![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
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
- […]
Aug 21, 2019:
- 5:50 PM Ticket #2339 (Wrong version of Clipper being installed into ChimeraX 0.9) created by
- […]
- 11:53 AM Ticket #2338 ("surface cap false": local variable 'update' referenced before assignment) created by
- […]
- 10:10 AM Ticket #2337 (View changes/resets when model shown) created by
- […]
- 6:47 AM Ticket #2336 (ChimeraX bug report submission) created by
- […]
Aug 20, 2019:
- 12:49 PM Ticket #2335 (Segfault in AtomicStructure.reorder_residues) closed by
- fixed: Was sending pointer objects to C++ layer rather than pointer values.
- 11:12 AM Ticket #2333 (UTF-16 file) closed by
- not a bug: Hi Pascal, The file you sent is in UTF-16 format with a 2-byte BOM …
- 10:58 AM Ticket #2332 (self._positions is None) closed by
- duplicate: duplicate of #2146
- 10:18 AM Ticket #2335 (Segfault in AtomicStructure.reorder_residues) created by
-
Happens whether the
new_orderresidues are from the same model or an … - 10:15 AM Ticket #2334 (Residues added to N-terminus of a chain do not appear in Model.polymers) created by
- If I use the (new today, still a bit messy) code below …
- 8:48 AM Ticket #2333 (UTF-16 file) created by
- […] 0_mapped.pb
- 8:38 AM ChangeLog edited by
- (diff)
- 6:29 AM Ticket #2332 (self._positions is None) created by
- […]
- 1:50 AM Ticket #2331 (Better session error reporting) created by
- […]
Aug 19, 2019:
- 7:18 PM Ticket #2249 (Occasional segmentation fault in MatchMaker?) closed by
- can't reproduce: Okay, I did fix _a_ memory leak having to do with chains/sequences, …
- 2:08 PM Ticket #2330 (Model Panel "close" button doesn't work) closed by
- fixed: Well, it's turns out the the 'close' command explicitly avoids closing …
- 12:33 PM Ticket #2330 (Model Panel "close" button doesn't work) created by
- Commands like “close #!2” as automatically generated by the Close …
- 12:21 PM Ticket #2328 (toggle-transparency map icon doesn't toggle transparency in some cases) closed by
- fixed: Fixed. If there are selected surfaces then the transparency icon …
- 12:03 PM Ticket #2325 (2D labels: session save: LabelModel class not found; also some ...) closed by
- fixed: The error saving a session with 2d labels was fixed last week. There …
- 11:40 AM Ticket #2324 (2D label pick: local variable 'lm' referenced before assignment) closed by
- fixed: Fixed. Error happened when using move label mouse mode and no 2d …
- 11:26 AM Ticket #2329 (Color sample wrong coloring when map has been moved.) closed by
- fixed: Fixed. Color sample code was trying to handle different positioning …
- 11:24 AM Ticket #2329 (Color sample wrong coloring when map has been moved.) created by
- […]
- 10:42 AM Ticket #2328 (toggle-transparency map icon doesn't toggle transparency in some cases) created by
- For testing, I have 3 models: atomic, volume1, hidden volume2. If …
- 10:35 AM Ticket #2326 (Qt crash drawing exposed window) closed by
- can't reproduce
- 10:01 AM Ticket #2327 (mmCIF: aniso_u values written in wrong order) created by
- If m is my starting model, and m2 is the same model after writing to …
- 9:33 AM Ticket #2326 (Qt crash drawing exposed window) created by
- […]
- 1:49 AM Ticket #2325 (2D labels: session save: LabelModel class not found; also some ...) created by
- […]
Aug 18, 2019:
- 6:32 AM Ticket #2324 (2D label pick: local variable 'lm' referenced before assignment) created by
- […]
Aug 16, 2019:
Aug 15, 2019:
- 11:15 AM Ticket #2322 (color target "All" semi-colors 2D labels) closed by
- fixed: Fixed. Color command was modulating 2d label colors -- didn't notice …
- 10:56 AM Ticket #2321 (Segger/map: cannot convert float infinity to integer) closed by
- fixed: Fixed. Segger fit to segments menu entry Group Regions by Chains was …
- 10:40 AM Ticket #2322 (color target "All" semi-colors 2D labels) created by
- I was experimenting to see whether color target All includes 2D …
- 10:30 AM Ticket #2318 (Crash during callback into Qt) closed by
- can't reproduce
- 7:11 AM Ticket #2320 (ISOLDE/ChimeraX 0.8 errors) closed by
- fixed: The errors listed here also should be fixed in the latest ISOLDE versions.
- 7:04 AM Ticket #2319 (ISOLDE: name '_f_sigf_chooser' is not defined) closed by
- fixed: My bad. This is an error in 1.0b2 that comes up if your input MTZ file …
- 6:03 AM Ticket #2321 (Segger/map: cannot convert float infinity to integer) created by
- […]
- 3:42 AM Ticket #2320 (ISOLDE/ChimeraX 0.8 errors) created by
- […]
- 2:19 AM Ticket #2319 (ISOLDE: name '_f_sigf_chooser' is not defined) created by
- […]
Aug 14, 2019:
- 6:50 PM Ticket #2318 (Crash during callback into Qt) created by
- […]
- 6:17 PM Ticket #2317 (OpenGL buffer "None" was not deleted) closed by
- fixed: Fixed. A Drawing was deleting the element (triangle) buffer when …
- 6:05 PM Ticket #2317 (OpenGL buffer "None" was not deleted) created by
- […]
- 1:45 PM Ticket #2313 (KeyError in map chooser) closed by
- fixed: Fixed. Fix available in the next daily build. Thanks for reporting …
- 1:20 PM Ticket #2312 (hide/show confusing) closed by
- can't reproduce: So a model is shown but "show #1/s1 cartoons" does not in some cases …
- 1:15 PM Ticket #2316 (Add fitmap include zeros option) closed by
- fixed: Fixed. Added fitmap command option "zeros true|false" default false. …
- 1:13 PM Ticket #2316 (Add fitmap include zeros option) created by
- […]
- 12:19 PM Ticket #2315 (fitmap fails when no surface exists) closed by
- fixed: Made fitmap command use "envelope false" if the map being fit has no …
- 12:00 PM Ticket #2315 (fitmap fails when no surface exists) created by
- […]
- 11:16 AM Ticket #2314 (MOLEonline in ChimeraX) closed by
- nonchimerax: Hi Eddie, ChimeraX is not just another incremental version of …
- 8:19 AM Ticket #2314 (MOLEonline in ChimeraX) created by
- […] mole_channels_oM5GDAPAYkqzANZqXz7qOw_4_chimera.py
- 4:04 AM Ticket #2313 (KeyError in map chooser) created by
- […]
Aug 13, 2019:
- 11:27 PM Ticket #2190 ("hat" symbol stripped from logged color command with reverse palette) closed by
- fixed: Error was in argument recognition code not saying it used the ^.
- 6:51 PM Ticket #2312 (hide/show confusing) created by
- […]
- 2:29 PM ChangeLog edited by
- (diff)
- 12:30 PM Ticket #2309 (Could not create OpenGL context) closed by
- nonchimerax: This ChimeraX error means computer does not have a graphics driver …
- 11:53 AM Ticket #2307 (color command undo for 2D labels) closed by
- fixed: Done. First I made the default color target not include labels. So …
- 11:21 AM Ticket #2311 (Implement "backrub" algorithm for rotamer optimization) created by
- A less pressing potential enhancement would be to include the …
- 10:31 AM Ticket #2305 (Picking: index out of bounds) closed by
- fixed: Fixed. If atoms are deleted and a pick is done before the graphics is …
- 6:11 AM Ticket #2310 (RFE: swapaa option to add hydrogens) created by
-
I can see
swapaabeing *really* useful for a lot of things (e.g. … - 12:34 AM Ticket #2309 (Could not create OpenGL context) created by
- […]
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