![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
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 …
Oct 8, 2019:
Oct 7, 2019:
- 11:39 AM Ticket #2481 (Error in Python shell event filter) closed by
- can't reproduce: Looking the code for qtconsole.eventFilter, this error would seem to …
Oct 4, 2019:
- 6:17 PM Ticket #2481 (Error in Python shell event filter) created by
- […]
- 2:41 PM Ticket #2480 (Startup errors do not appear in the log) closed by
- fixed: Tool startup was explicitly printing to stderr -- not logging the problem.
- 2:01 PM Ticket #2480 (Startup errors do not appear in the log) created by
- If a traceback occurs during startup and ChimeraX does manage to start …
- 12:30 PM Ticket #2479 (Toolbar won't display) created by
- […]
- 9:04 AM Ticket #2478 (CCD templates should us different XYZ fields) created by
- […]
Oct 3, 2019:
- 6:57 PM Ticket #2473 ("hide sel models" doesn't hide selected atomic model) closed by
- fixed: Fixed. Code to hide instances of models was causing this bug. It …
- 6:05 PM Ticket #2474 (color command could infer target is labels if only labels specified) closed by
- fixed: Done. Color command with only 2d labels specified now uses default …
- 5:43 PM Ticket #2477 (select clear doesn't clear sel checkboxes for object model (tested ...) closed by
- fixed: Fixed. Same bug as #2472.
- 5:41 PM Ticket #2472 (select clear doesn't clear sel checkboxes for 2D labels) closed by
- fixed: Fixed. The Model.clear_selection() method was not firing the …
- 5:40 PM Ticket #2473 ("hide sel models" doesn't hide selected atomic model) reopened by
- Oops. Closed the wrong ticket.
- 5:39 PM Ticket #2473 ("hide sel models" doesn't hide selected atomic model) closed by
- fixed: Fixed. The Model.clear_selection() method was not firing the …
- 4:16 PM Ticket #2477 (select clear doesn't clear sel checkboxes for object model (tested ...) created by
- Same issue as for #2472 with 2D labels except now with object from …
- 4:14 PM Ticket #2476 (weird command in history from opening file from URL) created by
- Harmless but weird-looking; If I use command: open …
- 3:44 PM Ticket #2475 (view #N command doesn't work on BILD models) created by
- Example: open 6cmn open …
- 2:24 PM Ticket #2474 (color command could infer target is labels if only labels specified) created by
- if you select 2D labels only, “color sel red” does nothing. If only …
- 2:20 PM Ticket #2473 ("hide sel models" doesn't hide selected atomic model) created by
- if I open an atomic model #1 and show a 3D label on something, then …
- 2:19 PM Ticket #2472 (select clear doesn't clear sel checkboxes for 2D labels) created by
- If I have two 2D labels #2.1 and #2.2, checking the selection box for …
- 1:46 PM 2019-10-03 created by
- 12:11 PM DeveloperMeetings edited by
- (diff)
- 11:31 AM Ticket #2468 (close tool → 'MainWindow' object has no attribute ...) closed by
- fixed: That dict only exists once the icon is used, so the new code needed to …
- 11:24 AM Ticket #2471 (Actions menu suggested text & organization) created by
- The Surface part would stay unchanged and is not mentioned. Actions …
- 11:24 AM Ticket #2464 (issues with ChimeraX) closed by
- nonchimerax: Yes, if what you want to do is use XLinkAnalyzer, then Chimera is the …
- 11:20 AM Ticket #2469 (close tool → 'MainWindow' object has no attribute ...) closed by
- duplicate
- 11:17 AM Ticket #2467 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') closed by
- duplicate
- 8:44 AM Ticket #2470 (ISOLDE delayed reaction: Error invoking kernel computeBondedForces) created by
- […]
- 7:45 AM Ticket #2469 (close tool → 'MainWindow' object has no attribute ...) created by
- […]
- 7:42 AM Ticket #2468 (close tool → 'MainWindow' object has no attribute ...) created by
- […]
- 6:37 AM Ticket #2467 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') created by
- […]
Oct 2, 2019:
- 5:23 PM Ticket #2248 (KeyError hiding tools when map series closed) closed by
- fixed
- 1:59 PM Ticket #2466 (pseudobonds to ribbons difficult to select and get balloon help for) created by
- The code to detect pseudobond picking needs to be updated to reflect …
- 12:54 PM Ticket #2465 (set silhouettes false → glBlitFramebuffer: invalid operation) closed by
- nonchimerax: You reported this same error 5 months ago, ticket #1888. As explained …
- 12:49 PM Ticket #2462 (MRC header value nsymbt is invalid) closed by
- nonchimerax: As the error message says the MRC header has an invalid value for …
- 12:40 PM Ticket #2463 (Opening saved session produces core dump) closed by
- can't reproduce: Looks like it might have died in Qt. Need the session.
- 8:19 AM Ticket #2465 (set silhouettes false → glBlitFramebuffer: invalid operation) created by
- […]
- 6:53 AM Ticket #2464 (issues with ChimeraX) created by
- […]
- 6:38 AM Ticket #2463 (Opening saved session produces core dump) created by
- […]
Oct 1, 2019:
- 6:31 PM Ticket #2462 (MRC header value nsymbt is invalid) created by
- […]
- 11:04 AM Ticket #2457 (glUniformMatrix4fv → invalid operation) closed by
- can't reproduce: OpenGL INVALID_OPERATION error setting a shader variable. Unclear how …
- 10:18 AM Ticket #2461 (Improve fitmap error message when multiple maps fit) created by
- Begin forwarded message: From: Oliver Clarke Subject: [Chimera-users] …
- 10:17 AM Ticket #2460 (Specify resolution in volume gaussian command instead of standard deviation) created by
- Begin forwarded message: From: Oliver Clarke Subject: [Chimera-users] …
- 10:15 AM Ticket #2459 (Add smoothing option to fitmap command) created by
- Begin forwarded message: From: Oliver Clarke Subject: [Chimera-users] …
- 9:42 AM Ticket #2446 (Camera stereo → glDrawBuffer: invalid operation) closed by
- fixed
- 8:48 AM Ticket #2458 (Clipper not saving in sessions) created by
- […]
- 7:58 AM Ticket #2457 (glUniformMatrix4fv → invalid operation) created by
- […]
- 1:51 AM Ticket #2456 (hbonds: accPhiPsi() takes exactly 8 arguments (9 given)) created by
- […]
Sep 30, 2019:
- 1:02 PM Ticket #2455 (Graphics/Orient now a placebo) closed by
- fixed: It now gives an error message -- in this case, "dV - unknown …
- 12:13 PM Ticket #2455 (Graphics/Orient now a placebo) created by
- […]
- 11:46 AM Ticket #2453 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') closed by
- duplicate
- 11:42 AM Ticket #2449 (2nd "camera stereo" → glDrawBuffer: invalid operation) closed by
- duplicate: Same bug as #2446 but with Quadro P5000 graphics. Will add a note to …
- 11:16 AM Ticket #2454 (RFE: Labels preference for (3D) label height) closed by
- fixed: Done. New settings is under the Labels tab in preferences "Height of …
- 10:27 AM Ticket #2454 (RFE: Labels preference for (3D) label height) created by
- There is already a Labels category in preferences. Since each user is …
Sep 27, 2019:
- 9:47 PM Ticket #2453 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') created by
- […]
- 8:43 PM Ticket #2450 (Various segmentation problems) closed by
- fixed: Fixed error opening segmentation (.seg) file written by Chimera. Fixed …
- 5:00 PM Ticket #2452 (protons not properly stripped in 3qm8 heme) created by
- The angle check is bad, possibly because alt locs are involved?
- 1:34 PM Ticket #2451 (Tiling not working for volumes) created by
- […]
- 11:52 AM Ticket #2450 (Various segmentation problems) created by
- […]
Sep 26, 2019:
- 12:48 PM Ticket #2449 (2nd "camera stereo" → glDrawBuffer: invalid operation) created by
- […]
- 11:53 AM Ticket #2448 ("swapaa interactive spec same" buggy) closed by
- fixed: It was a problem with the handling of "same" for swapaa interactive. …
- 11:46 AM Ticket #2447 (selection visible through opaque surface after BILD file opened) closed by
- not a bug: This is a feature, not a bug. A while back I made selection outlines …
- 11:39 AM Ticket #2448 ("swapaa interactive spec same" buggy) created by
- […]
- 11:30 AM Ticket #2447 (selection visible through opaque surface after BILD file opened) created by
- This is definitely an obscure situation, but reproducible... file as …
- 9:40 AM Ticket #2446 (Camera stereo → glDrawBuffer: invalid operation) created by
- […]
- 9:30 AM Ticket #2445 (Undesirable center of rotation) created by
- […]
- 8:36 AM Ticket #2444 (Weird import errors) created by
- […]
Sep 25, 2019:
- 3:46 PM Ticket #2443 ("graphics restart" failure) closed by
- duplicate: Same problem as #2442. Use ChimeraX daily build.
- 3:43 PM Ticket #2442 (camera stereo → glDrawBuffer: invalid operation) closed by
- can't reproduce: Please try the ChimeraX daily build. I believe I made a change a few …
- 3:12 PM Ticket #2443 ("graphics restart" failure) created by
- […]
- 2:47 PM Ticket #2441 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') closed by
- duplicate: Hi Bryan, This bug was only in the daily build for less than a day …
- 2:26 PM Ticket #2442 (camera stereo → glDrawBuffer: invalid operation) created by
- […]
- 2:11 PM Ticket #2441 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') created by
- […]
- 10:32 AM Ticket #2440 (GUI panels are all blank) closed by
- nonchimerax: From: Pascal Albanese UU Subject: Re: [chimerax-users] GUI not …
- 10:31 AM Ticket #2440 (GUI panels are all blank) created by
- On Sep 23, 2019, at 7:26 AM, Pascal Albanese UU wrote: Hi Chimera …
Sep 24, 2019:
- 7:12 PM Ticket #2439 (Linux crash) created by
- […]
- 12:36 PM Ticket #2438 (should object models (e.g. from BILD) be selectable?) created by
- This has many of the same pros and cons as making labels selectable …
- 11:31 AM Ticket #2437 (ISOLDE/Clipper: 'NXmapHandler' object has no attribute 'set_display_style') closed by
- duplicate: Duplicate of #2214.
- 11:30 AM Ticket #2436 (ISOLDE/Clipper: 'Atoms' object has no attribute 'transform') closed by
- duplicate
- 7:34 AM Ticket #2437 (ISOLDE/Clipper: 'NXmapHandler' object has no attribute 'set_display_style') created by
- […]
- 6:58 AM Ticket #2436 (ISOLDE/Clipper: 'Atoms' object has no attribute 'transform') created by
- […]
Sep 23, 2019:
- 11:38 AM Ticket #2435 (Select menu protein, nucleic acid, ribose should be under Chemistry ...) created by
- protein, nucleic acid, ribose are chemically defined and make more …
Sep 22, 2019:
- 9:58 AM Ticket #2434 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') closed by
- duplicate: Hi Ulrich, Thanks for reporting this problem. It is fixed in the …
Sep 21, 2019:
Sep 20, 2019:
- 3:50 PM Ticket #2432 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') closed by
- fixed: My apologies. The fix didn't make it into our central repository. …
- 2:58 PM Ticket #2432 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') created by
- […]
- 1:36 PM Ticket #2430 (Problem playing microscopy timepoints) closed by
- can't reproduce: The current ChimeraX daily build records a 360sbs movie of …
- 1:18 PM Ticket #2431 (Crash in free_keys_object/subtype_dealloc) closed by
- can't reproduce: pre-Qt 5.12.5
- 1:09 PM Ticket #2431 (Crash in free_keys_object/subtype_dealloc) created by
- […]
- 11:37 AM Ticket #2430 (Problem playing microscopy timepoints) created by
- […]
- 11:21 AM Ticket #2429 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') closed by
- duplicate: Hi Karim, Thanks for reporting this problem. It is fixed now, so if …
- 11:20 AM Ticket #2428 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') closed by
- fixed
- 11:18 AM Ticket #2427 (Crash due to NULL sseq.structure pointer) closed by
- can't reproduce
- 8:16 AM Ticket #2429 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') created by
- […]
- 4:40 AM Ticket #2428 (ImportError: cannot import name 'FileNameArg' from 'chimerax.core.commands') created by
- […]
- 1:47 AM Ticket #2427 (Crash due to NULL sseq.structure pointer) created by
- […]
Sep 19, 2019:
- 6:55 PM Ticket #2426 (Use special wildcards {t},{c},{z} for opening microscopy TIFF series) closed by
- fixed: Done. I added special wildcards {t}, {c}, {z} that can be used in the …
- 6:35 PM Ticket #2426 (Use special wildcards {t},{c},{z} for opening microscopy TIFF series) created by
- […]
- 10:27 AM Ticket #2425 (ISOLDE cannot find symbol atomstruct::Residue::find_atom) created by
- […]
- 9:17 AM Ticket #2424 (Array of coordinates is None) created by
- […]
- 3:32 AM Ticket #2423 (Sequence viewer fails on edited chain) created by
- […]
Sep 18, 2019:
- 3:54 PM Ticket #2376 (File history and/or "open" command converting \t to tab) closed by
- fixed: Fixed. Working on more general solution. Each *Arg class will …
- 3:49 PM Ticket #2422 (reorder file formats suffixes for open/save dialogs) closed by
- fixed: This is not a problem on Linux, because the file suffixes are not …
- 1:41 PM Ticket #2419 (Model.positions is None) closed by
- can't reproduce: This error saving a ChimeraX session is because something was …
- 1:30 PM Ticket #2421 ('MDFF_Mgr' object has no attribute '_c_pointer') closed by
- nonchimerax: Okey dokey. :-)
- 1:05 PM Ticket #2422 (reorder file formats suffixes for open/save dialogs) created by
- Would like the list of file format suffixes in the open/save dialogs …
- 11:37 AM Ticket #2421 ('MDFF_Mgr' object has no attribute '_c_pointer') created by
- […]
- 11:33 AM Ticket #2420 (Error with nucleotide/ring graphics after session restore) created by
- […] error2.png
- 11:22 AM Ticket #2418 (File→Open: unhashable type: 'set') closed by
- duplicate: Hi Thor, This problem was just fixed, so if you get the most recent …
- 11:20 AM Ticket #2417 (File→Open: unhashable type: 'set') closed by
- duplicate
- 11:19 AM Ticket #2416 (File→Open: unhashable type: 'set') closed by
- fixed: Conrad fixed this one yesterday. --Eric
- 11:18 AM Ticket #2415 (File→Open: unhashable type: 'set') closed by
- duplicate
- 10:49 AM Ticket #2419 (Model.positions is None) created by
- […] Screenshot from 2019-09-18 10-49-06.png
- 10:43 AM Ticket #2386 (Registration window obscured) closed by
- nonchimerax: This is Qt bug #49576, …
- 12:13 AM Ticket #2418 (File→Open: unhashable type: 'set') created by
- […]
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