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Timeline
Nov 17, 2016:
- 5:32 PM Ticket #479 (select sequence option also selected waters) closed by
- fixed: Fixed. Code saw the two waters in 1i50 chain K and decided all the …
- 4:02 PM Ticket #480 (maybe add "entity" (same molecular entity) operator to atomspecs) created by
- A sequence option was recently added to the "select" command and it is …
- 3:57 PM Ticket #479 (select sequence option also selected waters) created by
- open 1i50 select sequence /k ...shouldn't that only select the …
- 3:06 PM Ticket #478 (showing contacts residue plot broken today) closed by
- fixed: Fixed typo.
- 2:19 PM Ticket #478 (showing contacts residue plot broken today) created by
- After using "contacts", choosing any edge-context menu's "Residue …
Nov 16, 2016:
- 11:29 PM Ticket #472 (ChimeraX "open" command format-specification issues) closed by
- fixed: Part A was fixed by getting the fetch code to use the data format's …
- 6:10 PM Ticket #477 (cartoon: some tube-coil joins not so hot) created by
- Some of the tube-helix to coil junctions are pretty poor, e.g. 1a0s …
- 3:56 PM Ticket #239 (File... Save GUI save image adds ".cxs" before image suffix) closed by
- fixed: Must be dyslexic. Added logging the filename when saving an image via …
Nov 15, 2016:
- 4:56 PM Ticket #476 (Command history dialog appears at startup) created by
- The first time ChimeraX run after it is installed for the first time …
- 4:38 PM 2016-11-14 edited by
- (diff)
- 4:38 PM Ticket #447 (Transparency command on volumes undone when contour level changes) closed by
- fixed: Fixed
- 2:47 PM 2016-11-14 edited by
- (diff)
- 2:47 PM Ticket #449 (Volume planes on multiple data display is erratic) closed by
- wontfix: There are only 58 z planes in this data. So the command volume …
- 1:52 PM 2016-11-14 edited by
- (diff)
- 1:52 PM 2016-11-14 edited by
- (diff)
- 1:40 PM Ticket #327 (Log stops updating beyond 2 Mbyte size) closed by
- fixed: Conrad put in code to work around this that saves the log to a …
- 1:35 PM 2016-11-14 edited by
- (diff)
- 1:31 PM Ticket #49 (Better warning message if oculus fails to start) closed by
- fixed: Fixed.
- 11:58 AM Ticket #475 (crazy tube helices after dssp on 4hhb) created by
- open 4hhb rainbow dssp cartoon style modeh tube (the rainbow isn’t …
- 11:42 AM Ticket #474 ("save session filename" (no suffix) gives traceback) closed by
- fixed: Fixed.
- 11:29 AM Ticket #474 ("save session filename" (no suffix) gives traceback) created by
- As I understand it there are 3 ways to specify saving a session: save …
- 10:48 AM 2016-11-14 edited by
- (diff)
Nov 14, 2016:
- 5:38 PM Ticket #437 (OpenMM hangs and uses all system memory, tug atom mouse mode) closed by
- fixed: Hangs occur when simulation goes unstable in OpenMM. Tristan adapted …
- 5:36 PM Ticket #436 (Tool setup.py cannot register multiple extensions for file format) closed by
- fixed: Eric reports this is fixed.
- 5:35 PM Ticket #305 (RFE: connect to pyMLP, molecular lipophilicity potential evaluator) closed by
- fixed: Optimized about 6 months ago.
- 5:34 PM Ticket #287 (Image save shortcut, use different file names) closed by
- fixed: Done a year or more ago.
- 5:34 PM Ticket #233 (Does not start first time run on Mac) closed by
- worksforme: Have not observed this for at least 6 months.
- 5:33 PM Ticket #197 (testing2) closed by
- invalid
- 5:33 PM Ticket #119 (Put build scripts in chimera2 git repository) closed by
- fixed: Build scripts moved to their own repository.
- 5:32 PM Ticket #117 (Linux daily builds gives wx errors on startup) closed by
- invalid: Replaced wx with qt.
- 5:31 PM Ticket #93 (Drag and drop panel gives an error) closed by
- invalid: Wx has been replaced by Qt.
- 5:31 PM Ticket #64 (Multitouch trackpad support) closed by
- duplicate: Duplicate of #427. Toolkit is now Qt.
- 5:30 PM Ticket #53 (Make space navigator support a tool instead of in core) closed by
- fixed: Done.
- 5:29 PM Ticket #52 (Make oculus support a tool instead of in core) closed by
- fixed: Done.
- 5:29 PM Ticket #51 (Find oculus display more reliably) closed by
- invalid: VR toolkits now use direct rendering rather than extended display.
- 5:29 PM Ticket #70 (log tool doesn't cleanup when deleted) closed by
- fixed: The log is now session enduring (and has been for awhile).
- 5:28 PM Ticket #50 (Make oculus window full screen) closed by
- wontfix: VR toolkits now use direct rendering, not windows on extended display.
- 5:27 PM Ticket #20 (Sessions and Scenes Master Ticket) closed by
- duplicate: No longer using "master" tickets. Now use specific tickets for each issue.
- 5:26 PM Ticket #6 (Multitouch translation with two finger drag) closed by
- duplicate
- 5:25 PM Ticket #13 (Oculus rift refinements) closed by
- fixed: These features are now handled by the Oculus SDK.
- 5:24 PM Ticket #14 (Optimize saving STL surface files) closed by
- fixed: Done about a year ago.
- 5:23 PM Ticket #18 (3D Graphics Master Ticket) closed by
- duplicate: No longer using "master" tickets. Instead use individual tickets for …
- 5:23 PM Ticket #19 (User Interface Master Ticket) closed by
- duplicate: No longer using "master" tickets. Instead use individual tickets for …
- 5:22 PM Ticket #22 (ToolShed Master Ticket) closed by
- duplicate: No longer using "master" tickets. Instead use individual tickets for …
- 5:22 PM Ticket #23 (Help System Master Ticket) closed by
- duplicate: No longer using "master" tickets. Instead use individual tickets for …
- 5:22 PM Ticket #24 (TaskManager/Web Services Master Ticket) closed by
- duplicate: No longer using "master" tickets. Instead use individual tickets for …
- 5:21 PM Ticket #25 (Build System Master Ticket) closed by
- duplicate: No longer using "master" tickets. Instead use individual tickets for …
- 5:21 PM Ticket #26 (Sequence Data Master Ticket) closed by
- duplicate: No longer using "master" tickets. Instead use individual tickets for …
- 5:21 PM Ticket #27 (Volume Data Master Ticket) closed by
- duplicate: No longer using "master" tickets. Instead use individual tickets for …
- 5:20 PM Ticket #30 (Test Framework Master Ticket) closed by
- duplicate: No longer using "master" tickets. Instead use individual tickets for …
- 5:20 PM Ticket #33 (Volume Viewer Master Ticket) closed by
- duplicate: No longer using "master" tickets. Instead use individual tickets for …
- 5:20 PM Ticket #34 (Sequence Viewer Master Ticket) closed by
- duplicate: No longer using "master" tickets. Instead use individual tickets for …
- 5:19 PM Ticket #35 (mmCIF Reader Master Ticket) closed by
- duplicate: No longer using "master" tickets. Instead use individual tickets for …
- 5:19 PM Ticket #37 (Surfaces Master Ticket) closed by
- duplicate: No longer using "master" tickets. Instead use individual tickets for …
- 5:16 PM 2016-11-14 edited by
- (diff)
- 5:16 PM 2016-11-14 created by
- 5:14 PM Ticket #115 (Linux daily build does not include libwebkitgtk-1.0) closed by
- duplicate: Superceded by ticket #473.
- 5:14 PM Ticket #114 (Linux daily build does not include libjpeg62) closed by
- duplicate: Superceded by ticket #473.
- 5:10 PM Ticket #473 (Create Linux installer and distribute necessary system libraries) created by
- Need a linux installer for ChimeraX alpha release. Should include …
- 4:40 PM DeveloperMeetings edited by
- (diff)
- 4:33 PM DeveloperMeetings edited by
- (diff)
- 4:30 PM DeveloperMeetings2015 created by
- 4:26 PM DeveloperMeetings2014 created by
- 3:01 PM Ticket #462 (Rename open command explode option to "trajectory") closed by
- fixed: Fixed.
- 2:17 PM Ticket #172 (specifying surface model wrongly specifies its enclosed atoms) closed by
- fixed
- 2:15 PM Ticket #167 (volume color option rgba(r,g,b,a) does not work) closed by
- fixed
- 2:02 PM Ticket #332 (cannot save session) closed by
- fixed: menu uses save command.
- 1:56 PM FAI edited by
- (diff)
- 1:54 PM FAI edited by
- (diff)
- 1:53 PM FAI edited by
- (diff)
- 12:25 PM 2016-11-10 edited by
- (diff)
- 12:00 AM Milestone Core API Complete completed
Nov 10, 2016:
- 2:58 PM 2016-11-10 created by
- 2:14 PM DeveloperMeetings edited by
- (diff)
- 11:42 AM Ticket #436 (Tool setup.py cannot register multiple extensions for file format) reopened by
- Despite the fact that the setup.py.in for the alignments bundle …
- 9:02 AM Ticket #472 (ChimeraX "open" command format-specification issues) created by
- (A) how to specify mmtf is inconsistent from the other fetch formats. …
Nov 9, 2016:
- 4:51 PM Ticket #468 (sop zone doesn't work on non-square mesh) closed by
- fixed: Fixed. Special code to handle this case was ignoring the triangle mask.
Nov 4, 2016:
Nov 3, 2016:
- 6:07 PM Ticket #471 (Commands executed twice) created by
- Sometimes commands are executed twice when entered in the command line …
Nov 2, 2016:
- 11:01 AM Ticket #470 (Multiple copies of shell tool) created by
- The Shell menu entry used multiple times brings up multiple shells. …
Nov 1, 2016:
- 2:43 PM Ticket #397 (Missing bonds in mmCIF 1tna) closed by
- fixed: Decided to replace * with ' in atom names in mmCIF files to handle …
- 2:23 PM Ticket #467 (Density map toolbar thinks it is the mouse modes tool) closed by
- fixed: Fixed. Had used value of variable from outer scope, which, of course, …
- 2:19 PM Ticket #436 (Tool setup.py cannot register multiple extensions for file format) closed by
- fixed: Both .fa and .msf files can be opened.
- 2:08 PM Ticket #469 (HTML link to open local file should be interpreted relative to HTML ...) created by
- Currently ChimeraX interprets the local file location relative to its …
- 2:03 PM Ticket #468 (sop zone doesn't work on non-square mesh) created by
- If I set "vol all style mesh square f" then "sop zone" near some atoms …
- 10:25 AM Ticket #467 (Density map toolbar thinks it is the mouse modes tool) created by
- Menu Tools / Toolbar / Density Map Toolbar gives this bizarre error …
Oct 31, 2016:
- 3:07 PM Ticket #466 (Use map for CoordSets) created by
- For performance, change CoordSets from vector to map. As per T.G.: …
- 1:31 PM Ticket #415 (Model panel expands all hierarchy when models opened/closed) closed by
- fixed: All good things come to those who wait.
Oct 28, 2016:
- 12:09 PM Ticket #465 (atomic Collection.subtract() does not preserve element order) created by
- Subtracting collections of chains, residues, atoms does not preserve …
Oct 27, 2016:
- 4:47 PM Ticket #213 (mmCIF NMR ensembles don't propagate secondary structure) closed by
- fixed: Copy secondary structure assignments from first model to the others.
- 4:11 PM Ticket #455 (Capitalization of multi-character chain ids in atom specs) closed by
- fixed: Changed mmCIF reader to examine all letters in chain id for lowercase …
- 3:33 PM Ticket #455 (Capitalization of multi-character chain ids in atom specs) reopened by
- 2:50 PM 2016-10-27 created by
- 2:06 PM DeveloperMeetings edited by
- (diff)
- 11:31 AM Ticket #463 (Session save fails after blast results panel closed) closed by
- fixed: Fixed in 1e733ab. Was not calling base class "delete" …
- 11:19 AM Ticket #464 (mmCIF reader does not assign secondary structure to ensemble models) closed by
- duplicate: Duplicate of #213
- 11:10 AM Ticket #464 (mmCIF reader does not assign secondary structure to ensemble models) created by
- Opening 5ijn is extremely slow because we compute secondary structure …
Oct 26, 2016:
- 8:56 PM Ticket #454 (Crash showing cartoon) closed by
- fixed: Should be fixed in 667a8fa. Was not careful enough when …
- 6:35 PM Ticket #463 (Session save fails after blast results panel closed) created by
- After using the blast command and then closing the blast results panel …
- 4:46 PM Ticket #457 (Session restore error, atomic structure) closed by
- fixed: Fixed with commit 8cbc339f8786a9f05b17fc387c70e3a77c517136
- 3:15 PM Ticket #462 (Rename open command explode option to "trajectory") created by
- Easier to understand the open command option to put all coordinates in …
- 3:14 PM Ticket #461 (Ribbons don't update when coordinate set changes) created by
- Changing coordinate sets with the coordset command does not cause …
- 3:13 PM Ticket #460 (mmCIF reader does not have "explode" option to make coordinate sets) created by
- The mmcif reader needs to be able to put multiple models into …
- 3:04 PM Ticket #424 (mmCIF chain names) closed by
- fixed: Interim solution: For the pdbx_poly_seq_scheme information, added a …
- 12:39 PM Ticket #459 (extract_mmCIF_tables returned NULL without setting an error) closed by
- fixed: I wasn't able to reproduce that error with asym4.cif.bz2, but it was …
- 10:29 AM Ticket #459 (extract_mmCIF_tables returned NULL without setting an error) created by
- I've seen this error several times where extract_mmCIF_tables C++ code …
- 9:47 AM Ticket #458 (ChimeraX fetched data deleted by Mac OS upgrade) created by
- Upgrading Mac OS from 10.12 to 10.12.1 apparently deleted …
Oct 25, 2016:
- 5:05 PM Ticket #455 (Capitalization of multi-character chain ids in atom specs) closed by
- fixed: Added code to mmCIF reader to set the lower_case_chains flag if need be.
- 2:19 PM Ticket #457 (Session restore error, atomic structure) created by
- The attached nuclear pore asym3.cxs session from July 15 gives a …
- 11:01 AM Ticket #456 (Update surface zone when surface changes) created by
- On Oct 25, 2016, at 7:03 AM, Tristan Croll wrote: ... One more bug I …
Oct 24, 2016:
- 2:19 PM Ticket #455 (Capitalization of multi-character chain ids in atom specs) created by
- Begin forwarded message: From: Tristan Croll Subject: Bug: chain …
Oct 21, 2016:
- 7:05 PM Ticket #454 (Crash showing cartoon) created by
- Showing a cartoon on the attached 500,000 atom nuclear pore asym unit …
Oct 20, 2016:
Oct 19, 2016:
- 5:02 PM Ticket #453 (Undocked panels float above other apps on Mac) created by
- On the Mac undocked tool panels float above the main ChimeraX window …
Oct 18, 2016:
- 6:12 PM Ticket #452 (STL bundle fails to correctly read written STL file) closed by
- fixed: Fixed. C++ code with 2 assignments on one line where one took the …
- 4:02 PM Ticket #452 (STL bundle fails to correctly read written STL file) created by
- The STL bundle generates bad triangles when reading STL files ChimeraX …
- 11:55 AM Ticket #451 (cellpack fails creating surface) closed by
- fixed: Fixed. Incorrect numpy code to make several copies of a color array.
- 11:26 AM Ticket #451 (cellpack fails creating surface) created by
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