 PM Ticket #2439 (Linux crash) closed by
- worksforme: No response.
- 3:56 PM Ticket #2475 (view #N command doesn't work on BILD models) closed by
- fixed: Fixed. Problem was with getting the bounding box.
- 3:54 PM Ticket #2490 (Session restore: Basic Actions provides None in list of models for Objects) closed by
- can't reproduce: Need test the session that caused the problem.
- 3:06 PM Ticket #2479 (Toolbar won't display) closed by
- fixed
- 3:04 PM Ticket #2483 (mmCIF linking issues) closed by
- nonchimerax: The bug is in the Phenix struct_conn table. In there, for NAG, the …
- 2:13 PM Ticket #2478 (CCD templates should us different XYZ fields) closed by
- fixed: Done.
- 10:53 AM Ticket #2505 (Session save failed: AttributeError: 'Sequence' object has no ...) created by
- […]
- 10:15 AM Ticket #2504 (Crash drawing Qt widgets) closed by
- can't reproduce
- 7:40 AM Ticket #2504 (Crash drawing Qt widgets) created by
- […]
- 1:10 AM Ticket #2334 (Residues added to N-terminus of a chain do not appear in Model.polymers) closed by
- fixed: Ah - sorry about the unreproducability! I tried to make it …
Oct 15, 2019:
- 5:30 PM Ticket #2499 (macOS Catalina, opening file PermissionError) closed by
- can't reproduce: I have not been able to reproduce the Permission Error originally …
- 5:16 PM Ticket #2503 (On macOS Catalina ChimeraX asks for permission to access Desktop files ...) created by
- […]
- 2:47 PM Ticket #2500 (hbonds saltOnly: 'list' object has no attribute 'elements') closed by
- fixed: Thanks for reporting this problem. It is fixed now and the fix will …
- 11:27 AM Ticket #2502 (Copy/paste from Help) created by
- […]
- 9:42 AM Ticket #2501 (Widget redraw problem) created by
- […]
- 2:07 AM Ticket #2500 (hbonds saltOnly: 'list' object has no attribute 'elements') created by
- […]
Oct 14, 2019:
- 10:04 PM Ticket #2499 (macOS Catalina, opening file PermissionError) created by
- […]
- 9:00 PM Ticket #2494 (More 2D labels issues) closed by
- fixed: Fixed. Same bug as in #2493, trying to move a 2d label after closing …
- 8:57 PM Ticket #2493 (Many 2dlabel command problems) closed by
- fixed: Fixed remaining errors caused by closing a 2d label then trying to …
- 8:18 PM Ticket #2498 (Make hand mode to draw arrows in VR) created by
- Would be useful to be able to draw arrows in VR by dragging from head …
- 6:42 PM Ticket #2497 (Session restore with BILD model fails) created by
- […] test.cxs
- 6:39 PM Ticket #2496 (macOS Catalina can't verify daily build, signing problem) created by
- […] Screen Shot 2019-10-14 at 6.34.48 PM.png
- 3:49 PM Ticket #2495 (RFE: set independent) created by
- The following bug report has been submitted: Platform: …
- 2:33 PM Ticket #2494 (More 2D labels issues) created by
- The following bug report has been submitted: Platform: …
- 1:06 PM ChangeLog edited by
- (diff)
- 1:01 PM ChangeLog edited by
- (diff)
Oct 12, 2019:
Oct 11, 2019:
- 9:08 PM Ticket #2492 (Error closing RealSense camera) created by
- […]
- 2:33 PM Ticket #2491 (first model does not retain soft lighting when second model opened) closed by
- can't reproduce: The multishadow transform matrices are different when model #1 shows …
- 2:09 PM ChangeLog edited by
- (diff)
- 10:22 AM Ticket #2491 (first model does not retain soft lighting when second model opened) created by
- UCSF ChimeraX version: 0.91 (2019-10-10) Something strange happens to …
- 9:17 AM Ticket #2490 (Session restore: Basic Actions provides None in list of models for Objects) created by
- […]
- 7:59 AM Ticket #2489 (Control helix curvature) created by
- […]
Oct 10, 2019:
- 4:09 PM Ticket #2484 (Tile command: 'Volume' object has no attribute 'atomspec') closed by
- fixed: Fixed in 555d9bad4. The "atomspec" property was only …
- 10:02 AM Ticket #2488 (AddH: treat UNK as truncated amino acid) created by
- Since UNK is used as a placeholder for "unknown amino acid residue", …
Oct 9, 2019:
- 3:49 PM Ticket #2001 (poor superposition after modeller comparative) closed by
- fixed: The non-working-in-scripts problem opened as separate ticket #2487. …
- 3:21 PM Ticket #2486 (Crash in free_keys_object/subtype_dealloc) closed by
- can't reproduce: Would be nice if someone actually described what they were doing when …
- 3:19 PM Ticket #2485 (Crash in free_keys_object/subtype_dealloc) closed by
- can't reproduce
- 3:13 PM Ticket #2487 (Blocking Opal jobs need longer timeout) created by
- Blocking Modeller jobs fail because they take longer than 90 seconds …
- 2:36 PM Ticket #2486 (Crash in free_keys_object/subtype_dealloc) created by
- […]
- 1:58 PM Ticket #2485 (Crash in free_keys_object/subtype_dealloc) created by
- […]
- 1:47 PM Ticket #2484 (Tile command: 'Volume' object has no attribute 'atomspec') created by
- […]
- 11:12 AM Ticket #2482 (Save Segger segmentation: 'MainSaveDialog' object has no attribute ...) closed by
- fixed: Hi Thomas, This bug was fixed about 6 days after the version you …
- 3:51 AM Ticket #2470 (ISOLDE delayed reaction: Error invoking kernel computeBondedForces) closed by
- not a bug: This construct is now up and running smoothly on a GPU workstation.
- 1:41 AM Ticket #2483 (mmCIF linking issues) created by
- If I save a mmCIF file with disulfides and N-linked glycans from …
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