![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Sep 21, 2020:
- 11:57 PM Ticket #3746 (ChimeraX fails to start on macOS 11 beta 6) created by
- ChimeraX fails to start on macOS 11 beta 6 (20A5364e). Here is the …
- 5:12 PM Ticket #3745 (Can't find split-off atomic lib on Linux) created by
- […]
- 2:27 PM Ticket #3354 (Test update of bundles with binary (e.g. C++) components) closed by
- fixed: Okay, split pdb into pdb_lib and pdb. That's all of them.
- 5:05 AM Ticket #3744 (Cannot enter '@' in registration dialog) created by
- […]
Sep 20, 2020:
Sep 19, 2020:
Sep 18, 2020:
- 5:37 PM Ticket #3741 (devel install fails with new wheel version 0.35.1 module.) created by
- With PyPi wheel module version 0.35.1 bundle_builder fails apparently …
- 5:16 PM Ticket #3740 (Ghost head and hands of person who left 3-person VR meeting) created by
- […]
- 5:14 PM Ticket #3739 (Stuck VR hand controller during 3 person meeting) created by
- […]
- 5:12 PM Ticket #3738 (Tape-measure mouse mode not syncing) created by
- […]
- 5:10 PM Ticket #3737 ("Move selected models" mouse mode does not issue command) created by
- […]
- 12:36 PM Ticket #3736 (vr meeting: source code string cannot contain null bytes) created by
- […]
- 11:56 AM Ticket #3735 (vr meeting: float division by zero) created by
- […]
- 10:08 AM Ticket #3732 (Ribbon pick: index is out of bounds for axis) closed by
- duplicate: Duplicate. Fixed months ago.
- 5:48 AM Ticket #3734 (Have 'usage' report default value) created by
- […]
- 2:12 AM Ticket #3733 (Building with Conda-Forge?) created by
- I received the following email from John Chodera yesterday: …
- 12:18 AM Ticket #3732 (Ribbon pick: index is out of bounds for axis) created by
- […]
Sep 17, 2020:
- 4:35 PM Ticket #3725 (config/settings errors if multiple ChimeraXs starting up at once) closed by
- fixed: Embedded the PID into the temp file name used by "safe saving" which …
- 2:34 PM Ticket #3731 (residue_graph: edges should be a n x 2 array of unsigned ints) created by
- […]
- 2:20 PM Ticket #3730 (Account for symmetry in RMSD calculation) created by
- Such as in the rmsd command, but possibly also in other commands that …
- 2:18 PM Ticket #1896 (RFE: measure rmsd command) closed by
- fixed: Implemented basic rmsd command that does not account for symmetry. …
- 12:09 PM Ticket #3729 (flip peptide bond: Simulation must be running) created by
- […]
- 10:50 AM Ticket #3727 (Swapaa mouse mode using deleted residue) closed by
- fixed: Fixed. This is a weird rare case. Leucine 707 of 6m17 is a HETATM …
- 9:55 AM WikiStart edited by
- (diff)
- 9:54 AM WikiStart edited by
- (diff)
- 4:14 AM Ticket #3728 (Gratuitous re-registration of commands) created by
- […]
Sep 16, 2020:
- 8:22 PM Ticket #3727 (Swapaa mouse mode using deleted residue) created by
- […]
- 8:13 PM LinuxBuildSetup edited by
- (diff)
- 7:37 PM WindowsDevReq edited by
- (diff)
- 7:25 PM WindowsDevReq edited by
- (diff)
- 4:14 PM Ticket #3726 (Graphics hardware encountered an error) closed by
- duplicate: Same crash, same reporter, #3720.
- 3:31 PM Ticket #3726 (Graphics hardware encountered an error) created by
- […]
- 10:33 AM Ticket #3725 (config/settings errors if multiple ChimeraXs starting up at once) created by
- […]
- 9:40 AM Ticket #3720 (Graphics hardware crash) closed by
- can't reproduce: Searching online for gpusKillClientExt turns up no end of these kinds …
- 9:32 AM Ticket #3724 (Write failure raises OSError instead of IOError) created by
- […]
- 8:54 AM Ticket #3722 (Crash computing aromatic rings) closed by
- can't reproduce
- 8:52 AM Ticket #3721 (Crash computing aromatic rings) closed by
- can't reproduce
- 7:21 AM Ticket #3723 (Cannot rewrite settings file: "being used by another process") created by
- […]
- 7:21 AM Ticket #3722 (Crash computing aromatic rings) created by
- […]
- 7:12 AM Ticket #3721 (Crash computing aromatic rings) created by
- […]
Sep 15, 2020:
- 6:53 PM Ticket #3720 (Graphics hardware crash) created by
- […]
- 5:57 PM Ticket #3697 (Replace non-standard Windows numpy and scipy packages with PyPi ones) closed by
- fixed: Done. With PyPi numpy and scipy ChimeraX took 16.6 second to compute …
- 3:34 PM Ticket #3719 (Nucleotides: asking for distance from None) created by
- […]
- 11:02 AM Ticket #3715 (CIF: Missing column 'label_asym_id') closed by
- not a bug: Sorry, ChimeraX only loads mmCIF files, not small molecule CIF files. …
- 9:02 AM Ticket #3718 (Corrupted settings file?) created by
- […]
- 8:23 AM Ticket #3714 (swapBuffers crash) closed by
- can't reproduce
- 4:55 AM Ticket #3717 (ISOLDE: 'OpenMM_Thread_Handler' object has no attribute '_c_pointer') created by
- […]
- 1:46 AM Ticket #3716 (Error within error message) created by
- […]
- 1:19 AM Ticket #3715 (CIF: Missing column 'label_asym_id') created by
- […] Angew 04-20.cif
Sep 14, 2020:
- 8:27 PM Ticket #3714 (swapBuffers crash) created by
- […]
- 5:06 PM Ticket #3129 (Model panel confirm close) closed by
- fixed: If 'Close' would close multiple top-level models without them being …
- 3:05 PM Ticket #3713 (Crash with multiple displays) closed by
- nonchimerax: ChimeraX crashed in Apple's Metal graphics library and the crash …
- 1:22 PM Ticket #3713 (Crash with multiple displays) created by
- […]
- 9:19 AM Ticket #3711 (Crash in Clipper) closed by
- can't reproduce: Not much to go on there, without access to the offending data... I'm …
- 6:58 AM Ticket #3712 (Clipper map roaming overflow in computing bounds) created by
- […]
- 3:20 AM Ticket #3711 (Crash in Clipper) created by
- […]
Sep 13, 2020:
Sep 12, 2020:
Sep 11, 2020:
- 4:11 PM Ticket #3441 (somewhat unusual chain editing causes crash) closed by
- fixed: When chain C got merged into chain A, the chain C object got "demoted" …
- 10:34 AM Ticket #3704 (ISOLDE/Atomic version conflict) closed by
- not a bug: I think it's better to make the dependency on 1.6 instead of 1.6.0 …
- 9:16 AM Ticket #3707 (Crash rendering QtQuick scene graph from timer) closed by
- can't reproduce
- 9:02 AM Ticket #3706 (Error opening PDBQT) closed by
- fixed: Hi Andrew, Thanks for reporting this problem. It is fixed in the …
- 8:59 AM Ticket #3709 (Disabled ISOLDE menu) created by
- […]
- 7:42 AM Ticket #3708 (EMDB initial contour level) created by
- […]
- 7:14 AM Ticket #3707 (Crash rendering QtQuick scene graph from timer) created by
- […]
Sep 10, 2020:
- 8:32 PM Ticket #3706 (Error opening PDBQT) created by
- […] new1_1.pdbqt
- 7:04 PM Ticket #3705 (Bundle builder opaque error message) created by
- […]
- 4:28 PM Ticket #3694 (Crash adding then deleting residue) closed by
- fixed: For the specific case of a residue being added into the …
- 2:54 PM Ticket #3703 ("toolshed install" documentation error) closed by
- fixed: fixed in develop branch
- 2:52 PM Ticket #3704 (ISOLDE/Atomic version conflict) created by
- […]
- 2:45 PM Ticket #3703 ("toolshed install" documentation error) created by
- The syntax summary for "toolshed install" in its help page shows …
- 12:22 PM Ticket #3702 (make build-from-scratch fails) created by
- cd /Users/pett/src/chimerax/build/sync && rm */*.whl rm: */*.whl: No …
- 10:40 AM Milestone 1.1 completed
-
== Update mechanism (critical) ==
*
"Flatten" RBVI bundles …
Sep 9, 2020:
- 6:08 PM Ticket #3701 (SortedDIct.iloc deprecated) closed by
- fixed
- 4:23 PM Ticket #3701 (SortedDIct.iloc deprecated) created by
- […]
- 4:02 PM Ticket #3700 (Tape measure: 'Structure' object has no attribute 'session') closed by
- duplicate: Duplicate of #3457, fixed a few months ago.
- 3:25 PM Ticket #3688 (Segger obsolete import) closed by
- fixed: Fixed. Segger tar balls on plato mistakenly contained wheel files and …
- 12:56 PM Ticket #3700 (Tape measure: 'Structure' object has no attribute 'session') created by
- […]
- 10:59 AM ChangeLog edited by
- (diff)
- 5:46 AM Ticket #3699 (Starting simulation: clEnqueueNDRangeKernel (-4)) created by
- […]
- 4:18 AM Ticket #3698 (Libraries not found when generating bundle documentation) created by
- […]
Sep 8, 2020:
- 7:16 PM Ticket #3697 (Replace non-standard Windows numpy and scipy packages with PyPi ones) created by
- For unclear reasons we are using custom compiled numpy and scipy …
- 4:19 PM Ticket #3695 (Notes with markers) closed by
- fixed: Fixed in daily build and 1.1 release candidate. Markers with notes …
- 3:14 PM Ticket #3652 (Main graphics goes gray) closed by
- nonchimerax: Ok. Good. But the Nvidia graphics will give better performance than …
- 11:07 AM Ticket #3692 (Crash during popup window) closed by
- can't reproduce: User has 3 screens. Possibly a Qt bug related to the popup (atom …
- 10:58 AM Ticket #3691 (Map pixel-size precision) closed by
- nonchimerax: It is using the full precision pixel size that you set, it only …
- 9:43 AM Ticket #3696 (ISOLDE color-picker problem) created by
- […]
- 9:02 AM Ticket #3693 (Crash popping up atom spec or tooltip) closed by
- can't reproduce
- 4:47 AM Ticket #3695 (Notes with markers) created by
- […]
- 1:45 AM Ticket #3694 (Crash adding then deleting residue) created by
- […]
Sep 6, 2020:
- 7:18 PM Ticket #3693 (Crash popping up atom spec or tooltip) created by
- […]
- 5:35 PM Ticket #3692 (Crash during popup window) created by
- […]
- 1:10 AM Ticket #3691 (Map pixel-size precision) created by
- […]
Sep 4, 2020:
- 6:54 PM Ticket #3362 (Run command from VR wand button press) closed by
- fixed: vr button command can assign any command to any VR controller button. …
- 6:51 PM Ticket #2602 (View command includes vr room camera) closed by
- fixed: Fixed. Made vr room camera not contribute to scene bounds and …
- 6:48 PM Ticket #2833 (VR room camera depth cue is wrong) closed by
- fixed: Fixed. VR room camera was being included in scene bounds. Made it …
- 6:33 PM Ticket #2835 (View all misbehaves in VR) closed by
- fixed: Fixed. Problem was that the gui panels were included in the bounds …
- 6:30 PM Ticket #2810 (Make device realsense enable vr room camera) closed by
- fixed: Made realsense command start vr room camera Feb 10, 2020.
- 5:54 PM Ticket #2811 (Volume image black backing face for augmented reality videos) closed by
- fixed: Added as volume command option backingColor (can be a color or "none") …
- 5:35 PM Ticket #2170 (Better VR button assignments for Oculus hand controllers) closed by
- fixed: Fixed on July 5, 2019. Allowed hand controllers to have default …
- 5:31 PM Ticket #1580 (Make VR grip button move models) closed by
- fixed: Oculus grip button became move models on July 5, 2019.
- 5:27 PM Ticket #1573 (Turn off depth cueing for VR meeting head and hands) closed by
- fixed: Fixed. Disabled depth cue on VR face model. This was long overdue, …
- 5:12 PM Ticket #1137 (Add popup menu display in VR gui panel) closed by
- fixed: This was added Sept 23, 2019.
- 3:53 PM Ticket #3242 (ctrl-click selects all atoms with same name in a residue) closed by
- fixed: Now uses the much uglier @@serial_number=N specifier when necessary.
- 2:38 PM Ticket #3690 (ChimeraX hangs at startup, white window, two displays, Windows 10) created by
- […]
- 11:58 AM Ticket #3585 (AddH: unusual positioning) closed by
- not a bug: For /L5:1907, one proton is positioned to H-bond with /L5:1885@O2' and …
- 11:32 AM Ticket #3689 (Another Segger obsolete import) closed by
- duplicate: Same as #3688. Bug in ChimeraX nightly build system on Linux is …
- 2:09 AM Ticket #3689 (Another Segger obsolete import) created by
- […]
- 1:47 AM Ticket #3688 (Segger obsolete import) created by
- […]
Sep 3, 2020:
- 6:37 PM Ticket #3687 (Find a way for VR meeting to handle firewalls) created by
- For two people at different universities to have a VR meeting one …
- 3:34 PM Ticket #3686 (Non-obvious menu) closed by
- fixed: Fixed in 1.2. I removed the white menubar background from the Segment …
- 3:03 PM Ticket #3685 (geometry/graphics memory leak) closed by
- fixed: Believed fixed, but up to you to test since I don't have a test case …
- 11:04 AM Ticket #3665 (Toolshed updates: Connection refused) closed by
- fixed: Revised to always to do updates asynchronously.
- 8:31 AM Ticket #3686 (Non-obvious menu) created by
- […]
- 2:29 AM Ticket #3685 (geometry/graphics memory leak) created by
- […]
- 2:09 AM Ticket #3684 (mmCIF memory leak) created by
- […]
Sep 2, 2020:
- 7:24 PM Ticket #3675 (Only lower left quadrant of graphics shown, external display) closed by
- fixed: Fixed in nightly build, not in 1.1 release candidate. Won't fix in …
- 5:07 PM Ticket #3683 (Startup hangs on Windows when initial size spans two screens) created by
- […]
- 3:48 PM Ticket #3682 (Crash when screen removed) created by
- […]
- 2:17 PM ChangeLog edited by
- (diff)
- 9:19 AM Ticket #3671 (Crash during geometry change) closed by
- can't reproduce: Thanks for the report and feedback though! --Eric
Sep 1, 2020:
- 8:05 PM Ticket #3678 (surface cap coloring by zone not saved in session) closed by
- fixed: Fixed in 1.2, not in 1.1 (too risky).. Saved cap models in sessions. …
- 6:58 PM Ticket #3680 (Clip plane adjustment: Cut fraction is out of range) closed by
- fixed: Fixed. Using sharp edges option with colorzone sometimes caused …
- 5:59 PM Ticket #3681 (Molecule Display toolbar icons in different orders, sometimes ...) created by
- See attached screenshots showing the Molecule Display tool with …
- 5:47 PM Ticket #3677 (per-model clipping status not saved in session) closed by
- fixed: Fixed in 1.2. The allow_clipping attribute was not saved in sessions. …
- 5:05 PM Ticket #2723 (Lazy managers) closed by
- fixed: A manager with the attribute autostart="false" is lazy.
- 4:31 PM Ticket #3680 (Clip plane adjustment: Cut fraction is out of range) created by
- […] bfactorclip.cxc
- 2:17 PM Ticket #3679 (Unit testing framework?) created by
- API changes in the update to ChimeraX 1.1 have broken both Clipper and …
- 1:34 PM Ticket #3672 (Deleting residue involved in sequence alignment: list indices must be ...) closed by
- fixed: Thanks for the report. Fixed in both develop and release branches.
- 1:33 PM Ticket #3678 (surface cap coloring by zone not saved in session) created by
- Same cxc setup file, png file of how it looked when I saved the …
- 1:29 PM Ticket #3677 (per-model clipping status not saved in session) created by
- The attached session was saved with atomic model clipping off, surface …
- 12:55 PM Ticket #3676 (Out-of-date mmCIF templates) created by
- […]
- 11:40 AM Ticket #3673 (Need additional trigger-blocking control) closed by
- fixed: As per your suggestion, added manual_block/release() calls, on both …
- 11:17 AM Ticket #3675 (Only lower left quadrant of graphics shown, external display) created by
- […] chimerax bug.pptx
- 10:05 AM Ticket #3674 (Create a video about how to create a bundle) created by
- Would be nice to have a 3 minute video showing all the steps to create …
- 7:04 AM Ticket #3673 (Need additional trigger-blocking control) created by
- […]
- 5:44 AM Ticket #3672 (Deleting residue involved in sequence alignment: list indices must be ...) created by
- […]
Aug 31, 2020:
- 8:38 PM Ticket #3671 (Crash during geometry change) created by
- […]
- 1:37 PM Ticket #3670 (chimerax 1.0 installation) created by
- […]
- 1:20 PM Ticket #3271 (Line-ending issues for resaved PDB files) closed by
- fixed: The endings are now uniformly just newline. Fix available in next …
- 11:23 AM Ticket #3669 (Crash during display change) closed by
- can't reproduce
- 11:11 AM Ticket #2289 (Suppress log scrolling if log link clicked) closed by
- fixed: Fixed on develop and release branches.
- 8:52 AM Ticket #3668 (Problem restoring session) closed by
- duplicate: Hi Ben, Thanks for reporting this problem. It was fixed on October …
- 6:14 AM Ticket #3669 (Crash during display change) created by
- […]
Aug 30, 2020:
- 11:57 PM Ticket #3661 (Make ChimeraX start faster, takes 5 seconds) closed by
- fixed: Found the culprit. Revised code that dealt with the available bundle …
- 11:44 PM Ticket #3662 (Re-install not reinstalling) closed by
- fixed: Should be fixed :-). Add code to rebuild installed bundle cache if …
- 11:15 PM Ticket #3666 (Installed bundle not used until restart) closed by
- fixed: Needed to create the "user" site-packages/chimerax namespace directory …
- 6:02 PM Ticket #3668 (Problem restoring session) created by
- […]
Aug 29, 2020:
- 2:29 AM Ticket #3664 (Drag select ignoring 'pickable' attribute) closed by
-
fixed: Yep - explicitly adding
pickable=Falseto each drawing did the trick.
Aug 28, 2020:
- 2:07 PM Ticket #3663 (Typo in graphics/drawing.py) closed by
- fixed: Fixed in 1.1 release branch and in develop. Apparently no code was …
- 1:19 PM Ticket #3667 (non-terminal O3' should not get protonated) created by
- e.g. /R;127 in 1eyg
- 9:17 AM Ticket #3666 (Installed bundle not used until restart) created by
- After installing the BlastProtein bundle from the toolshed (and never …
- 8:57 AM Ticket #3665 (Toolshed updates: Connection refused) created by
- […]
- 8:28 AM Ticket #3664 (Drag select ignoring 'pickable' attribute) created by
- […]
- 8:22 AM Ticket #3663 (Typo in graphics/drawing.py) created by
- […]
- 5:00 AM Ticket #3662 (Re-install not reinstalling) created by
- […]
- 1:57 AM Ticket #3659 (Failure to correct ligand when no CCD template available) closed by
- fixed: The first traceback here: `AttributeError: 'PositionRestraintMgr' …
Aug 27, 2020:
- 10:54 PM Ticket #3660 (bundle install failure) closed by
- fixed: Available BundleInfo instance needed to be converted to …
- 5:53 PM Ticket #3661 (Make ChimeraX start faster, takes 5 seconds) created by
- […]
- 3:32 PM Ticket #3660 (bundle install failure) created by
- […]
- 12:30 PM Ticket #3659 (Failure to correct ligand when no CCD template available) created by
- […]
- 10:40 AM Ticket #3173 (BLAST PDB web services being removed November 2020) closed by
- fixed: Updated Blast Protein to use GraphQL, so all information is retrieved …
- 9:10 AM Ticket #3658 (Crash opening 128 volumes) created by
- […]
Aug 26, 2020:
- 4:35 PM ChangeLog edited by
- (diff)
- 3:33 PM NeteSOW edited by
- (diff)
- 12:17 PM Ticket #2289 (Suppress log scrolling if log link clicked) reopened by
- The problem of scrolling to the bottom of the Log from clicking …
- 9:51 AM Ticket #3657 (Crash showing tooltip) closed by
- can't reproduce
- 9:49 AM Ticket #3655 (Crash while showing window) closed by
- can't reproduce
Aug 25, 2020:
- 6:09 PM Ticket #3657 (Crash showing tooltip) created by
- […]
- 5:46 PM Ticket #3656 (Make OBJ reader handle ".mtl" material files using colors and textures) created by
- Would be interesting to be able to open OBJ files with textures on …
- 5:04 PM Ticket #3655 (Crash while showing window) created by
- […]
- 1:18 PM Ticket #3654 (Mis-named hydrogens) closed by
- fixed: Fixed. Pushed to both develop and release branches.
- 11:58 AM Ticket #3651 (Two, two commands in one) closed by
- fixed: Okay, pushed fixes to both develop and release.
- 9:56 AM Ticket #3654 (Mis-named hydrogens) created by
- […]
- 4:34 AM Ticket #3653 (HETATM vs. ATOM) created by
- […]
- 2:02 AM Ticket #3652 (Main graphics goes gray) created by
- […] bug.PNG
Aug 24, 2020:
- 6:02 PM Ticket #3651 (Two, two commands in one) created by
- […]
- 4:50 PM Ticket #3218 (Duplicate residues created in Chain) closed by
- fixed: F86 can be polymeric, but its phosphorus is named P1, so loosened …
- 3:49 PM Ticket #3650 (degenerate structure) closed by
- nonchimerax: Hi Valentyn, As per the log message "Structure has degenerate atomic …
- 3:22 PM Ticket #3650 (degenerate structure) created by
- […]
- 2:28 PM Ticket #3649 (radio button non-existent) closed by
- duplicate
- 2:20 PM Ticket #3646 (Attempt to option-group check button which is None) closed by
- can't reproduce: Seems impossible looking hard at the code. Would need an actual …
- 2:11 PM Ticket #3649 (radio button non-existent) created by
- […]
- 2:10 PM Ticket #3648 (radio button non-existent) created by
- […]
- 1:55 PM Ticket #3647 (Read Amber format) created by
- as per summary
- 1:26 PM Ticket #3646 (Attempt to option-group check button which is None) created by
- […]
- 10:40 AM Ticket #3642 (Bad IDATM typing) closed by
- not a bug: The residue was named 'A' (e.g. adenosine in RNA) when it shouldn't …
Aug 23, 2020:
- 2:19 PM Ticket #3276 (nucleotide sugar-tubes disconnected from ribbon in restored session) closed by
- fixed: Fixed. I made Structure update_graphics_if_needed() public and had …
Aug 22, 2020:
- 11:26 AM Ticket #3341 (Memory error in libqsvg.so on exit) closed by
- fixed: Great! I assuming that the switch to building all Linux binary wheels …
- 10:08 AM ChangeLog edited by
- (diff)
- 9:10 AM Ticket #3645 (Crash setting chain ID) closed by
- can't reproduce: Need a _tad_ more info…
- 12:45 AM Ticket #3645 (Crash setting chain ID) created by
- […]
Note:
See TracTimeline
for information about the timeline view.
