![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
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
- […]
Sep 17, 2019:
- 9:28 PM Ticket #2409 (File→Open: unhashable type: 'set') closed by
- fixed: Fixed in d1cafaf2d. Code added to report formats …
- 2:17 PM Ticket #2417 (File→Open: unhashable type: 'set') created by
- […]
- 1:26 PM Ticket #2405 (2dlabels creation/deletion sometimes not shown in Model Panel) closed by
- fixed: Okay, model panel updates properly when "global tool unhide" occurs
- 12:47 PM Ticket #2416 (File→Open: unhashable type: 'set') created by
- […]
- 12:33 PM Ticket #2415 (File→Open: unhashable type: 'set') created by
- […]
- 11:43 AM Ticket #2414 (File→Open: unhashable type: 'set') closed by
- duplicate: duplicate of #2409
- 11:37 AM Ticket #2413 (Crash in free_keys_object/subtype_dealloc) closed by
- can't reproduce
- 8:27 AM Ticket #2414 (File→Open: unhashable type: 'set') created by
- […]
- 12:01 AM Ticket #2411 (Template fetching broken?) closed by
- worksforme: Looks like a temporary failure. Just worked for me from home.
- 12:00 AM Ticket #2412 (Superfluous argument quoting) closed by
- fixed: Fixed. _whitespace only find leading whitespace. Added …
Sep 16, 2019:
- 9:03 PM Ticket #2413 (Crash in free_keys_object/subtype_dealloc) created by
- […]
- 4:39 PM Ticket #2179 (Non-graphics windows blank after structure load) closed by
- can't reproduce
- 4:23 PM Ticket #2375 (Shell tab-completion attempts import of non-Python libs) closed by
- nonchimerax: I don't think there's anything I can do about this.
- 3:20 PM Ticket #2410 (self._positions is None) closed by
- duplicate: Duplicate. Fixed a while ago.
- 2:10 PM Ticket #2412 (Superfluous argument quoting) created by
- The changes to argument processing/logging now cause unneeded …
- 2:05 PM Ticket #2411 (Template fetching broken?) created by
- […]
- 11:48 AM Ticket #2406 (Bad startup-command error handling) closed by
- fixed: Hi Daniel, There is something wrong with the commands you told …
- 11:36 AM Ticket #2404 (Toolbar context menu Hide Tool and Help don't work in full-window mode) closed by
- duplicate: Largely a duplicate of #2297. Noted in #2297 to check this ticket to …
- 11:30 AM Ticket #2403 (Bad error reporting for startup-command errors) closed by
- fixed
- 11:19 AM Ticket #2401 (seq view setting change: 'OptionalRGBAOption' object has no attribute 'get') closed by
- duplicate
Sep 15, 2019:
- 6:38 PM Ticket #2410 (self._positions is None) created by
- […]
- 6:32 AM Ticket #2409 (File→Open: unhashable type: 'set') created by
- […]
Sep 14, 2019:
- 2:16 PM Ticket #2408 (Cannot use Lenobo explorer for VR) created by
- […]
- 12:40 AM Ticket #2407 (Problem saving session involving Clipper) created by
- […]
Sep 13, 2019:
- 1:57 PM Ticket #2370 ((atomic) model: self.positions is None) closed by
- can't reproduce: It appears some ChimeraX tool tried to save a closed model in the …
- 1:54 PM Ticket #2399 (Crash handling Qt event) closed by
- nonchimerax: This is a crash in the OpenGL graphics driver. Apple's OpenGL …
- 10:58 AM Ticket #2402 (ViewDockX should facilitate correct receptor vs. ligand classification ...) closed by
- fixed: Fixed in Maestro tool version 1.3 as discussed in the comments for #2343.
- 10:45 AM Ticket #2343 (ViewDockX up/down arrow actions should log the corresponding commands) closed by
- fixed: Okay, receptors from Maestro files no longer get ViewDock attributes …
- 10:08 AM Ticket #2406 (Bad startup-command error handling) created by
- […]
Sep 12, 2019:
- 11:44 PM Ticket #2395 (open of filetype in unloaded bundle should let user install bundle) closed by
- fixed: Fixed in f10025b5b. The text can probably stand some …
- 4:39 PM Ticket #2405 (2dlabels creation/deletion sometimes not shown in Model Panel) created by
- Image attached: I created a label with symbols and another with text, …
- 3:51 PM Ticket #2404 (Toolbar context menu Hide Tool and Help don't work in full-window mode) created by
- By full-window mode I mean when you use the icon to make the graphics …
- 2:06 PM Ticket #2403 (Bad error reporting for startup-command errors) created by
- […]
- 12:03 PM Ticket #2402 (ViewDockX should facilitate correct receptor vs. ligand classification ...) created by
- Suggestions are that ViewDockX should either: (A) read the …
- 12:38 AM Ticket #2401 (seq view setting change: 'OptionalRGBAOption' object has no attribute 'get') created by
- […]
Sep 11, 2019:
- 5:15 PM Ticket #2400 (KeyError from item chooser) closed by
- duplicate: Hi, I believe this problem was fixed on 8/14, so just after the …
- 9:17 AM Ticket #2400 (KeyError from item chooser) created by
- […]
- 8:33 AM Ticket #2398 (2D label fading broken) closed by
- duplicate: Hi Gabor, This problem was fixed just yesterday, so as you noticed it …
- 7:56 AM Ticket #2399 (Crash handling Qt event) created by
- […]
- 12:40 AM Ticket #2398 (2D label fading broken) created by
- […]
Sep 10, 2019:
- 7:59 PM Ticket #2397 (Crash in save-image dialog?) closed by
- nonchimerax: Appears to have crashed on mouse button release on a QToolButton that …
- 7:52 PM Ticket #2396 (Crash in graphics driver (chrome backend?) after ctypes call) closed by
- nonchimerax: Crash in Mac graphics driver. Unfortunately Apple graphics drivers …
- 4:25 PM Ticket #2298 (2dlabels fading broken) closed by
- fixed
- 8:29 AM ChangeLog edited by
- (diff)
- 7:39 AM Ticket #2397 (Crash in save-image dialog?) created by
- […]
- 2:53 AM Ticket #2396 (Crash in graphics driver (chrome backend?) after ctypes call) created by
- […]
Sep 9, 2019:
- 5:10 PM Ticket #2380 (surface hide/show wonky) closed by
- fixed: Fixed. Would be useful if the documentation clarified that "surface …
- 3:54 PM Ticket #2388 (surface coloring error after swapaa) closed by
- fixed: Fixed. Tried to use remembered molecular surface atom patch colors …
- 3:26 PM Ticket #2390 (Changing 2D label to be very large fails) closed by
- fixed: Fixed. Error was from label with empty text, resulting in 0 size …
- 2:00 PM Ticket #2395 (open of filetype in unloaded bundle should let user install bundle) created by
- Like the case when a command is typed that is provided by a bundle …
- 12:46 PM Ticket #2391 (Surface cap not colored) closed by
- not a bug: To color a surface cap you would have to use the color zone command. …
- 12:38 PM Ticket #2393 (open 0069 fromDatabase emdb: MRC file is truncated) closed by
- not a bug: As the error message says, the MRC file was truncated. In fact I can …
- 11:37 AM Ticket #2392 (2D labels: local variable 'lm' referenced before assignment) closed by
- duplicate: Hi Stephan, Thanks for reporting this problem. We fixed this issue …
- 9:45 AM Ticket #2394 (Residues added to protein chain save out of order in PDB) created by
- If I add a residue to a protein chain (e.g. to the N-terminus using …
- 7:35 AM Ticket #2393 (open 0069 fromDatabase emdb: MRC file is truncated) created by
- […]
- 3:45 AM Ticket #2392 (2D labels: local variable 'lm' referenced before assignment) created by
- […]
- 1:16 AM Ticket #2391 (Surface cap not colored) created by
- […]
Sep 6, 2019:
- 3:45 PM Ticket #2390 (Changing 2D label to be very large fails) created by
- […]
- 3:06 PM Ticket #2384 (Excessive status output) closed by
- fixed: Cut way back on the status message output by having swapaa silence the …
- 3:04 PM Ticket #2385 (Wrong default criteria) closed by
- fixed: Upgraded the way the 'd' criteria is handled. If one map is open, …
- 2:13 PM Ticket #2389 (Graphics buffer deletion problem for "split" after "surface") closed by
- duplicate: Fixed yesterday but last night's builds failed. Duplicate of #2383.
- 2:04 PM Ticket #2381 (Add hbonds clear and distance clear subcommands) closed by
- fixed: Implemented "dist/hb delete" as equivalents for ~dist/~hb
- 1:57 PM Ticket #2389 (Graphics buffer deletion problem for "split" after "surface") created by
- […]
- 1:12 PM Ticket #2387 (Alt loc issues) closed by
- fixed: ChimeraX chooses alt locs by looking at connected groups of alt locs …
- 10:40 AM Ticket #2388 (surface coloring error after swapaa) created by
- […]
- 3:12 AM Ticket #2387 (Alt loc issues) created by
- […]
- 1:33 AM Ticket #2386 (Registration window obscured) created by
- […]
Sep 5, 2019:
- 11:52 PM Ticket #2385 (Wrong default criteria) created by
- […]
- 11:37 PM Ticket #2384 (Excessive status output) created by
- […]
- 10:49 PM Ticket #2383 (surface close causes OpenGL buffer delete error) closed by
- fixed: Fixed. OpenGL buffers not deleted due to indentation error. Bug …
- 10:13 PM Ticket #2382 (mlp error: ValueError: list.remove(x): x not in list) closed by
- fixed: Fixed I think. Could not reproduce. The mlp command created volume …
- 5:56 PM Ticket #2383 (surface close causes OpenGL buffer delete error) created by
- […]
- 5:21 PM Ticket #2382 (mlp error: ValueError: list.remove(x): x not in list) created by
- […]
- 5:20 PM Ticket #2379 (traceback when closing seq viewer with multiple chains associated) closed by
- fixed: A previous fix to stop a memory leak resulting in some data structures …
- 5:13 PM Ticket #2381 (Add hbonds clear and distance clear subcommands) created by
- […]
- 5:06 PM Ticket #2378 (Crash in free_keys_object/subtype_dealloc) closed by
- can't reproduce: This crash seems to be reported roughly once a week, with no …
- 4:48 PM Ticket #2380 (surface hide/show wonky) created by
- "surface show" seems busted. Ergo: open 3fx2 surface shows …
- 4:35 PM Ticket #2379 (traceback when closing seq viewer with multiple chains associated) created by
- […] seqbug.cxs
- 2:11 PM Ticket #2378 (Crash in free_keys_object/subtype_dealloc) created by
- […]
- 12:29 PM Ticket #2377 (Add command to assign VR buttons) closed by
- fixed: I added the command "vr button" to assign VR hand controller buttons …
- 12:18 PM Ticket #2377 (Add command to assign VR buttons) created by
- […]
- 3:17 AM Ticket #2376 (File history and/or "open" command converting \t to tab) created by
- […]
Sep 4, 2019:
- 5:41 PM Ticket #2108 (Session adds non-statemanager to list of state managers) closed by
- fixed: After a lot of headache-inducing code examination, concluded it would …
- 10:45 AM 2019-08-29 created by
- 10:25 AM DeveloperMeetings edited by
- (diff)
- 3:37 AM Ticket #2375 (Shell tab-completion attempts import of non-Python libs) created by
- […]
Sep 3, 2019:
- 5:23 PM Ticket #2371 (FileNotFoundError re-reading map file) closed by
- duplicate: Newer ChimeraX versions give a user-friendly error message describing …
- 4:17 PM Ticket #2360 (Show clipping caps: Array argument has non-numeric values) closed by
- duplicate: Duplicate of #2277. Fixed a month ago.
- 2:40 PM Ticket #2369 (swapaa failure for non-rotameric side chains) closed by
- fixed: Logic to check for no rotamers was no longer correct due to changes to …
- 2:14 PM Ticket #2367 (volume eraser: output array is read-only) closed by
- duplicate: Hi Stephan, Thanks for reporting this problem. It was fixed 6 days …
- 2:10 PM Ticket #2366 (Bad pointer freed) closed by
- duplicate: Seems to be the exact same crash as #2356. Would be nice to have more …
- 12:52 PM Ticket #2374 (ISOLDE: multiple different errors) created by
- […]
- 8:57 AM Ticket #2373 (Registration failure) created by
- […]
- 7:03 AM Ticket #2372 (Crash during script execution) created by
- […] SAGA-intro.cxc
- 5:10 AM Ticket #2371 (FileNotFoundError re-reading map file) created by
- […]
- 2:51 AM Ticket #2370 ((atomic) model: self.positions is None) created by
- […]
- 2:43 AM Ticket #2369 (swapaa failure for non-rotameric side chains) created by
- […]
- 2:38 AM Ticket #2368 (Handling missing structure pseudobonds when editing chains) created by
- More of a query than anything else: when adding a residue to a chain …
- 12:23 AM Ticket #2367 (volume eraser: output array is read-only) created by
- […]
- 12:04 AM Ticket #2331 (Better session error reporting) closed by
- fixed: Added code to keep track of where data is saved from in a session, and …
Aug 31, 2019:
Aug 30, 2019:
- 4:05 PM Ticket #2365 (Make 2D labels selectable) created by
- […]
- 3:06 PM Ticket #2364 (Make graphics subcommands for quality, silhouettes, framerate...) closed by
- fixed
- 2:52 PM Ticket #2364 (Make graphics subcommands for quality, silhouettes, framerate...) created by
- […]
- 2:43 PM Ticket #2363 (Don't show silhouettes on mesh surfaces) created by
- […]
- 11:29 AM Ticket #2362 (Make default silhouette thickness 2 on retina displays) closed by
- fixed: Done. Default silhouette thickness on retina displays is now 2. On …
- 11:18 AM Ticket #2362 (Make default silhouette thickness 2 on retina displays) created by
- […]
- 11:12 AM Ticket #2361 (Silhouette edges not shown on molecule under transparent surface) closed by
- fixed: Fixed. ChimeraX is not showing silhouette edges on molecules behind …
- 11:02 AM Ticket #2361 (Silhouette edges not shown on molecule under transparent surface) created by
- […]
- 10:45 AM Ticket #2360 (Show clipping caps: Array argument has non-numeric values) created by
- […]
Aug 29, 2019:
- 11:00 AM Ticket #2356 (Bad pointer freed) closed by
- can't reproduce: Classic Python C-stack -- difficult to tell what Python code was executing.
- 10:46 AM Ticket #2359 (Optimize ribbon drawing) created by
- As per ticket #2355, _update_ribbon_graphics takes 27ms/frame to …
- 10:43 AM Ticket #2355 (Suggestion: track visible atoms/ribbons/bonds on C++ side) closed by
- not a bug: Will open a ticket about optimizing ribbon graphics
Aug 28, 2019:
- 6:16 PM Ticket #2357 (Error copying map with "volume scale" command) closed by
- fixed: Fixed. volume scale command copied volume colors but not threshold …
- 5:00 PM Ticket #2357 (Error copying map with "volume scale" command) created by
- […]
- 3:53 PM Ticket #2351 (volume eraser: output array is read-only) closed by
- fixed: Fixed. Session restore of a map whose array is included in the …
- 3:52 PM Ticket #2356 (Bad pointer freed) created by
- […]
- 3:36 PM Ticket #2338 ("surface cap false": local variable 'update' referenced before assignment) closed by
- fixed: Fixed. "surface cap false" did not work unless offset or subdivision …
- 3:29 PM Ticket #2337 (View changes/resets when model shown) closed by
- duplicate: Probably fixed. On August 15, 2019 I fixed a bug where view would …
- 8:34 AM Ticket #2354 (ISOLDE in old ChimeraX 0.9 daily) closed by
- not a bug: Same daily build as #2352, but different user directory. Still, since …
- 8:29 AM Ticket #2355 (Suggestion: track visible atoms/ribbons/bonds on C++ side) created by
- For big models, there's currently a fairly large fixed overhead to …
- 4:11 AM Ticket #2354 (ISOLDE in old ChimeraX 0.9 daily) created by
- […]
Aug 27, 2019:
- 12:46 PM Ticket #2353 (mistake) closed by
- not a bug: It's too easy to hit Submit instead of Cancel on the bug reporter
- 12:44 PM Ticket #2353 (mistake) created by
- […]
- 1:43 AM Ticket #2344 (Wrong Clipper?) closed by
- duplicate: Yup. Same issue.
Aug 26, 2019:
- 12:21 PM Ticket #2352 (ISOLDE environment preparation -- running a command: Expected a keyword) closed by
- not a bug: Oh, I see. It *is* an API change, but in the wrong direction. They're …
- 11:27 AM Ticket #2350 (KeyError in model chooser) closed by
- duplicate: Already fixed as of 8/14
- 11:26 AM Ticket #2349 (KeyError in model chooser) closed by
- duplicate: Already fixed as of 8/14
- 11:24 AM Ticket #2348 (Keyrror in model chooser) closed by
- duplicate: Already fixed as of 8/14
Aug 25, 2019:
- 11:17 PM Ticket #2352 (ISOLDE environment preparation -- running a command: Expected a keyword) created by
- […]
- 10:13 AM Ticket #2351 (volume eraser: output array is read-only) created by
- […]
Aug 23, 2019:
- 7:36 PM Ticket #2327 (mmCIF: aniso_u values written in wrong order) closed by
- fixed: This broke on October 1 2018 with the commit that: "change Python …
- 1:25 PM Ticket #2346 (ViewDockX error if non-structures open) closed by
- fixed: Fixed in 7ae015db. ViewDockX was not ignoring changes to …
- 11:48 AM Ticket #2350 (KeyError in model chooser) created by
- […]
- 11:47 AM Ticket #2349 (KeyError in model chooser) created by
- […]
- 11:47 AM Ticket #2348 (Keyrror in model chooser) created by
- […]
- 11:21 AM Ticket #2345 (Wrong Clipper?) closed by
- duplicate
- 10:34 AM Ticket #2340 (Qt crash) closed by
- can't reproduce: Hi Ricardo, Thanks for getting back to me. I just tried dragging …
- 2:04 AM Ticket #2347 (Wrong version of Clipper installed) closed by
- duplicate
Aug 22, 2019:
- 4:19 PM Ticket #2347 (Wrong version of Clipper installed) created by
- […]
- 1:03 PM Ticket #2346 (ViewDockX error if non-structures open) created by
- […]
- 12:37 PM Ticket #2345 (Wrong Clipper?) created by
- […]
- 12:37 PM Ticket #2344 (Wrong Clipper?) created by
- […]
- 11:21 AM Ticket #2343 (ViewDockX up/down arrow actions should log the corresponding commands) created by
- ViewDockX up/down arrow actions should log the corresponding commands. …
- 11:20 AM Ticket #2342 (API inconsistency copying residue with blank insertion code) closed by
- fixed: Now it massages an empty insertion code to a blank before passing it …
- 11:11 AM Ticket #2341 (Command-history deletion bug) closed by
- duplicate: Fixed back in December
- 9:04 AM Ticket #2342 (API inconsistency copying residue with blank insertion code) created by
- If I try to create a new residue based on an existing one: […] …
- 8:25 AM Ticket #2341 (Command-history deletion bug) created by
- […]
- 6:16 AM Ticket #2339 (Wrong version of Clipper being installed into ChimeraX 0.9) closed by
- duplicate: Duplicate of #2214.
- 5:55 AM Ticket #2340 (Qt crash) created by
- […]
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