![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
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
- […]
Aug 12, 2019:
- 5:27 PM Ticket #2304 (Molmap: divide by zero) closed by
- fixed: Fixed. User tried 0 resolution and 0 grid spacing in molmap. Not …
- 3:59 PM Ticket #2306 (weird initial model placement if 2d labels created first) closed by
- fixed: Fixed. Camera view was only set when first model opened. If a 2D …
- 3:49 PM Ticket #2035 (Nucleotides tethers: Bond drawing: cylinder and endpoint arrays differ ...) closed by
- can't reproduce: Need test case.
- 3:43 PM Ticket #2294 (DICOM segmentation dims CT brightness) closed by
- fixed: Fixed. Blended 3d texture was created with initial rgba values, then …
- 3:38 PM Ticket #2180 (QTimer not in QThread (offscreen rendering not working)) closed by
- fixed: Turns out my problem was due to having LD_LIBRARY_PATH set and a …
- 3:34 PM Ticket #2302 (mmCIF write: citation_author is None) closed by
- fixed: Fixed in the next daily build. Very curious about the original CIF …
- 3:20 PM Ticket #2268 (Error opening mmCIF: basic_string::_M_construct null not valid) closed by
- can't reproduce: No response and not able to reproduce.
- 3:17 PM Ticket #2308 (no log scroll after 'close') closed by
- fixed: Bug was due to spurious "link_clicked". The url was a data: url that …
- 2:57 PM Ticket #2185 (AddH option to use residue templates for guidance) closed by
- fixed: Implemented as 'template' keyword for addh (default false). The …
- 11:51 AM Ticket #2303 ('save' command 'models' keyword wrong/mishandled) closed by
- fixed: 'save' was only passing off 'models' keyword to underlying functions …
- 11:07 AM Ticket #2308 (no log scroll after 'close') created by
- If the log is long enough to scroll, if I type 'close' and the 'open …
- 10:32 AM Ticket #2293 (cannot save session with volume eraser sphere?) closed by
- fixed: Fixed. Was trying to save eraser sphere model. Made it not save the …
- 10:05 AM 2019-08-08 edited by
- (diff)
- 9:25 AM Ticket #2307 (color command undo for 2D labels) created by
- Since the general "color" command now works on 2D labels it is much …
- 9:09 AM Ticket #2306 (weird initial model placement if 2d labels created first) created by
- If I start ChimeraX then use these commands in this order: 2d text …
- 12:48 AM Ticket #2305 (Picking: index out of bounds) created by
- […]
Aug 11, 2019:
Aug 9, 2019:
- 2:15 PM Ticket #2296 ('MolecularSurface' object has no attribute 'gaussian_level') closed by
- fixed: Fixed. Error happened because session was restored with molecular …
- 1:12 PM Ticket #2301 (bare 'label delete' gives error) closed by
- fixed: Fixed. Also I made "2dlabels delete" with no arguments delete all labels.
- 6:56 AM Ticket #2303 ('save' command 'models' keyword wrong/mishandled) created by
- […]
- 4:02 AM Ticket #2302 (mmCIF write: citation_author is None) created by
- […]
Aug 8, 2019:
- 4:27 PM Ticket #2301 (bare 'label delete' gives error) created by
- […]
- 3:14 PM Ticket #2300 (extra wait command w/o frame count halts script) closed by
- fixed: Greg took the bull by the horns and fixed this just now.
- 2:57 PM 2019-08-08 created by
- 2:07 PM DeveloperMeetings edited by
- (diff)
- 1:54 PM Ticket #2299 (extra wait command w/o frame count halts script) closed by
- duplicate: accidentally clicked something and made this ticket twice
- 1:53 PM Ticket #2300 (extra wait command w/o frame count halts script) created by
- For example, the attached script just has these commands 2d text …
- 1:50 PM Ticket #2299 (extra wait command w/o frame count halts script) created by
- 10:57 AM Ticket #2298 (2dlabels fading broken) created by
- 2dlabels text start xpos .2 ypos .2 2dlabels #1 size 40 color red …
Aug 7, 2019:
- 5:25 PM Ticket #2297 (Showing all tools suppressed during global tool hide) created by
- […]
- 10:05 AM Ticket #2296 ('MolecularSurface' object has no attribute 'gaussian_level') created by
- […]
- 12:25 AM Ticket #2295 (Crash in OpenGL) created by
- […]
Aug 6, 2019:
- 5:39 PM Ticket #2294 (DICOM segmentation dims CT brightness) created by
- […]
- 5:32 PM Ticket #2292 (2D labels 'frames' problem: local variable 'bg2' referenced before ...) closed by
- fixed
- 4:51 PM Ticket #2293 (cannot save session with volume eraser sphere?) created by
- […]
- 3:24 PM Ticket #2282 (Make 2D labels models) closed by
- fixed: Done. Made 2d labels each be a model under a "2D labels" grouping …
- 3:05 PM Ticket #2292 (2D labels 'frames' problem: local variable 'bg2' referenced before ...) created by
- […]
- 8:00 AM Ticket #2291 (Tile command: 'Volume' object has no attribute 'atomspec') created by
- […]
Aug 5, 2019:
- 5:40 PM Ticket #2211 (dialogs completely gray after being shown and hidden once) closed by
- fixed: Fixed by reverting to earlier Qt.
- 5:39 PM Ticket #2289 (Suppress log scrolling if log link clicked) closed by
- fixed
- 5:38 PM Ticket #2162 (Side View: self.view.render is None) closed by
- can't reproduce: Ack. Didn't notice that this was an anonymous bug report. Unable to …
- 3:54 PM Ticket #2290 (Basic Actions: showing ribbons unintuitive) created by
- […]
- 3:31 PM Ticket #2217 (Restored models for Objects of Basic Actions are None) closed by
- wontfix: No response. The guess is that this was a bug when saving the session …
- 3:24 PM Ticket #2176 (Session restore: "named views" is None) closed by
- wontfix: This is most likely due to a bug in the original session saving. …
- 2:46 PM Ticket #2285 (RFE: Add wildcard option in ExtraFiles portion of bundle_info.xml) closed by
- fixed: Since ignorance of the law is not a defense, I plead guilty that I did …
- 1:07 PM Ticket #2289 (Suppress log scrolling if log link clicked) created by
- […]
- 12:47 PM Ticket #2288 (traceback interactively moving clip plane after coloring by map value ...) closed by
- fixed: Fixed. Molecular surface mouse pick was mistakenly think the picked …
- 11:45 AM Ticket #2288 (traceback interactively moving clip plane after coloring by map value ...) created by
- […] 3eebB.dx
- 11:39 AM Ticket #2286 (Swapaa seg fault (in Ring::aromatic)) closed by
- fixed: Rings weren't being marked as "dirty" when atoms/bonds deleted.
- 10:11 AM Ticket #2287 (Swapaa: template atom is None) closed by
- duplicate: This was fixed on Thursday (so fixed as of the 8/2 builds)
- 9:42 AM Ticket #2287 (Swapaa: template atom is None) created by
- […]
- 9:36 AM Ticket #2286 (Swapaa seg fault (in Ring::aromatic)) created by
- […]
- 2:53 AM Ticket #2285 (RFE: Add wildcard option in ExtraFiles portion of bundle_info.xml) created by
-
I'd like to suggest the following amendment to
get_extrafiles()in …
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