![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Timeline
Feb 28, 2020:
- 10:16 PM Ticket #2880 (GCC 7.3 breaks ISOLDE) closed by
- fixed
- 3:37 PM Ticket #2899 (Accidental submission) closed by
- duplicate
- 3:36 PM Ticket #2898 (Shell does not start) closed by
- duplicate: I don't think you were in fact working from a complete rebuild (or …
- 2:02 PM Ticket #2895 (Crash during close) closed by
- fixed: Prevent firing of delayed Sequence triggers if no one is listening to …
- 1:06 PM Ticket #2899 (Accidental submission) created by
- […]
- 11:20 AM Ticket #2891 (Sequence viewer: 'OptionalRGBAOption' object has no attribute 'get') closed by
- duplicate
- 11:20 AM Ticket #2891 (Sequence viewer: 'OptionalRGBAOption' object has no attribute 'get') reopened by
- 11:17 AM Ticket #2891 (Sequence viewer: 'OptionalRGBAOption' object has no attribute 'get') closed by
- duplicate
- 10:13 AM Ticket #2894 (Errors when typing commands after conference close) closed by
- fixed: Fixed in d87ae6ba9. Forgot to turn off command relay when …
Feb 27, 2020:
- 11:08 PM Ticket #2898 (Shell does not start) created by
- […]
- 6:33 PM Ticket #2897 (Closing Side View opens empty dialog/window) created by
- […]
- 5:31 PM Ticket #2896 (generic attribute selection slow) created by
- […]
- 5:26 PM Ticket #2895 (Crash during close) created by
- […]
- 5:16 PM Ticket #2783 (Disconnecting already-disconnected tooltip slot when click outside ...) closed by
- fixed: This apparently "fixed itself" with later versions of the packages …
- 4:52 PM Ticket #2894 (Errors when typing commands after conference close) created by
- […]
- 4:51 PM Ticket #2893 (conference does not send models to participants) created by
- […]
- 4:49 PM Ticket #2892 (conference does not send models to participant) created by
- […]
- 2:03 PM Ticket #2891 (Sequence viewer: 'OptionalRGBAOption' object has no attribute 'get') created by
- […]
- 12:52 PM Ticket #2889 (Crash drawing Qt interface) closed by
- duplicate: duplicate of #2888
- 11:00 AM ChangeLog edited by
- (diff)
Feb 26, 2020:
- 8:22 PM Ticket #2886 (error showing image map colored by index-map segmentation) closed by
- fixed: Fixed. Segmentation coloring on a map which was never shown in image …
- 6:42 PM Ticket #2890 (Font startup cost) created by
- […]
- 5:14 PM Ticket #2889 (Crash drawing Qt interface) created by
- […]
- 4:51 PM Ticket #2888 (Crash drawing Qt interface) created by
- […]
- 4:42 PM Ticket #2887 (No daily build for Generic Linux 64-bit) created by
- […]
- 11:22 AM Ticket #2886 (error showing image map colored by index-map segmentation) created by
- […]
- 11:13 AM Ticket #2885 (2D arrows not restored from old sessions) closed by
- fixed
- 10:38 AM Ticket #2881 (Shell does not start) closed by
- fixed: Fixed in 6d8525e5c. Added jupyter-client 5.3.4 as …
- 10:28 AM Ticket #2885 (2D arrows not restored from old sessions) created by
- […] arrows.cxs
Feb 25, 2020:
- 8:09 PM Ticket #2884 (OpenMM: Error initializing context: clGetDeviceIDs) created by
- […]
- 5:08 PM Ticket #2882 (Update download page to say macOS 10.13 is required) closed by
- fixed: Changes on the preview site. Will be on main site tomorrow.
- 4:54 PM Ticket #2883 ("seg colors" command traceback if specifying surface model with map keyword) closed by
- fixed: Fixed. The segmentation colors command was trying to give an error …
- 4:15 PM Ticket #2883 ("seg colors" command traceback if specifying surface model with map keyword) created by
- […]
- 1:07 PM Ticket #2867 (Error finding files in same folder as session file (previously: Error ...) closed by
- fixed: If you eventually are able to reproduce the session restore error …
- 1:05 PM Ticket #2882 (Update download page to say macOS 10.13 is required) created by
- Download page needs update, says macOS 10.12 is required when in fact …
- 11:43 AM ChangeLog edited by
- (diff)
- 11:42 AM ChangeLog edited by
- (diff)
Feb 24, 2020:
- 11:51 PM Ticket #2881 (Shell does not start) created by
- […]
- 11:50 PM Ticket #2880 (GCC 7.3 breaks ISOLDE) created by
- […]
- 6:22 PM Ticket #2879 (openmm/swig: type object 'object' has no attribute '__getattr__') created by
- […]
- 1:57 PM Ticket #2868 (Trac browse source unusably slow) closed by
- fixed
- 10:52 AM Ticket #2878 (Crash in free_keys_object/subtype_dealloc) closed by
- can't reproduce
Feb 23, 2020:
- 12:50 PM Ticket #2878 (Crash in free_keys_object/subtype_dealloc) created by
- […]
- 11:32 AM Ticket #2869 (incorrect undo of roll specific model) closed by
- fixed: Fixed in 49f498967. Make multi-frame turns use the same …
Feb 22, 2020:
- 6:26 PM Ticket #2877 (VR sometimes freezes when resizing panels) created by
- VR sometimes freezes for several seconds when resizing panels by …
- 6:08 PM Ticket #2876 (core import hook makes non-equivalent classes) created by
- The input hook that allows "from chimerax.core.ui import …
- 5:58 PM Ticket #2875 (ISOLDE imports obsolete MainToolWindow from core.ui) created by
- […]
- 7:51 AM Ticket #2874 (Crash drawing Qt widgets) created by
- […]
Feb 21, 2020:
- 12:24 PM Ticket #2873 (PyQt icon image not changing) created by
- Probably won’t be able to get to the bottom of this myself until I get …
- 11:10 AM Ticket #2801 (Model Panel width too narrow) closed by
- fixed: The latest hacky solution seems to work on Windows too.
- 10:02 AM Ticket #2872 (Make button to update metal coordination bonds) created by
- Would like a way to update metal coordination bonds when atoms of a …
Feb 20, 2020:
- 2:59 PM Ticket #2864 (Model Panel: 'Close' sometimes closes parent) closed by
- fixed: Hi Tony, Thanks for pointing out this problem. Fixed in tomorrow's …
- 2:24 PM Ticket #2871 (Add speech recognition for running commands in VR) created by
- Conrad has added the speech ChimeraX bundle that uses the PyPi …
- 1:41 PM Ticket #2865 (Problem saving MRC/PDB: name 'model' is not defined) closed by
- fixed: Fixed. The error message was supposed to say you specified a model …
- 1:05 PM Ticket #2870 (ChimeraX Help Viewer (browser) behaving strangely) created by
- (1) now when I start Help Viewer from the Help menu or by opening a …
- 12:02 PM Ticket #2866 (Crash in free_keys_object/subtype_dealloc) closed by
- can't reproduce
- 11:45 AM Ticket #2869 (incorrect undo of roll specific model) created by
- The attached session square-assembly.cxs has two models #2.1 and #2.2 …
- 11:21 AM Ticket #2868 (Trac browse source unusably slow) created by
- Takes about 2 minutes to show ChimeraX Trac web page Browse Source. …
- 9:51 AM Ticket #2206 (Hang initializing bundles (bad cache?)) closed by
- can't reproduce: I was unable to reproduce this problem under a variety of different …
- 9:49 AM Ticket #2214 (Incorrect version of Clipper installed in ChimeraX 0.9) closed by
- fixed: Switched over to new scheme for tying bundles to specific ChimeraX …
- 9:47 AM Ticket #1305 (Need mechanism for restarting ChimeraX after installing in-use bundle) closed by
- fixed: Fixed in 71769061. When a package/module is already in …
- 8:18 AM Ticket #2867 (Error finding files in same folder as session file (previously: Error ...) created by
- […]
- 4:33 AM Ticket #2866 (Crash in free_keys_object/subtype_dealloc) created by
- […]
Feb 19, 2020:
- 11:14 PM Ticket #2865 (Problem saving MRC/PDB: name 'model' is not defined) created by
- […]
- 10:02 PM Ticket #2864 (Model Panel: 'Close' sometimes closes parent) created by
- […] closing_children.zip
- 4:32 PM ChangeLog edited by
- (diff)
- 3:41 PM Ticket #2861 (Consecutive "view myname" commands only does first) closed by
- fixed: Fixed. The problem was not really related to clipping planes. It was …
- 1:14 PM Ticket #2801 (Model Panel width too narrow) reopened by
- Now the Model Panel starts out too wide on Windows, about 750 pixels wide.
- 6:21 AM Ticket #2863 (Side View: self.view.render is None) created by
- […]
- 1:52 AM Ticket #2862 (view names need to be prevented from being the same as 'view' keywords) created by
- […]
- 1:44 AM Ticket #2861 (Consecutive "view myname" commands only does first) created by
- […] bug.cxc
Feb 18, 2020:
- 9:19 PM Ticket #2860 (Dead pseudobond group being saved in session) created by
- […]
- 5:32 PM Ticket #2801 (Model Panel width too narrow) closed by
- fixed: Okay, now that Model Panel will just stay the same width instead of …
- 2:20 PM Ticket #2856 (Surface cap update: 'NoneType' object has no attribute 'update_direction') closed by
- can't reproduce: Session restore appears to have put None in clip plane list in …
- 12:04 PM Ticket #2859 (Atoms/Bonds→Delete deletes all atoms if non-empty selection has no ...) closed by
- fixed
- 11:07 AM Ticket #2858 (Crash in free_keys_object/subtype_dealloc) closed by
- duplicate
- 10:45 AM Ticket #2859 (Atoms/Bonds→Delete deletes all atoms if non-empty selection has no ...) created by
- […]
- 7:06 AM Ticket #2858 (Crash in free_keys_object/subtype_dealloc) created by
- […]
Feb 16, 2020:
- 10:32 PM Ticket #2857 (Error showing VR tool window) closed by
- fixed: Fixed. Log panel was squished to zero size by creation of Build …
- 10:25 PM Ticket #2857 (Error showing VR tool window) created by
- […]
- 9:06 PM Ticket #2856 (Surface cap update: 'NoneType' object has no attribute 'update_direction') created by
- […]
- 6:34 PM Ticket #2855 (Command to run tests deprecated) created by
- On Windows building every bundle gives a deprecation warning when …
- 6:28 PM WindowsDevReq edited by
- (diff)
- 5:08 PM Ticket #2854 (Toolbar customization bug with multiple sections) created by
- […] Screen Shot 2020-02-17 at 12.05.31 PM.png
- 4:28 PM Ticket #2853 (Windows build should not require pre-installed Python) created by
- In order to encourage outside developers our Windows build should not …
Feb 14, 2020:
- 4:18 PM Ticket #2851 (Undocked tools have no titlebar in VR) closed by
- fixed: Fixed by making VR add titlebars to docked and undocked widgets.
- 4:12 PM Ticket #2801 (Model Panel width too narrow) reopened by
- In Feb 13 Windows ChimeraX Model Panel still shrinks in width so that …
- 1:43 PM Ticket #2849 (Menu pane positioned wrong in VR) closed by
- fixed: Fixed. This is because the QMenu was created without a parent so the …
- 1:33 PM Ticket #2852 (Add "Show atoms" graphics window context menu) created by
- […]
- 12:34 PM Ticket #2848 (Cascaded menus broken in VR) closed by
- fixed: Fixed. Made click and release on VR user interface panels update …
- 10:56 AM Ticket #2851 (Undocked tools have no titlebar in VR) created by
- If a tools is undocked it does not show a titlebar in VR. The …
- 10:56 AM Ticket #2850 (_openmm could not be found) created by
- […]
Feb 13, 2020:
- 6:39 PM Ticket #2849 (Menu pane positioned wrong in VR) created by
- […]
- 6:36 PM Ticket #2848 (Cascaded menus broken in VR) created by
- […]
- 5:48 PM Ticket #2847 (Snapshot icons to save PDB, mmCIF, or session) created by
- Might have toolbar icons to save a structure to a PDB or mmCIF file on …
- 5:24 PM Ticket #2846 (VR laser pointer for picking) created by
- Wilian notes in the message below that VR bond rotation is difficult …
- 4:34 PM Ticket #2845 (VR hand controllers swapped, Oculus Rift S) created by
- […]
- 4:13 PM Ticket #2790 (Long atom spec → grako recursion error) closed by
- fixed: Fixed by increasing maximum stack size while parsing atom specifications.
- 2:02 PM Ticket #2572 (Atom matching occurring in input order rather than name order) closed by
- fixed: "align" command now asks for the implied atoms to be sorted.
- 1:11 PM Ticket #2844 (Crash/hang encoding movie) closed by
- fixed: Fixed. Movie encoding was running ffmpeg which apparently looks for …
- 11:54 AM Ticket #2844 (Crash/hang encoding movie) created by
- […]
- 11:44 AM Ticket #2843 (Crash showing 316 million triangle surface) closed by
- nonchimerax: On a 590 million triangle surface (ticket #2842) it gave a OpenGL out …
- 11:42 AM Ticket #2842 (OpenGL out of memory on 590 million triangles) closed by
- nonchimerax
- 11:33 AM Ticket #2843 (Crash showing 316 million triangle surface) created by
- […]
- 11:29 AM Ticket #2842 (OpenGL out of memory on 590 million triangles) created by
- […]
- 10:57 AM Ticket #2838 (Build Structure executing old (Chimera1) code) closed by
- fixed
- 10:40 AM Ticket #2841 (Help Viewer crash?) closed by
- duplicate
- 10:34 AM Ticket #2840 (Sequence header session-restore problem) closed by
- not a bug: Hi Leonie, It looks like this is a session from a newer version of …
- 12:09 AM Ticket #2841 (Help Viewer crash?) created by
- […]
Feb 12, 2020:
- 10:06 PM Ticket #2840 (Sequence header session-restore problem) created by
- […]
- 6:50 PM Ticket #2839 (update_buffer_data: cannot allocate huge array) created by
- […]
- 5:59 PM Ticket #2838 (Build Structure executing old (Chimera1) code) created by
- […]
- 5:47 PM Ticket #2827 (Crash while using Help Viewer) closed by
- worksforme: We have update the version of the Qt user interface toolkit in the …
- 3:29 PM Ticket #2801 (Model Panel width too narrow) closed by
- fixed
- 2:35 PM Ticket #2834 (Settings save failure when saving non-default color) closed by
- fixed: Happened because repr() of a Color was not eval()able (numpy string …
- 11:27 AM Ticket #2836 (Crash either initializing graphics or when screen changed) closed by
- can't reproduce: Crash in Qt. It was deleting a QScreen and in handleScreenRemoved() …
- 10:08 AM Ticket #2837 (Crash displaying ISOLDE ramachandran plot) created by
- […]
- 9:59 AM Ticket #2836 (Crash either initializing graphics or when screen changed) created by
- […]
- 9:22 AM Ticket #2835 (View all misbehaves in VR) created by
- When I use the view all toolbar icon in VR my molecule recedes further …
- 6:09 AM Ticket #2834 (Settings save failure when saving non-default color) created by
- […]
Feb 11, 2020:
- 7:16 PM Ticket #2833 (VR room camera depth cue is wrong) created by
- Showing a volume surface in VR with the VR room camera enabled shows …
- 5:03 PM Ticket #2832 (Chain trace creation delayed in scripts) created by
- […] thr.cxc
- 11:55 AM Ticket #2829 (Bogus bundle reviews) closed by
- fixed: There is no easy way to delete only some of the ratings, so I deleted …
- 11:21 AM Ticket #2831 (Residue::find_atom() being looked for in isolde/libmolc.so) closed by
- duplicate: duplicate of #2825
- 1:26 AM Ticket #2831 (Residue::find_atom() being looked for in isolde/libmolc.so) created by
- […]
Feb 10, 2020:
- 4:56 PM Ticket #2830 (Allow Toolshed uploads with dependencies on daily build bundles) created by
- […]
- 4:29 PM Ticket #2829 (Bogus bundle reviews) created by
- […]
- 3:10 PM Ticket #2828 (Rotamer dialog column sorting not numerical) created by
- If I calculate clashes for Arg rotamers at 3gws residue 346 (Leu) and …
- 11:45 AM Ticket #2826 (Crash drawing Qt widgets) closed by
- duplicate: Apparent duplicate of #2826
- 11:03 AM Ticket #2827 (Crash while using Help Viewer) created by
- […]
- 11:01 AM Ticket #2826 (Crash drawing Qt widgets) created by
- […]
- 10:18 AM Ticket #2824 (Crash in free_keys_object/subtype_dealloc) closed by
- can't reproduce
- 9:59 AM Ticket #2825 (Residue::find_atom() being looked for in isolde/libmolc.so) created by
- […]
Feb 8, 2020:
Feb 7, 2020:
- 11:58 AM Ticket #2821 (sym to generate mmCIF assembly loses bfactor info) closed by
- fixed
- 10:47 AM Ticket #2822 (Write PDB: out-of-range on a string) closed by
- can't reproduce: Would need a session file (also, version is 0.9)
- 10:44 AM Ticket #2820 (SideVIew self.view.render is None) closed by
- duplicate
- 10:43 AM Ticket #2819 (SideVIew self.view.render is None) closed by
- duplicate
- 8:23 AM Ticket #2823 (Nucleotides trying to save dead Residue in session) created by
- […]
- 4:21 AM Ticket #2822 (Write PDB: out-of-range on a string) created by
- […]
Feb 6, 2020:
- 3:59 PM Ticket #2821 (sym to generate mmCIF assembly loses bfactor info) created by
- For example, open 6oyy sym #1 assembly 1 copies t close #1 color …
- 3:26 PM Ticket #2820 (SideVIew self.view.render is None) created by
- […]
- 3:26 PM Ticket #2819 (SideVIew self.view.render is None) created by
- […]
- 11:57 AM Ticket #2816 (SideVIew self.view.render is None) closed by
- duplicate: dup of #2813
- 11:40 AM Ticket #2814 (SideVIew self.view.render is None) closed by
- duplicate: dup of #2813
- 11:16 AM Ticket #2818 (Improve sample bundle code) created by
- The sample bundle found at …
- 9:39 AM Ticket #2817 (SideVIew self.view.render is None) created by
- […]
Feb 5, 2020:
- 7:00 PM Ticket #2816 (SideVIew self.view.render is None) created by
- […]
- 5:45 PM Ticket #2815 (VR buttons cause shadow recomputation) closed by
- fixed: Fixed.
- 5:41 PM Ticket #2815 (VR buttons cause shadow recomputation) created by
- […]
- 5:27 PM Ticket #2814 (SideVIew self.view.render is None) created by
- […]
- 4:46 PM Ticket #2813 (SideVIew self.view.render is None) created by
- […]
- 3:20 PM Ticket #2812 (Better handling of missing background depth in augmented reality videos) created by
- I need a mechanism to assure complete depth information for the …
- 3:08 PM Ticket #2811 (Volume image black backing face for augmented reality videos) created by
- Add mode where back of volume image display can be made opaque black …
- 3:03 PM Ticket #2810 (Make device realsense enable vr room camera) created by
- For making augmented reality videos it would simplify setup if the …
- 1:58 PM Ticket #2800 (Add "Undock tool" menu entry) closed by
- fixed: Menu item added for tools with no title bars
- 11:36 AM Ticket #2808 (Crash in glDrawArrays_ACC_Exec) closed by
- can't reproduce: Can't reproduce
- 11:33 AM Ticket #2807 ('NoneType' object has no attribute 'needs_update' after 2D labels closed) closed by
- fixed: Hi Shiran, This bug was fixed just yesterday, so if you get the …
- 11:21 AM Ticket #2809 (make ChimeraX website documentation URL point to vdocs) created by
- If possible, it would be great if we could make the URLs …
- 2:51 AM Ticket #2808 (Crash in glDrawArrays_ACC_Exec) created by
- […]
- 2:12 AM Ticket #2807 ('NoneType' object has no attribute 'needs_update' after 2D labels closed) created by
- […]
Feb 4, 2020:
- 6:06 PM Ticket #2806 (Refactor bundleinfo.xml) created by
- 6:00 PM Ticket #2805 (Update toolshed to Python3 and more recent django) created by
- 5:57 PM Ticket #2804 (Update ChimeraX dependencies) created by
- Dependency updates Python 3.8 QT 5.14 MSVC Linux …
- 5:29 PM Ticket #2803 (Dead 2D label being updated) closed by
- fixed
- 4:48 PM Ticket #2802 (saving session w/ 2D arrows gives RuntimeError: Unable to restore ...) closed by
- fixed
- 4:15 PM Ticket #2799 (Normals parellel to Z axis inverted) closed by
- fixed: Fixed. Same bug as #2793. Cylinders pointing along -z were not …
- 4:01 PM Ticket #2793 (Stick bond not circular) closed by
- fixed: Fixed. Bond drawing rotates a cylinder and when the bond points …
- 2:33 PM Ticket #2803 (Dead 2D label being updated) created by
- […]
- 1:38 PM Ticket #2802 (saving session w/ 2D arrows gives RuntimeError: Unable to restore ...) created by
- […]
- 12:46 PM Ticket #2795 (Problem with intra-mol excluded H-bond detection) closed by
- fixed: Has mistyped 'if' as 'is'
- 11:37 AM Ticket #2801 (Model Panel width too narrow) created by
- […]
- 11:35 AM Ticket #2800 (Add "Undock tool" menu entry) created by
- […]
- 8:37 AM Ticket #2799 (Normals parellel to Z axis inverted) created by
- […]
- 5:52 AM Ticket #2798 (Arcane version-conflict reporting) created by
- […]
- 4:42 AM Ticket #2797 (Missing clip caps for models with non-rotation position matrices ...) created by
- […]
Feb 3, 2020:
- 5:03 PM Ticket #2796 (Crash opening structure in conjunction with ISOLDE) created by
- […]
- 12:59 PM ChangeLog edited by
- (diff)
- 12:50 PM Ticket #2795 (Problem with intra-mol excluded H-bond detection) created by
- […]
- 10:29 AM Ticket #2792 (Attempt to save dead Residue in session) closed by
- can't reproduce: Bug from version before code to provide more extensive error …
- 10:17 AM Ticket #2794 (SideVIew self.view.render is None) created by
- […]
- 8:35 AM Ticket #2793 (Stick bond not circular) created by
- […] acetone.zip
Feb 2, 2020:
Jan 31, 2020:
- 4:55 PM Ticket #2471 (Actions menu suggested text & organization) closed by
- fixed: Okay, implemented.
- 2:32 PM Ticket #2790 (Long atom spec → grako recursion error) created by
- […]
Jan 30, 2020:
- 4:05 PM Ticket #1815 (style selAtom gives keyword error) closed by
- not a bug
- 2:57 PM Ticket #2789 (Attempted instantiation of HeaderSequence during session save) created by
- […]
- 1:40 PM Ticket #2788 (KeyError removing tool from _tool_instances dict) closed by
- can't reproduce
- 11:48 AM Ticket #2788 (KeyError removing tool from _tool_instances dict) created by
- […]
Jan 29, 2020:
- 12:47 PM Ticket #2786 (Multiple "vr false" → 'SteamVRCamera' object has no attribute ...) closed by
- fixed: Fixed SteamVR camera was being created when "vr false" issued, but …
- 12:17 PM Ticket #2787 (Saved images appear faded compared to graphics window, need color profiles) created by
- […]
- 10:00 AM Ticket #2786 (Multiple "vr false" → 'SteamVRCamera' object has no attribute ...) created by
- […]
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